changeset 2:5ac3ca7ad18b draft default tip

Updated Test Data
author geert-vandeweyer
date Sat, 02 Aug 2014 10:24:42 -0400
parents 15437246f588
children
files test-data-orig/cuffcompare_in1.gtf test-data-orig/cuffcompare_in1_liftover_mapped.bed test-data-orig/cuffcompare_in1_liftover_unmapped.bed test-data-orig/cuffcompare_in1_mult_liftover_mapped.bed test-data-orig/cuffcompare_in1_mult_liftover_unmapped.bed test-data-orig/cuffcompare_in2.gtf test-data-orig/cuffcompare_in3.gtf test-data-orig/cuffcompare_out1.tmap test-data-orig/cuffcompare_out2.refmap test-data-orig/cuffcompare_out3.tmap test-data-orig/cuffcompare_out4.refmap test-data-orig/cuffcompare_out5.gtf test-data-orig/cuffcompare_out6.tracking test-data-orig/cuffcompare_out7.txt test-data-orig/cuffmerge_out1.gtf test-data/cuffcompare_out5.gtf test-data/cuffcompare_out6.tracking test-data/cuffcompare_out7.txt test-data/cuffmerge_out1.gtf
diffstat 19 files changed, 1034 insertions(+), 169 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data-orig/cuffcompare_in1.gtf	Sat Aug 02 10:24:42 2014 -0400
@@ -0,0 +1,100 @@
+chr1	Cufflinks	transcript	3111450	3111490	1000	.	.	gene_id "CUFF.1"; transcript_id "CUFF.1.1"; FPKM "20.6079364877"; frac "1.000000"; conf_lo "0.000000"; conf_hi "49.751960"; cov "1.317073";
+chr1	Cufflinks	exon	3111450	3111490	1000	.	.	gene_id "CUFF.1"; transcript_id "CUFF.1.1"; exon_number "1"; FPKM "20.6079364877"; frac "1.000000"; conf_lo "0.000000"; conf_hi "49.751960"; cov "1.317073";
+chr1	Cufflinks	transcript	3111546	3111576	1000	.	.	gene_id "CUFF.3"; transcript_id "CUFF.3.1"; FPKM "27.2556579354"; frac "1.000000"; conf_lo "0.000000"; conf_hi "65.800979"; cov "1.741935";
+chr1	Cufflinks	exon	3111546	3111576	1000	.	.	gene_id "CUFF.3"; transcript_id "CUFF.3.1"; exon_number "1"; FPKM "27.2556579354"; frac "1.000000"; conf_lo "0.000000"; conf_hi "65.800979"; cov "1.741935";
+chr1	Cufflinks	transcript	3200326	3200352	1000	.	.	gene_id "CUFF.5"; transcript_id "CUFF.5.1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	exon	3200326	3200352	1000	.	.	gene_id "CUFF.5"; transcript_id "CUFF.5.1"; exon_number "1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	transcript	3200023	3200191	1000	.	.	gene_id "CUFF.7"; transcript_id "CUFF.7.1"; FPKM "9.9991171124"; frac "1.000000"; conf_lo "0.000000"; conf_hi "19.998234"; cov "0.639053";
+chr1	Cufflinks	exon	3200023	3200191	1000	.	.	gene_id "CUFF.7"; transcript_id "CUFF.7.1"; exon_number "1"; FPKM "9.9991171124"; frac "1.000000"; conf_lo "0.000000"; conf_hi "19.998234"; cov "0.639053";
+chr1	Cufflinks	transcript	3201078	3201481	1000	.	.	gene_id "CUFF.9"; transcript_id "CUFF.9.1"; FPKM "17.7768957078"; frac "1.000000"; conf_lo "9.153835"; conf_hi "26.399957"; cov "1.136139";
+chr1	Cufflinks	exon	3201078	3201481	1000	.	.	gene_id "CUFF.9"; transcript_id "CUFF.9.1"; exon_number "1"; FPKM "17.7768957078"; frac "1.000000"; conf_lo "9.153835"; conf_hi "26.399957"; cov "1.136139";
+chr1	Cufflinks	transcript	3201673	3201699	1000	.	.	gene_id "CUFF.11"; transcript_id "CUFF.11.1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	exon	3201673	3201699	1000	.	.	gene_id "CUFF.11"; transcript_id "CUFF.11.1"; exon_number "1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	transcript	3204755	3204833	1000	.	.	gene_id "CUFF.13"; transcript_id "CUFF.13.1"; FPKM "10.6952581772"; frac "1.000000"; conf_lo "0.000000"; conf_hi "25.820637"; cov "0.683544";
+chr1	Cufflinks	exon	3204755	3204833	1000	.	.	gene_id "CUFF.13"; transcript_id "CUFF.13.1"; exon_number "1"; FPKM "10.6952581772"; frac "1.000000"; conf_lo "0.000000"; conf_hi "25.820637"; cov "0.683544";
+chr1	Cufflinks	transcript	3212214	3212292	1000	.	.	gene_id "CUFF.15"; transcript_id "CUFF.15.1"; FPKM "10.6952581772"; frac "1.000000"; conf_lo "0.000000"; conf_hi "25.820637"; cov "0.683544";
+chr1	Cufflinks	exon	3212214	3212292	1000	.	.	gene_id "CUFF.15"; transcript_id "CUFF.15.1"; exon_number "1"; FPKM "10.6952581772"; frac "1.000000"; conf_lo "0.000000"; conf_hi "25.820637"; cov "0.683544";
+chr1	Cufflinks	transcript	3213096	3213192	1000	.	.	gene_id "CUFF.17"; transcript_id "CUFF.17.1"; FPKM "8.7105710927"; frac "1.000000"; conf_lo "0.000000"; conf_hi "21.029179"; cov "0.556701";
+chr1	Cufflinks	exon	3213096	3213192	1000	.	.	gene_id "CUFF.17"; transcript_id "CUFF.17.1"; exon_number "1"; FPKM "8.7105710927"; frac "1.000000"; conf_lo "0.000000"; conf_hi "21.029179"; cov "0.556701";
+chr1	Cufflinks	transcript	3212368	3212439	1000	.	.	gene_id "CUFF.19"; transcript_id "CUFF.19.1"; FPKM "29.3376873610"; frac "1.000000"; conf_lo "3.097262"; conf_hi "55.578113"; cov "1.875000";
+chr1	Cufflinks	exon	3212368	3212439	1000	.	.	gene_id "CUFF.19"; transcript_id "CUFF.19.1"; exon_number "1"; FPKM "29.3376873610"; frac "1.000000"; conf_lo "3.097262"; conf_hi "55.578113"; cov "1.875000";
+chr1	Cufflinks	transcript	3243019	3243079	1000	.	.	gene_id "CUFF.21"; transcript_id "CUFF.21.1"; FPKM "13.8512359999"; frac "1.000000"; conf_lo "0.000000"; conf_hi "33.439842"; cov "0.885246";
+chr1	Cufflinks	exon	3243019	3243079	1000	.	.	gene_id "CUFF.21"; transcript_id "CUFF.21.1"; exon_number "1"; FPKM "13.8512359999"; frac "1.000000"; conf_lo "0.000000"; conf_hi "33.439842"; cov "0.885246";
+chr1	Cufflinks	transcript	3243348	3243401	1000	.	.	gene_id "CUFF.23"; transcript_id "CUFF.23.1"; FPKM "23.4701498888"; frac "1.000000"; conf_lo "0.000000"; conf_hi "50.571145"; cov "1.500000";
+chr1	Cufflinks	exon	3243348	3243401	1000	.	.	gene_id "CUFF.23"; transcript_id "CUFF.23.1"; exon_number "1"; FPKM "23.4701498888"; frac "1.000000"; conf_lo "0.000000"; conf_hi "50.571145"; cov "1.500000";
+chr1	Cufflinks	transcript	3242634	3242923	1000	.	.	gene_id "CUFF.25"; transcript_id "CUFF.25.1"; FPKM "14.5676792413"; frac "1.000000"; conf_lo "5.354270"; conf_hi "23.781089"; cov "0.931034";
+chr1	Cufflinks	exon	3242634	3242923	1000	.	.	gene_id "CUFF.25"; transcript_id "CUFF.25.1"; exon_number "1"; FPKM "14.5676792413"; frac "1.000000"; conf_lo "5.354270"; conf_hi "23.781089"; cov "0.931034";
+chr1	Cufflinks	transcript	3256975	3257011	1000	.	.	gene_id "CUFF.27"; transcript_id "CUFF.27.1"; FPKM "34.2537322701"; frac "1.000000"; conf_lo "0.000000"; conf_hi "73.806535"; cov "2.189189";
+chr1	Cufflinks	exon	3256975	3257011	1000	.	.	gene_id "CUFF.27"; transcript_id "CUFF.27.1"; exon_number "1"; FPKM "34.2537322701"; frac "1.000000"; conf_lo "0.000000"; conf_hi "73.806535"; cov "2.189189";
+chr1	Cufflinks	transcript	3189900	3190041	1000	.	.	gene_id "CUFF.29"; transcript_id "CUFF.29.1"; FPKM "107.1032192108"; frac "1.000000"; conf_lo "71.402146"; conf_hi "142.804292"; cov "6.845070";
+chr1	Cufflinks	exon	3189900	3190041	1000	.	.	gene_id "CUFF.29"; transcript_id "CUFF.29.1"; exon_number "1"; FPKM "107.1032192108"; frac "1.000000"; conf_lo "71.402146"; conf_hi "142.804292"; cov "6.845070";
+chr1	Cufflinks	transcript	3190273	3190303	1000	.	.	gene_id "CUFF.31"; transcript_id "CUFF.31.1"; FPKM "122.6504607091"; frac "1.000000"; conf_lo "40.883487"; conf_hi "204.417435"; cov "7.838710";
+chr1	Cufflinks	exon	3190273	3190303	1000	.	.	gene_id "CUFF.31"; transcript_id "CUFF.31.1"; exon_number "1"; FPKM "122.6504607091"; frac "1.000000"; conf_lo "40.883487"; conf_hi "204.417435"; cov "7.838710";
+chr1	Cufflinks	transcript	3190455	3190481	1000	.	.	gene_id "CUFF.33"; transcript_id "CUFF.33.1"; FPKM "109.5273661476"; frac "1.000000"; conf_lo "26.732460"; conf_hi "192.322273"; cov "7.000000";
+chr1	Cufflinks	exon	3190455	3190481	1000	.	.	gene_id "CUFF.33"; transcript_id "CUFF.33.1"; exon_number "1"; FPKM "109.5273661476"; frac "1.000000"; conf_lo "26.732460"; conf_hi "192.322273"; cov "7.000000";
+chr1	Cufflinks	transcript	3191539	3191669	1000	.	.	gene_id "CUFF.35"; transcript_id "CUFF.35.1"; FPKM "96.7471827476"; frac "1.000000"; conf_lo "61.420107"; conf_hi "132.074259"; cov "6.183206";
+chr1	Cufflinks	exon	3191539	3191669	1000	.	.	gene_id "CUFF.35"; transcript_id "CUFF.35.1"; exon_number "1"; FPKM "96.7471827476"; frac "1.000000"; conf_lo "61.420107"; conf_hi "132.074259"; cov "6.183206";
+chr1	Cufflinks	transcript	3191877	3191945	1000	.	.	gene_id "CUFF.37"; transcript_id "CUFF.37.1"; FPKM "104.0850125502"; frac "1.000000"; conf_lo "53.596365"; conf_hi "154.573660"; cov "6.652174";
+chr1	Cufflinks	exon	3191877	3191945	1000	.	.	gene_id "CUFF.37"; transcript_id "CUFF.37.1"; exon_number "1"; FPKM "104.0850125502"; frac "1.000000"; conf_lo "53.596365"; conf_hi "154.573660"; cov "6.652174";
+chr1	Cufflinks	transcript	3192442	3192494	1000	.	.	gene_id "CUFF.39"; transcript_id "CUFF.39.1"; FPKM "23.9129829055"; frac "1.000000"; conf_lo "0.000000"; conf_hi "51.525317"; cov "1.528302";
+chr1	Cufflinks	exon	3192442	3192494	1000	.	.	gene_id "CUFF.39"; transcript_id "CUFF.39.1"; exon_number "1"; FPKM "23.9129829055"; frac "1.000000"; conf_lo "0.000000"; conf_hi "51.525317"; cov "1.528302";
+chr1	Cufflinks	transcript	3192551	3192629	1000	.	.	gene_id "CUFF.41"; transcript_id "CUFF.41.1"; FPKM "10.6952581772"; frac "1.000000"; conf_lo "0.000000"; conf_hi "25.820637"; cov "0.683544";
+chr1	Cufflinks	exon	3192551	3192629	1000	.	.	gene_id "CUFF.41"; transcript_id "CUFF.41.1"; exon_number "1"; FPKM "10.6952581772"; frac "1.000000"; conf_lo "0.000000"; conf_hi "25.820637"; cov "0.683544";
+chr1	Cufflinks	transcript	3192732	3192811	1000	.	.	gene_id "CUFF.43"; transcript_id "CUFF.43.1"; FPKM "10.5615674500"; frac "1.000000"; conf_lo "0.000000"; conf_hi "25.497879"; cov "0.675000";
+chr1	Cufflinks	exon	3192732	3192811	1000	.	.	gene_id "CUFF.43"; transcript_id "CUFF.43.1"; exon_number "1"; FPKM "10.5615674500"; frac "1.000000"; conf_lo "0.000000"; conf_hi "25.497879"; cov "0.675000";
+chr1	Cufflinks	transcript	3192941	3193042	1000	.	.	gene_id "CUFF.45"; transcript_id "CUFF.45.1"; FPKM "20.7089557842"; frac "1.000000"; conf_lo "2.186303"; conf_hi "39.231609"; cov "1.323529";
+chr1	Cufflinks	exon	3192941	3193042	1000	.	.	gene_id "CUFF.45"; transcript_id "CUFF.45.1"; exon_number "1"; FPKM "20.7089557842"; frac "1.000000"; conf_lo "2.186303"; conf_hi "39.231609"; cov "1.323529";
+chr1	Cufflinks	transcript	3194186	3194226	1000	.	.	gene_id "CUFF.47"; transcript_id "CUFF.47.1"; FPKM "20.6079364877"; frac "1.000000"; conf_lo "0.000000"; conf_hi "49.751960"; cov "1.317073";
+chr1	Cufflinks	exon	3194186	3194226	1000	.	.	gene_id "CUFF.47"; transcript_id "CUFF.47.1"; exon_number "1"; FPKM "20.6079364877"; frac "1.000000"; conf_lo "0.000000"; conf_hi "49.751960"; cov "1.317073";
+chr1	Cufflinks	transcript	3194303	3194329	1000	.	.	gene_id "CUFF.49"; transcript_id "CUFF.49.1"; FPKM "15.6467665925"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.940300"; cov "1.000000";
+chr1	Cufflinks	exon	3194303	3194329	1000	.	.	gene_id "CUFF.49"; transcript_id "CUFF.49.1"; exon_number "1"; FPKM "15.6467665925"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.940300"; cov "1.000000";
+chr1	Cufflinks	transcript	3195084	3195110	1000	.	.	gene_id "CUFF.51"; transcript_id "CUFF.51.1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	exon	3195084	3195110	1000	.	.	gene_id "CUFF.51"; transcript_id "CUFF.51.1"; exon_number "1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	transcript	3195451	3195477	1000	.	.	gene_id "CUFF.53"; transcript_id "CUFF.53.1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	exon	3195451	3195477	1000	.	.	gene_id "CUFF.53"; transcript_id "CUFF.53.1"; exon_number "1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	transcript	3197090	3197116	1000	.	.	gene_id "CUFF.55"; transcript_id "CUFF.55.1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	exon	3197090	3197116	1000	.	.	gene_id "CUFF.55"; transcript_id "CUFF.55.1"; exon_number "1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	transcript	3197247	3197273	1000	.	.	gene_id "CUFF.57"; transcript_id "CUFF.57.1"; FPKM "15.6467665925"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.940300"; cov "1.000000";
+chr1	Cufflinks	exon	3197247	3197273	1000	.	.	gene_id "CUFF.57"; transcript_id "CUFF.57.1"; exon_number "1"; FPKM "15.6467665925"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.940300"; cov "1.000000";
+chr1	Cufflinks	transcript	3197347	3197373	1000	.	.	gene_id "CUFF.59"; transcript_id "CUFF.59.1"; FPKM "15.6467665925"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.940300"; cov "1.000000";
+chr1	Cufflinks	exon	3197347	3197373	1000	.	.	gene_id "CUFF.59"; transcript_id "CUFF.59.1"; exon_number "1"; FPKM "15.6467665925"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.940300"; cov "1.000000";
+chr1	Cufflinks	transcript	3277191	3277218	1000	.	.	gene_id "CUFF.61"; transcript_id "CUFF.61.1"; FPKM "45.2638604998"; frac "1.000000"; conf_lo "0.000000"; conf_hi "97.530065"; cov "2.892857";
+chr1	Cufflinks	exon	3277191	3277218	1000	.	.	gene_id "CUFF.61"; transcript_id "CUFF.61.1"; exon_number "1"; FPKM "45.2638604998"; frac "1.000000"; conf_lo "0.000000"; conf_hi "97.530065"; cov "2.892857";
+chr1	Cufflinks	transcript	3278237	3278263	1000	.	.	gene_id "CUFF.63"; transcript_id "CUFF.63.1"; FPKM "15.6467665925"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.940300"; cov "1.000000";
+chr1	Cufflinks	exon	3278237	3278263	1000	.	.	gene_id "CUFF.63"; transcript_id "CUFF.63.1"; exon_number "1"; FPKM "15.6467665925"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.940300"; cov "1.000000";
+chr1	Cufflinks	transcript	3280687	3280741	1000	.	.	gene_id "CUFF.65"; transcript_id "CUFF.65.1"; FPKM "15.3622799272"; frac "1.000000"; conf_lo "0.000000"; conf_hi "37.087825"; cov "0.981818";
+chr1	Cufflinks	exon	3280687	3280741	1000	.	.	gene_id "CUFF.65"; transcript_id "CUFF.65.1"; exon_number "1"; FPKM "15.3622799272"; frac "1.000000"; conf_lo "0.000000"; conf_hi "37.087825"; cov "0.981818";
+chr1	Cufflinks	transcript	3290489	3290553	1000	.	.	gene_id "CUFF.67"; transcript_id "CUFF.67.1"; FPKM "12.9988522461"; frac "1.000000"; conf_lo "0.000000"; conf_hi "31.382005"; cov "0.830769";
+chr1	Cufflinks	exon	3290489	3290553	1000	.	.	gene_id "CUFF.67"; transcript_id "CUFF.67.1"; exon_number "1"; FPKM "12.9988522461"; frac "1.000000"; conf_lo "0.000000"; conf_hi "31.382005"; cov "0.830769";
+chr1	Cufflinks	transcript	3290940	3291023	1000	.	.	gene_id "CUFF.69"; transcript_id "CUFF.69.1"; FPKM "10.0586356666"; frac "1.000000"; conf_lo "0.000000"; conf_hi "24.283695"; cov "0.642857";
+chr1	Cufflinks	exon	3290940	3291023	1000	.	.	gene_id "CUFF.69"; transcript_id "CUFF.69.1"; exon_number "1"; FPKM "10.0586356666"; frac "1.000000"; conf_lo "0.000000"; conf_hi "24.283695"; cov "0.642857";
+chr1	Cufflinks	transcript	3291089	3291186	1000	.	.	gene_id "CUFF.71"; transcript_id "CUFF.71.1"; FPKM "8.6216877142"; frac "1.000000"; conf_lo "0.000000"; conf_hi "20.814595"; cov "0.551020";
+chr1	Cufflinks	exon	3291089	3291186	1000	.	.	gene_id "CUFF.71"; transcript_id "CUFF.71.1"; exon_number "1"; FPKM "8.6216877142"; frac "1.000000"; conf_lo "0.000000"; conf_hi "20.814595"; cov "0.551020";
+chr1	Cufflinks	transcript	3299610	3299664	1000	.	.	gene_id "CUFF.73"; transcript_id "CUFF.73.1"; FPKM "15.3622799272"; frac "1.000000"; conf_lo "0.000000"; conf_hi "37.087825"; cov "0.981818";
+chr1	Cufflinks	exon	3299610	3299664	1000	.	.	gene_id "CUFF.73"; transcript_id "CUFF.73.1"; exon_number "1"; FPKM "15.3622799272"; frac "1.000000"; conf_lo "0.000000"; conf_hi "37.087825"; cov "0.981818";
+chr1	Cufflinks	transcript	3300052	3300078	1000	.	.	gene_id "CUFF.75"; transcript_id "CUFF.75.1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	exon	3300052	3300078	1000	.	.	gene_id "CUFF.75"; transcript_id "CUFF.75.1"; exon_number "1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	transcript	3319000	3319051	1000	.	.	gene_id "CUFF.77"; transcript_id "CUFF.77.1"; FPKM "16.2485653076"; frac "1.000000"; conf_lo "0.000000"; conf_hi "39.227507"; cov "1.038462";
+chr1	Cufflinks	exon	3319000	3319051	1000	.	.	gene_id "CUFF.77"; transcript_id "CUFF.77.1"; exon_number "1"; FPKM "16.2485653076"; frac "1.000000"; conf_lo "0.000000"; conf_hi "39.227507"; cov "1.038462";
+chr1	Cufflinks	transcript	3355888	3355914	1000	.	.	gene_id "CUFF.79"; transcript_id "CUFF.79.1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	exon	3355888	3355914	1000	.	.	gene_id "CUFF.79"; transcript_id "CUFF.79.1"; exon_number "1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	transcript	3363215	3363278	1000	.	.	gene_id "CUFF.81"; transcript_id "CUFF.81.1"; FPKM "13.2019593124"; frac "1.000000"; conf_lo "0.000000"; conf_hi "31.872349"; cov "0.843750";
+chr1	Cufflinks	exon	3363215	3363278	1000	.	.	gene_id "CUFF.81"; transcript_id "CUFF.81.1"; exon_number "1"; FPKM "13.2019593124"; frac "1.000000"; conf_lo "0.000000"; conf_hi "31.872349"; cov "0.843750";
+chr1	Cufflinks	transcript	3363754	3363849	1000	.	.	gene_id "CUFF.83"; transcript_id "CUFF.83.1"; FPKM "13.2019593124"; frac "1.000000"; conf_lo "0.000000"; conf_hi "28.446269"; cov "0.843750";
+chr1	Cufflinks	exon	3363754	3363849	1000	.	.	gene_id "CUFF.83"; transcript_id "CUFF.83.1"; exon_number "1"; FPKM "13.2019593124"; frac "1.000000"; conf_lo "0.000000"; conf_hi "28.446269"; cov "0.843750";
+chr1	Cufflinks	transcript	3367136	3367162	1000	.	.	gene_id "CUFF.85"; transcript_id "CUFF.85.1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	exon	3367136	3367162	1000	.	.	gene_id "CUFF.85"; transcript_id "CUFF.85.1"; exon_number "1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	transcript	3367334	3367382	1000	.	.	gene_id "CUFF.87"; transcript_id "CUFF.87.1"; FPKM "17.2433754285"; frac "1.000000"; conf_lo "0.000000"; conf_hi "41.629191"; cov "1.102041";
+chr1	Cufflinks	exon	3367334	3367382	1000	.	.	gene_id "CUFF.87"; transcript_id "CUFF.87.1"; exon_number "1"; FPKM "17.2433754285"; frac "1.000000"; conf_lo "0.000000"; conf_hi "41.629191"; cov "1.102041";
+chr1	Cufflinks	transcript	3377212	3377262	1000	.	.	gene_id "CUFF.89"; transcript_id "CUFF.89.1"; FPKM "16.5671646274"; frac "1.000000"; conf_lo "0.000000"; conf_hi "39.996674"; cov "1.058824";
+chr1	Cufflinks	exon	3377212	3377262	1000	.	.	gene_id "CUFF.89"; transcript_id "CUFF.89.1"; exon_number "1"; FPKM "16.5671646274"; frac "1.000000"; conf_lo "0.000000"; conf_hi "39.996674"; cov "1.058824";
+chr1	Cufflinks	transcript	3391326	3391352	1000	.	.	gene_id "CUFF.91"; transcript_id "CUFF.91.1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	exon	3391326	3391352	1000	.	.	gene_id "CUFF.91"; transcript_id "CUFF.91.1"; exon_number "1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	transcript	3435842	3435880	1000	.	.	gene_id "CUFF.93"; transcript_id "CUFF.93.1"; FPKM "21.6647537435"; frac "1.000000"; conf_lo "0.000000"; conf_hi "52.303342"; cov "1.384615";
+chr1	Cufflinks	exon	3435842	3435880	1000	.	.	gene_id "CUFF.93"; transcript_id "CUFF.93.1"; exon_number "1"; FPKM "21.6647537435"; frac "1.000000"; conf_lo "0.000000"; conf_hi "52.303342"; cov "1.384615";
+chr1	Cufflinks	transcript	3447762	3447788	1000	.	.	gene_id "CUFF.95"; transcript_id "CUFF.95.1"; FPKM "46.9402997776"; frac "1.000000"; conf_lo "0.000000"; conf_hi "101.142289"; cov "3.000000";
+chr1	Cufflinks	exon	3447762	3447788	1000	.	.	gene_id "CUFF.95"; transcript_id "CUFF.95.1"; exon_number "1"; FPKM "46.9402997776"; frac "1.000000"; conf_lo "0.000000"; conf_hi "101.142289"; cov "3.000000";
+chr1	Cufflinks	transcript	3450907	3450965	1000	.	.	gene_id "CUFF.97"; transcript_id "CUFF.97.1"; FPKM "21.4811541355"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.285454"; cov "1.372881";
+chr1	Cufflinks	exon	3450907	3450965	1000	.	.	gene_id "CUFF.97"; transcript_id "CUFF.97.1"; exon_number "1"; FPKM "21.4811541355"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.285454"; cov "1.372881";
+chr1	Cufflinks	transcript	3451052	3451109	1000	.	.	gene_id "CUFF.99"; transcript_id "CUFF.99.1"; FPKM "14.5676792413"; frac "1.000000"; conf_lo "0.000000"; conf_hi "35.169489"; cov "0.931034";
+chr1	Cufflinks	exon	3451052	3451109	1000	.	.	gene_id "CUFF.99"; transcript_id "CUFF.99.1"; exon_number "1"; FPKM "14.5676792413"; frac "1.000000"; conf_lo "0.000000"; conf_hi "35.169489"; cov "0.931034";
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data-orig/cuffcompare_in1_liftover_mapped.bed	Sat Aug 02 10:24:42 2014 -0400
@@ -0,0 +1,86 @@
+chr1	Cufflinks	transcript	3022555	3022596	1000	.	.	gene_id "CUFF.1"; transcript_id "CUFF.1.1"; FPKM "20.6079364877"; frac "1.000000"; conf_lo "0.000000"; conf_hi "49.751960"; cov "1.317073";
+chr1	Cufflinks	exon	3022555	3022596	1000	.	.	gene_id "CUFF.1"; transcript_id "CUFF.1.1"; exon_number "1"; FPKM "20.6079364877"; frac "1.000000"; conf_lo "0.000000"; conf_hi "49.751960"; cov "1.317073";
+chr1	Cufflinks	transcript	3117334	3117360	1000	.	.	gene_id "CUFF.5"; transcript_id "CUFF.5.1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	exon	3117334	3117360	1000	.	.	gene_id "CUFF.5"; transcript_id "CUFF.5.1"; exon_number "1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	transcript	3117031	3117199	1000	.	.	gene_id "CUFF.7"; transcript_id "CUFF.7.1"; FPKM "9.9991171124"; frac "1.000000"; conf_lo "0.000000"; conf_hi "19.998234"; cov "0.639053";
+chr1	Cufflinks	exon	3117031	3117199	1000	.	.	gene_id "CUFF.7"; transcript_id "CUFF.7.1"; exon_number "1"; FPKM "9.9991171124"; frac "1.000000"; conf_lo "0.000000"; conf_hi "19.998234"; cov "0.639053";
+chr1	Cufflinks	transcript	3118118	3118521	1000	.	.	gene_id "CUFF.9"; transcript_id "CUFF.9.1"; FPKM "17.7768957078"; frac "1.000000"; conf_lo "9.153835"; conf_hi "26.399957"; cov "1.136139";
+chr1	Cufflinks	exon	3118118	3118521	1000	.	.	gene_id "CUFF.9"; transcript_id "CUFF.9.1"; exon_number "1"; FPKM "17.7768957078"; frac "1.000000"; conf_lo "9.153835"; conf_hi "26.399957"; cov "1.136139";
+chr1	Cufflinks	transcript	3118713	3118739	1000	.	.	gene_id "CUFF.11"; transcript_id "CUFF.11.1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	exon	3118713	3118739	1000	.	.	gene_id "CUFF.11"; transcript_id "CUFF.11.1"; exon_number "1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	transcript	3121789	3121867	1000	.	.	gene_id "CUFF.13"; transcript_id "CUFF.13.1"; FPKM "10.6952581772"; frac "1.000000"; conf_lo "0.000000"; conf_hi "25.820637"; cov "0.683544";
+chr1	Cufflinks	exon	3121789	3121867	1000	.	.	gene_id "CUFF.13"; transcript_id "CUFF.13.1"; exon_number "1"; FPKM "10.6952581772"; frac "1.000000"; conf_lo "0.000000"; conf_hi "25.820637"; cov "0.683544";
+chr1	Cufflinks	transcript	3128503	3128581	1000	.	.	gene_id "CUFF.15"; transcript_id "CUFF.15.1"; FPKM "10.6952581772"; frac "1.000000"; conf_lo "0.000000"; conf_hi "25.820637"; cov "0.683544";
+chr1	Cufflinks	exon	3128503	3128581	1000	.	.	gene_id "CUFF.15"; transcript_id "CUFF.15.1"; exon_number "1"; FPKM "10.6952581772"; frac "1.000000"; conf_lo "0.000000"; conf_hi "25.820637"; cov "0.683544";
+chr1	Cufflinks	transcript	3129386	3129482	1000	.	.	gene_id "CUFF.17"; transcript_id "CUFF.17.1"; FPKM "8.7105710927"; frac "1.000000"; conf_lo "0.000000"; conf_hi "21.029179"; cov "0.556701";
+chr1	Cufflinks	exon	3129386	3129482	1000	.	.	gene_id "CUFF.17"; transcript_id "CUFF.17.1"; exon_number "1"; FPKM "8.7105710927"; frac "1.000000"; conf_lo "0.000000"; conf_hi "21.029179"; cov "0.556701";
+chr1	Cufflinks	transcript	3128657	3128728	1000	.	.	gene_id "CUFF.19"; transcript_id "CUFF.19.1"; FPKM "29.3376873610"; frac "1.000000"; conf_lo "3.097262"; conf_hi "55.578113"; cov "1.875000";
+chr1	Cufflinks	exon	3128657	3128728	1000	.	.	gene_id "CUFF.19"; transcript_id "CUFF.19.1"; exon_number "1"; FPKM "29.3376873610"; frac "1.000000"; conf_lo "3.097262"; conf_hi "55.578113"; cov "1.875000";
+chr1	Cufflinks	transcript	3162445	3162500	1000	.	.	gene_id "CUFF.23"; transcript_id "CUFF.23.1"; FPKM "23.4701498888"; frac "1.000000"; conf_lo "0.000000"; conf_hi "50.571145"; cov "1.500000";
+chr1	Cufflinks	exon	3162445	3162500	1000	.	.	gene_id "CUFF.23"; transcript_id "CUFF.23.1"; exon_number "1"; FPKM "23.4701498888"; frac "1.000000"; conf_lo "0.000000"; conf_hi "50.571145"; cov "1.500000";
+chr1	Cufflinks	transcript	3176998	3177034	1000	.	.	gene_id "CUFF.27"; transcript_id "CUFF.27.1"; FPKM "34.2537322701"; frac "1.000000"; conf_lo "0.000000"; conf_hi "73.806535"; cov "2.189189";
+chr1	Cufflinks	exon	3176998	3177034	1000	.	.	gene_id "CUFF.27"; transcript_id "CUFF.27.1"; exon_number "1"; FPKM "34.2537322701"; frac "1.000000"; conf_lo "0.000000"; conf_hi "73.806535"; cov "2.189189";
+chr1	Cufflinks	transcript	3107191	3107612	1000	.	.	gene_id "CUFF.29"; transcript_id "CUFF.29.1"; FPKM "107.1032192108"; frac "1.000000"; conf_lo "71.402146"; conf_hi "142.804292"; cov "6.845070";
+chr1	Cufflinks	exon	3107191	3107612	1000	.	.	gene_id "CUFF.29"; transcript_id "CUFF.29.1"; exon_number "1"; FPKM "107.1032192108"; frac "1.000000"; conf_lo "71.402146"; conf_hi "142.804292"; cov "6.845070";
+chr1	Cufflinks	transcript	3107844	3107874	1000	.	.	gene_id "CUFF.31"; transcript_id "CUFF.31.1"; FPKM "122.6504607091"; frac "1.000000"; conf_lo "40.883487"; conf_hi "204.417435"; cov "7.838710";
+chr1	Cufflinks	exon	3107844	3107874	1000	.	.	gene_id "CUFF.31"; transcript_id "CUFF.31.1"; exon_number "1"; FPKM "122.6504607091"; frac "1.000000"; conf_lo "40.883487"; conf_hi "204.417435"; cov "7.838710";
+chr1	Cufflinks	transcript	3108025	3108051	1000	.	.	gene_id "CUFF.33"; transcript_id "CUFF.33.1"; FPKM "109.5273661476"; frac "1.000000"; conf_lo "26.732460"; conf_hi "192.322273"; cov "7.000000";
+chr1	Cufflinks	exon	3108025	3108051	1000	.	.	gene_id "CUFF.33"; transcript_id "CUFF.33.1"; exon_number "1"; FPKM "109.5273661476"; frac "1.000000"; conf_lo "26.732460"; conf_hi "192.322273"; cov "7.000000";
+chr1	Cufflinks	transcript	3109111	3109241	1000	.	.	gene_id "CUFF.35"; transcript_id "CUFF.35.1"; FPKM "96.7471827476"; frac "1.000000"; conf_lo "61.420107"; conf_hi "132.074259"; cov "6.183206";
+chr1	Cufflinks	exon	3109111	3109241	1000	.	.	gene_id "CUFF.35"; transcript_id "CUFF.35.1"; exon_number "1"; FPKM "96.7471827476"; frac "1.000000"; conf_lo "61.420107"; conf_hi "132.074259"; cov "6.183206";
+chr1	Cufflinks	transcript	3109989	3110041	1000	.	.	gene_id "CUFF.39"; transcript_id "CUFF.39.1"; FPKM "23.9129829055"; frac "1.000000"; conf_lo "0.000000"; conf_hi "51.525317"; cov "1.528302";
+chr1	Cufflinks	exon	3109989	3110041	1000	.	.	gene_id "CUFF.39"; transcript_id "CUFF.39.1"; exon_number "1"; FPKM "23.9129829055"; frac "1.000000"; conf_lo "0.000000"; conf_hi "51.525317"; cov "1.528302";
+chr1	Cufflinks	transcript	3110098	3110176	1000	.	.	gene_id "CUFF.41"; transcript_id "CUFF.41.1"; FPKM "10.6952581772"; frac "1.000000"; conf_lo "0.000000"; conf_hi "25.820637"; cov "0.683544";
+chr1	Cufflinks	exon	3110098	3110176	1000	.	.	gene_id "CUFF.41"; transcript_id "CUFF.41.1"; exon_number "1"; FPKM "10.6952581772"; frac "1.000000"; conf_lo "0.000000"; conf_hi "25.820637"; cov "0.683544";
+chr1	Cufflinks	transcript	3110280	3110358	1000	.	.	gene_id "CUFF.43"; transcript_id "CUFF.43.1"; FPKM "10.5615674500"; frac "1.000000"; conf_lo "0.000000"; conf_hi "25.497879"; cov "0.675000";
+chr1	Cufflinks	exon	3110280	3110358	1000	.	.	gene_id "CUFF.43"; transcript_id "CUFF.43.1"; exon_number "1"; FPKM "10.5615674500"; frac "1.000000"; conf_lo "0.000000"; conf_hi "25.497879"; cov "0.675000";
+chr1	Cufflinks	transcript	3110488	3110589	1000	.	.	gene_id "CUFF.45"; transcript_id "CUFF.45.1"; FPKM "20.7089557842"; frac "1.000000"; conf_lo "2.186303"; conf_hi "39.231609"; cov "1.323529";
+chr1	Cufflinks	exon	3110488	3110589	1000	.	.	gene_id "CUFF.45"; transcript_id "CUFF.45.1"; exon_number "1"; FPKM "20.7089557842"; frac "1.000000"; conf_lo "2.186303"; conf_hi "39.231609"; cov "1.323529";
+chr1	Cufflinks	transcript	3111332	3111358	1000	.	.	gene_id "CUFF.49"; transcript_id "CUFF.49.1"; FPKM "15.6467665925"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.940300"; cov "1.000000";
+chr1	Cufflinks	exon	3111332	3111358	1000	.	.	gene_id "CUFF.49"; transcript_id "CUFF.49.1"; exon_number "1"; FPKM "15.6467665925"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.940300"; cov "1.000000";
+chr1	Cufflinks	transcript	3112113	3112139	1000	.	.	gene_id "CUFF.51"; transcript_id "CUFF.51.1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	exon	3112113	3112139	1000	.	.	gene_id "CUFF.51"; transcript_id "CUFF.51.1"; exon_number "1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	transcript	3112479	3112505	1000	.	.	gene_id "CUFF.53"; transcript_id "CUFF.53.1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	exon	3112479	3112505	1000	.	.	gene_id "CUFF.53"; transcript_id "CUFF.53.1"; exon_number "1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	transcript	3114116	3114142	1000	.	.	gene_id "CUFF.55"; transcript_id "CUFF.55.1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	exon	3114116	3114142	1000	.	.	gene_id "CUFF.55"; transcript_id "CUFF.55.1"; exon_number "1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	transcript	3114273	3114299	1000	.	.	gene_id "CUFF.57"; transcript_id "CUFF.57.1"; FPKM "15.6467665925"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.940300"; cov "1.000000";
+chr1	Cufflinks	exon	3114273	3114299	1000	.	.	gene_id "CUFF.57"; transcript_id "CUFF.57.1"; exon_number "1"; FPKM "15.6467665925"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.940300"; cov "1.000000";
+chr1	Cufflinks	transcript	3114373	3114399	1000	.	.	gene_id "CUFF.59"; transcript_id "CUFF.59.1"; FPKM "15.6467665925"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.940300"; cov "1.000000";
+chr1	Cufflinks	exon	3114373	3114399	1000	.	.	gene_id "CUFF.59"; transcript_id "CUFF.59.1"; exon_number "1"; FPKM "15.6467665925"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.940300"; cov "1.000000";
+chr1	Cufflinks	transcript	3201794	3201848	1000	.	.	gene_id "CUFF.65"; transcript_id "CUFF.65.1"; FPKM "15.3622799272"; frac "1.000000"; conf_lo "0.000000"; conf_hi "37.087825"; cov "0.981818";
+chr1	Cufflinks	exon	3201794	3201848	1000	.	.	gene_id "CUFF.65"; transcript_id "CUFF.65.1"; exon_number "1"; FPKM "15.3622799272"; frac "1.000000"; conf_lo "0.000000"; conf_hi "37.087825"; cov "0.981818";
+chr1	Cufflinks	transcript	3211077	3211141	1000	.	.	gene_id "CUFF.67"; transcript_id "CUFF.67.1"; FPKM "12.9988522461"; frac "1.000000"; conf_lo "0.000000"; conf_hi "31.382005"; cov "0.830769";
+chr1	Cufflinks	exon	3211077	3211141	1000	.	.	gene_id "CUFF.67"; transcript_id "CUFF.67.1"; exon_number "1"; FPKM "12.9988522461"; frac "1.000000"; conf_lo "0.000000"; conf_hi "31.382005"; cov "0.830769";
+chr1	Cufflinks	transcript	3211528	3211611	1000	.	.	gene_id "CUFF.69"; transcript_id "CUFF.69.1"; FPKM "10.0586356666"; frac "1.000000"; conf_lo "0.000000"; conf_hi "24.283695"; cov "0.642857";
+chr1	Cufflinks	exon	3211528	3211611	1000	.	.	gene_id "CUFF.69"; transcript_id "CUFF.69.1"; exon_number "1"; FPKM "10.0586356666"; frac "1.000000"; conf_lo "0.000000"; conf_hi "24.283695"; cov "0.642857";
+chr1	Cufflinks	transcript	3211677	3211774	1000	.	.	gene_id "CUFF.71"; transcript_id "CUFF.71.1"; FPKM "8.6216877142"; frac "1.000000"; conf_lo "0.000000"; conf_hi "20.814595"; cov "0.551020";
+chr1	Cufflinks	exon	3211677	3211774	1000	.	.	gene_id "CUFF.71"; transcript_id "CUFF.71.1"; exon_number "1"; FPKM "8.6216877142"; frac "1.000000"; conf_lo "0.000000"; conf_hi "20.814595"; cov "0.551020";
+chr1	Cufflinks	transcript	3220199	3220253	1000	.	.	gene_id "CUFF.73"; transcript_id "CUFF.73.1"; FPKM "15.3622799272"; frac "1.000000"; conf_lo "0.000000"; conf_hi "37.087825"; cov "0.981818";
+chr1	Cufflinks	exon	3220199	3220253	1000	.	.	gene_id "CUFF.73"; transcript_id "CUFF.73.1"; exon_number "1"; FPKM "15.3622799272"; frac "1.000000"; conf_lo "0.000000"; conf_hi "37.087825"; cov "0.981818";
+chr1	Cufflinks	transcript	3220641	3220667	1000	.	.	gene_id "CUFF.75"; transcript_id "CUFF.75.1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	exon	3220641	3220667	1000	.	.	gene_id "CUFF.75"; transcript_id "CUFF.75.1"; exon_number "1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	transcript	3240464	3240515	1000	.	.	gene_id "CUFF.77"; transcript_id "CUFF.77.1"; FPKM "16.2485653076"; frac "1.000000"; conf_lo "0.000000"; conf_hi "39.227507"; cov "1.038462";
+chr1	Cufflinks	exon	3240464	3240515	1000	.	.	gene_id "CUFF.77"; transcript_id "CUFF.77.1"; exon_number "1"; FPKM "16.2485653076"; frac "1.000000"; conf_lo "0.000000"; conf_hi "39.227507"; cov "1.038462";
+chr1	Cufflinks	transcript	3277601	3277627	1000	.	.	gene_id "CUFF.79"; transcript_id "CUFF.79.1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	exon	3277601	3277627	1000	.	.	gene_id "CUFF.79"; transcript_id "CUFF.79.1"; exon_number "1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	transcript	3285318	3285381	1000	.	.	gene_id "CUFF.81"; transcript_id "CUFF.81.1"; FPKM "13.2019593124"; frac "1.000000"; conf_lo "0.000000"; conf_hi "31.872349"; cov "0.843750";
+chr1	Cufflinks	exon	3285318	3285381	1000	.	.	gene_id "CUFF.81"; transcript_id "CUFF.81.1"; exon_number "1"; FPKM "13.2019593124"; frac "1.000000"; conf_lo "0.000000"; conf_hi "31.872349"; cov "0.843750";
+chr1	Cufflinks	transcript	3285858	3285953	1000	.	.	gene_id "CUFF.83"; transcript_id "CUFF.83.1"; FPKM "13.2019593124"; frac "1.000000"; conf_lo "0.000000"; conf_hi "28.446269"; cov "0.843750";
+chr1	Cufflinks	exon	3285858	3285953	1000	.	.	gene_id "CUFF.83"; transcript_id "CUFF.83.1"; exon_number "1"; FPKM "13.2019593124"; frac "1.000000"; conf_lo "0.000000"; conf_hi "28.446269"; cov "0.843750";
+chr1	Cufflinks	transcript	3289268	3289294	1000	.	.	gene_id "CUFF.85"; transcript_id "CUFF.85.1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	exon	3289268	3289294	1000	.	.	gene_id "CUFF.85"; transcript_id "CUFF.85.1"; exon_number "1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	transcript	3289466	3289514	1000	.	.	gene_id "CUFF.87"; transcript_id "CUFF.87.1"; FPKM "17.2433754285"; frac "1.000000"; conf_lo "0.000000"; conf_hi "41.629191"; cov "1.102041";
+chr1	Cufflinks	exon	3289466	3289514	1000	.	.	gene_id "CUFF.87"; transcript_id "CUFF.87.1"; exon_number "1"; FPKM "17.2433754285"; frac "1.000000"; conf_lo "0.000000"; conf_hi "41.629191"; cov "1.102041";
+chr1	Cufflinks	transcript	3300382	3300432	1000	.	.	gene_id "CUFF.89"; transcript_id "CUFF.89.1"; FPKM "16.5671646274"; frac "1.000000"; conf_lo "0.000000"; conf_hi "39.996674"; cov "1.058824";
+chr1	Cufflinks	exon	3300382	3300432	1000	.	.	gene_id "CUFF.89"; transcript_id "CUFF.89.1"; exon_number "1"; FPKM "16.5671646274"; frac "1.000000"; conf_lo "0.000000"; conf_hi "39.996674"; cov "1.058824";
+chr1	Cufflinks	transcript	3317446	3317472	1000	.	.	gene_id "CUFF.91"; transcript_id "CUFF.91.1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	exon	3317446	3317472	1000	.	.	gene_id "CUFF.91"; transcript_id "CUFF.91.1"; exon_number "1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	transcript	3365246	3365284	1000	.	.	gene_id "CUFF.93"; transcript_id "CUFF.93.1"; FPKM "21.6647537435"; frac "1.000000"; conf_lo "0.000000"; conf_hi "52.303342"; cov "1.384615";
+chr1	Cufflinks	exon	3365246	3365284	1000	.	.	gene_id "CUFF.93"; transcript_id "CUFF.93.1"; exon_number "1"; FPKM "21.6647537435"; frac "1.000000"; conf_lo "0.000000"; conf_hi "52.303342"; cov "1.384615";
+chr1	Cufflinks	transcript	3377607	3377633	1000	.	.	gene_id "CUFF.95"; transcript_id "CUFF.95.1"; FPKM "46.9402997776"; frac "1.000000"; conf_lo "0.000000"; conf_hi "101.142289"; cov "3.000000";
+chr1	Cufflinks	exon	3377607	3377633	1000	.	.	gene_id "CUFF.95"; transcript_id "CUFF.95.1"; exon_number "1"; FPKM "46.9402997776"; frac "1.000000"; conf_lo "0.000000"; conf_hi "101.142289"; cov "3.000000";
+chr1	Cufflinks	transcript	3381259	3381317	1000	.	.	gene_id "CUFF.97"; transcript_id "CUFF.97.1"; FPKM "21.4811541355"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.285454"; cov "1.372881";
+chr1	Cufflinks	exon	3381259	3381317	1000	.	.	gene_id "CUFF.97"; transcript_id "CUFF.97.1"; exon_number "1"; FPKM "21.4811541355"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.285454"; cov "1.372881";
+chr1	Cufflinks	transcript	3381404	3381474	1000	.	.	gene_id "CUFF.99"; transcript_id "CUFF.99.1"; FPKM "14.5676792413"; frac "1.000000"; conf_lo "0.000000"; conf_hi "35.169489"; cov "0.931034";
+chr1	Cufflinks	exon	3381404	3381474	1000	.	.	gene_id "CUFF.99"; transcript_id "CUFF.99.1"; exon_number "1"; FPKM "14.5676792413"; frac "1.000000"; conf_lo "0.000000"; conf_hi "35.169489"; cov "0.931034";
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data-orig/cuffcompare_in1_liftover_unmapped.bed	Sat Aug 02 10:24:42 2014 -0400
@@ -0,0 +1,28 @@
+# Deleted in new
+chr1	Cufflinks	transcript	3111546	3111576	1000	.	.	gene_id "CUFF.3"; transcript_id "CUFF.3.1"; FPKM "27.2556579354"; frac "1.000000"; conf_lo "0.000000"; conf_hi "65.800979"; cov "1.741935";
+# Deleted in new
+chr1	Cufflinks	exon	3111546	3111576	1000	.	.	gene_id "CUFF.3"; transcript_id "CUFF.3.1"; exon_number "1"; FPKM "27.2556579354"; frac "1.000000"; conf_lo "0.000000"; conf_hi "65.800979"; cov "1.741935";
+# Partially deleted in new
+chr1	Cufflinks	transcript	3243019	3243079	1000	.	.	gene_id "CUFF.21"; transcript_id "CUFF.21.1"; FPKM "13.8512359999"; frac "1.000000"; conf_lo "0.000000"; conf_hi "33.439842"; cov "0.885246";
+# Partially deleted in new
+chr1	Cufflinks	exon	3243019	3243079	1000	.	.	gene_id "CUFF.21"; transcript_id "CUFF.21.1"; exon_number "1"; FPKM "13.8512359999"; frac "1.000000"; conf_lo "0.000000"; conf_hi "33.439842"; cov "0.885246";
+# Partially deleted in new
+chr1	Cufflinks	transcript	3242634	3242923	1000	.	.	gene_id "CUFF.25"; transcript_id "CUFF.25.1"; FPKM "14.5676792413"; frac "1.000000"; conf_lo "5.354270"; conf_hi "23.781089"; cov "0.931034";
+# Partially deleted in new
+chr1	Cufflinks	exon	3242634	3242923	1000	.	.	gene_id "CUFF.25"; transcript_id "CUFF.25.1"; exon_number "1"; FPKM "14.5676792413"; frac "1.000000"; conf_lo "5.354270"; conf_hi "23.781089"; cov "0.931034";
+# Partially deleted in new
+chr1	Cufflinks	transcript	3191877	3191945	1000	.	.	gene_id "CUFF.37"; transcript_id "CUFF.37.1"; FPKM "104.0850125502"; frac "1.000000"; conf_lo "53.596365"; conf_hi "154.573660"; cov "6.652174";
+# Partially deleted in new
+chr1	Cufflinks	exon	3191877	3191945	1000	.	.	gene_id "CUFF.37"; transcript_id "CUFF.37.1"; exon_number "1"; FPKM "104.0850125502"; frac "1.000000"; conf_lo "53.596365"; conf_hi "154.573660"; cov "6.652174";
+# Partially deleted in new
+chr1	Cufflinks	transcript	3194186	3194226	1000	.	.	gene_id "CUFF.47"; transcript_id "CUFF.47.1"; FPKM "20.6079364877"; frac "1.000000"; conf_lo "0.000000"; conf_hi "49.751960"; cov "1.317073";
+# Partially deleted in new
+chr1	Cufflinks	exon	3194186	3194226	1000	.	.	gene_id "CUFF.47"; transcript_id "CUFF.47.1"; exon_number "1"; FPKM "20.6079364877"; frac "1.000000"; conf_lo "0.000000"; conf_hi "49.751960"; cov "1.317073";
+# Deleted in new
+chr1	Cufflinks	transcript	3277191	3277218	1000	.	.	gene_id "CUFF.61"; transcript_id "CUFF.61.1"; FPKM "45.2638604998"; frac "1.000000"; conf_lo "0.000000"; conf_hi "97.530065"; cov "2.892857";
+# Deleted in new
+chr1	Cufflinks	exon	3277191	3277218	1000	.	.	gene_id "CUFF.61"; transcript_id "CUFF.61.1"; exon_number "1"; FPKM "45.2638604998"; frac "1.000000"; conf_lo "0.000000"; conf_hi "97.530065"; cov "2.892857";
+# Deleted in new
+chr1	Cufflinks	transcript	3278237	3278263	1000	.	.	gene_id "CUFF.63"; transcript_id "CUFF.63.1"; FPKM "15.6467665925"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.940300"; cov "1.000000";
+# Deleted in new
+chr1	Cufflinks	exon	3278237	3278263	1000	.	.	gene_id "CUFF.63"; transcript_id "CUFF.63.1"; exon_number "1"; FPKM "15.6467665925"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.940300"; cov "1.000000";
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data-orig/cuffcompare_in1_mult_liftover_mapped.bed	Sat Aug 02 10:24:42 2014 -0400
@@ -0,0 +1,92 @@
+chr1	Cufflinks	transcript	3022555	3022596	1000	.	.	gene_id "CUFF.1"; transcript_id "CUFF.1.1"; FPKM "20.6079364877"; frac "1.000000"; conf_lo "0.000000"; conf_hi "49.751960"; cov "1.317073";
+chr1	Cufflinks	exon	3022555	3022596	1000	.	.	gene_id "CUFF.1"; transcript_id "CUFF.1.1"; exon_number "1"; FPKM "20.6079364877"; frac "1.000000"; conf_lo "0.000000"; conf_hi "49.751960"; cov "1.317073";
+chr1	Cufflinks	transcript	3117334	3117360	1000	.	.	gene_id "CUFF.5"; transcript_id "CUFF.5.1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	exon	3117334	3117360	1000	.	.	gene_id "CUFF.5"; transcript_id "CUFF.5.1"; exon_number "1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	transcript	3117031	3117199	1000	.	.	gene_id "CUFF.7"; transcript_id "CUFF.7.1"; FPKM "9.9991171124"; frac "1.000000"; conf_lo "0.000000"; conf_hi "19.998234"; cov "0.639053";
+chr1	Cufflinks	exon	3117031	3117199	1000	.	.	gene_id "CUFF.7"; transcript_id "CUFF.7.1"; exon_number "1"; FPKM "9.9991171124"; frac "1.000000"; conf_lo "0.000000"; conf_hi "19.998234"; cov "0.639053";
+chr1	Cufflinks	transcript	3118118	3118521	1000	.	.	gene_id "CUFF.9"; transcript_id "CUFF.9.1"; FPKM "17.7768957078"; frac "1.000000"; conf_lo "9.153835"; conf_hi "26.399957"; cov "1.136139";
+chr1	Cufflinks	exon	3118118	3118521	1000	.	.	gene_id "CUFF.9"; transcript_id "CUFF.9.1"; exon_number "1"; FPKM "17.7768957078"; frac "1.000000"; conf_lo "9.153835"; conf_hi "26.399957"; cov "1.136139";
+chr1	Cufflinks	transcript	3118713	3118739	1000	.	.	gene_id "CUFF.11"; transcript_id "CUFF.11.1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	exon	3118713	3118739	1000	.	.	gene_id "CUFF.11"; transcript_id "CUFF.11.1"; exon_number "1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	transcript	3121789	3121867	1000	.	.	gene_id "CUFF.13"; transcript_id "CUFF.13.1"; FPKM "10.6952581772"; frac "1.000000"; conf_lo "0.000000"; conf_hi "25.820637"; cov "0.683544";
+chr1	Cufflinks	exon	3121789	3121867	1000	.	.	gene_id "CUFF.13"; transcript_id "CUFF.13.1"; exon_number "1"; FPKM "10.6952581772"; frac "1.000000"; conf_lo "0.000000"; conf_hi "25.820637"; cov "0.683544";
+chr1	Cufflinks	transcript	3128503	3128581	1000	.	.	gene_id "CUFF.15"; transcript_id "CUFF.15.1"; FPKM "10.6952581772"; frac "1.000000"; conf_lo "0.000000"; conf_hi "25.820637"; cov "0.683544";
+chr1	Cufflinks	exon	3128503	3128581	1000	.	.	gene_id "CUFF.15"; transcript_id "CUFF.15.1"; exon_number "1"; FPKM "10.6952581772"; frac "1.000000"; conf_lo "0.000000"; conf_hi "25.820637"; cov "0.683544";
+chr1	Cufflinks	transcript	3129386	3129482	1000	.	.	gene_id "CUFF.17"; transcript_id "CUFF.17.1"; FPKM "8.7105710927"; frac "1.000000"; conf_lo "0.000000"; conf_hi "21.029179"; cov "0.556701";
+chr1	Cufflinks	exon	3129386	3129482	1000	.	.	gene_id "CUFF.17"; transcript_id "CUFF.17.1"; exon_number "1"; FPKM "8.7105710927"; frac "1.000000"; conf_lo "0.000000"; conf_hi "21.029179"; cov "0.556701";
+chr1	Cufflinks	transcript	3128657	3128728	1000	.	.	gene_id "CUFF.19"; transcript_id "CUFF.19.1"; FPKM "29.3376873610"; frac "1.000000"; conf_lo "3.097262"; conf_hi "55.578113"; cov "1.875000";
+chr1	Cufflinks	exon	3128657	3128728	1000	.	.	gene_id "CUFF.19"; transcript_id "CUFF.19.1"; exon_number "1"; FPKM "29.3376873610"; frac "1.000000"; conf_lo "3.097262"; conf_hi "55.578113"; cov "1.875000";
+chr1	Cufflinks	transcript	3162123	3162179	1000	.	.	gene_id "CUFF.21"; transcript_id "CUFF.21.1"; FPKM "13.8512359999"; frac "1.000000"; conf_lo "0.000000"; conf_hi "33.439842"; cov "0.885246";
+chr1	Cufflinks	exon	3162123	3162179	1000	.	.	gene_id "CUFF.21"; transcript_id "CUFF.21.1"; exon_number "1"; FPKM "13.8512359999"; frac "1.000000"; conf_lo "0.000000"; conf_hi "33.439842"; cov "0.885246";
+chr1	Cufflinks	transcript	3162445	3162500	1000	.	.	gene_id "CUFF.23"; transcript_id "CUFF.23.1"; FPKM "23.4701498888"; frac "1.000000"; conf_lo "0.000000"; conf_hi "50.571145"; cov "1.500000";
+chr1	Cufflinks	exon	3162445	3162500	1000	.	.	gene_id "CUFF.23"; transcript_id "CUFF.23.1"; exon_number "1"; FPKM "23.4701498888"; frac "1.000000"; conf_lo "0.000000"; conf_hi "50.571145"; cov "1.500000";
+chr1	Cufflinks	transcript	3161752	3162025	1000	.	.	gene_id "CUFF.25"; transcript_id "CUFF.25.1"; FPKM "14.5676792413"; frac "1.000000"; conf_lo "5.354270"; conf_hi "23.781089"; cov "0.931034";
+chr1	Cufflinks	exon	3161752	3162025	1000	.	.	gene_id "CUFF.25"; transcript_id "CUFF.25.1"; exon_number "1"; FPKM "14.5676792413"; frac "1.000000"; conf_lo "5.354270"; conf_hi "23.781089"; cov "0.931034";
+chr1	Cufflinks	transcript	3176998	3177034	1000	.	.	gene_id "CUFF.27"; transcript_id "CUFF.27.1"; FPKM "34.2537322701"; frac "1.000000"; conf_lo "0.000000"; conf_hi "73.806535"; cov "2.189189";
+chr1	Cufflinks	exon	3176998	3177034	1000	.	.	gene_id "CUFF.27"; transcript_id "CUFF.27.1"; exon_number "1"; FPKM "34.2537322701"; frac "1.000000"; conf_lo "0.000000"; conf_hi "73.806535"; cov "2.189189";
+chr1	Cufflinks	transcript	3107191	3107612	1000	.	.	gene_id "CUFF.29"; transcript_id "CUFF.29.1"; FPKM "107.1032192108"; frac "1.000000"; conf_lo "71.402146"; conf_hi "142.804292"; cov "6.845070";
+chr1	Cufflinks	exon	3107191	3107612	1000	.	.	gene_id "CUFF.29"; transcript_id "CUFF.29.1"; exon_number "1"; FPKM "107.1032192108"; frac "1.000000"; conf_lo "71.402146"; conf_hi "142.804292"; cov "6.845070";
+chr1	Cufflinks	transcript	3107844	3107874	1000	.	.	gene_id "CUFF.31"; transcript_id "CUFF.31.1"; FPKM "122.6504607091"; frac "1.000000"; conf_lo "40.883487"; conf_hi "204.417435"; cov "7.838710";
+chr1	Cufflinks	exon	3107844	3107874	1000	.	.	gene_id "CUFF.31"; transcript_id "CUFF.31.1"; exon_number "1"; FPKM "122.6504607091"; frac "1.000000"; conf_lo "40.883487"; conf_hi "204.417435"; cov "7.838710";
+chr1	Cufflinks	transcript	3108025	3108051	1000	.	.	gene_id "CUFF.33"; transcript_id "CUFF.33.1"; FPKM "109.5273661476"; frac "1.000000"; conf_lo "26.732460"; conf_hi "192.322273"; cov "7.000000";
+chr1	Cufflinks	exon	3108025	3108051	1000	.	.	gene_id "CUFF.33"; transcript_id "CUFF.33.1"; exon_number "1"; FPKM "109.5273661476"; frac "1.000000"; conf_lo "26.732460"; conf_hi "192.322273"; cov "7.000000";
+chr1	Cufflinks	transcript	3109111	3109241	1000	.	.	gene_id "CUFF.35"; transcript_id "CUFF.35.1"; FPKM "96.7471827476"; frac "1.000000"; conf_lo "61.420107"; conf_hi "132.074259"; cov "6.183206";
+chr1	Cufflinks	exon	3109111	3109241	1000	.	.	gene_id "CUFF.35"; transcript_id "CUFF.35.1"; exon_number "1"; FPKM "96.7471827476"; frac "1.000000"; conf_lo "61.420107"; conf_hi "132.074259"; cov "6.183206";
+chr1	Cufflinks	transcript	3109449	3109512	1000	.	.	gene_id "CUFF.37"; transcript_id "CUFF.37.1"; FPKM "104.0850125502"; frac "1.000000"; conf_lo "53.596365"; conf_hi "154.573660"; cov "6.652174";
+chr1	Cufflinks	exon	3109449	3109512	1000	.	.	gene_id "CUFF.37"; transcript_id "CUFF.37.1"; exon_number "1"; FPKM "104.0850125502"; frac "1.000000"; conf_lo "53.596365"; conf_hi "154.573660"; cov "6.652174";
+chr1	Cufflinks	transcript	3109989	3110041	1000	.	.	gene_id "CUFF.39"; transcript_id "CUFF.39.1"; FPKM "23.9129829055"; frac "1.000000"; conf_lo "0.000000"; conf_hi "51.525317"; cov "1.528302";
+chr1	Cufflinks	exon	3109989	3110041	1000	.	.	gene_id "CUFF.39"; transcript_id "CUFF.39.1"; exon_number "1"; FPKM "23.9129829055"; frac "1.000000"; conf_lo "0.000000"; conf_hi "51.525317"; cov "1.528302";
+chr1	Cufflinks	transcript	3110098	3110176	1000	.	.	gene_id "CUFF.41"; transcript_id "CUFF.41.1"; FPKM "10.6952581772"; frac "1.000000"; conf_lo "0.000000"; conf_hi "25.820637"; cov "0.683544";
+chr1	Cufflinks	exon	3110098	3110176	1000	.	.	gene_id "CUFF.41"; transcript_id "CUFF.41.1"; exon_number "1"; FPKM "10.6952581772"; frac "1.000000"; conf_lo "0.000000"; conf_hi "25.820637"; cov "0.683544";
+chr1	Cufflinks	transcript	3110280	3110358	1000	.	.	gene_id "CUFF.43"; transcript_id "CUFF.43.1"; FPKM "10.5615674500"; frac "1.000000"; conf_lo "0.000000"; conf_hi "25.497879"; cov "0.675000";
+chr1	Cufflinks	exon	3110280	3110358	1000	.	.	gene_id "CUFF.43"; transcript_id "CUFF.43.1"; exon_number "1"; FPKM "10.5615674500"; frac "1.000000"; conf_lo "0.000000"; conf_hi "25.497879"; cov "0.675000";
+chr1	Cufflinks	transcript	3110488	3110589	1000	.	.	gene_id "CUFF.45"; transcript_id "CUFF.45.1"; FPKM "20.7089557842"; frac "1.000000"; conf_lo "2.186303"; conf_hi "39.231609"; cov "1.323529";
+chr1	Cufflinks	exon	3110488	3110589	1000	.	.	gene_id "CUFF.45"; transcript_id "CUFF.45.1"; exon_number "1"; FPKM "20.7089557842"; frac "1.000000"; conf_lo "2.186303"; conf_hi "39.231609"; cov "1.323529";
+chr1	Cufflinks	transcript	3111332	3111358	1000	.	.	gene_id "CUFF.49"; transcript_id "CUFF.49.1"; FPKM "15.6467665925"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.940300"; cov "1.000000";
+chr1	Cufflinks	exon	3111332	3111358	1000	.	.	gene_id "CUFF.49"; transcript_id "CUFF.49.1"; exon_number "1"; FPKM "15.6467665925"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.940300"; cov "1.000000";
+chr1	Cufflinks	transcript	3112113	3112139	1000	.	.	gene_id "CUFF.51"; transcript_id "CUFF.51.1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	exon	3112113	3112139	1000	.	.	gene_id "CUFF.51"; transcript_id "CUFF.51.1"; exon_number "1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	transcript	3112479	3112505	1000	.	.	gene_id "CUFF.53"; transcript_id "CUFF.53.1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	exon	3112479	3112505	1000	.	.	gene_id "CUFF.53"; transcript_id "CUFF.53.1"; exon_number "1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	transcript	3114116	3114142	1000	.	.	gene_id "CUFF.55"; transcript_id "CUFF.55.1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	exon	3114116	3114142	1000	.	.	gene_id "CUFF.55"; transcript_id "CUFF.55.1"; exon_number "1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	transcript	3114273	3114299	1000	.	.	gene_id "CUFF.57"; transcript_id "CUFF.57.1"; FPKM "15.6467665925"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.940300"; cov "1.000000";
+chr1	Cufflinks	exon	3114273	3114299	1000	.	.	gene_id "CUFF.57"; transcript_id "CUFF.57.1"; exon_number "1"; FPKM "15.6467665925"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.940300"; cov "1.000000";
+chr1	Cufflinks	transcript	3114373	3114399	1000	.	.	gene_id "CUFF.59"; transcript_id "CUFF.59.1"; FPKM "15.6467665925"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.940300"; cov "1.000000";
+chr1	Cufflinks	exon	3114373	3114399	1000	.	.	gene_id "CUFF.59"; transcript_id "CUFF.59.1"; exon_number "1"; FPKM "15.6467665925"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.940300"; cov "1.000000";
+chr1	Cufflinks	transcript	3201794	3201848	1000	.	.	gene_id "CUFF.65"; transcript_id "CUFF.65.1"; FPKM "15.3622799272"; frac "1.000000"; conf_lo "0.000000"; conf_hi "37.087825"; cov "0.981818";
+chr1	Cufflinks	exon	3201794	3201848	1000	.	.	gene_id "CUFF.65"; transcript_id "CUFF.65.1"; exon_number "1"; FPKM "15.3622799272"; frac "1.000000"; conf_lo "0.000000"; conf_hi "37.087825"; cov "0.981818";
+chr1	Cufflinks	transcript	3211077	3211141	1000	.	.	gene_id "CUFF.67"; transcript_id "CUFF.67.1"; FPKM "12.9988522461"; frac "1.000000"; conf_lo "0.000000"; conf_hi "31.382005"; cov "0.830769";
+chr1	Cufflinks	exon	3211077	3211141	1000	.	.	gene_id "CUFF.67"; transcript_id "CUFF.67.1"; exon_number "1"; FPKM "12.9988522461"; frac "1.000000"; conf_lo "0.000000"; conf_hi "31.382005"; cov "0.830769";
+chr1	Cufflinks	transcript	3211528	3211611	1000	.	.	gene_id "CUFF.69"; transcript_id "CUFF.69.1"; FPKM "10.0586356666"; frac "1.000000"; conf_lo "0.000000"; conf_hi "24.283695"; cov "0.642857";
+chr1	Cufflinks	exon	3211528	3211611	1000	.	.	gene_id "CUFF.69"; transcript_id "CUFF.69.1"; exon_number "1"; FPKM "10.0586356666"; frac "1.000000"; conf_lo "0.000000"; conf_hi "24.283695"; cov "0.642857";
+chr1	Cufflinks	transcript	3211677	3211774	1000	.	.	gene_id "CUFF.71"; transcript_id "CUFF.71.1"; FPKM "8.6216877142"; frac "1.000000"; conf_lo "0.000000"; conf_hi "20.814595"; cov "0.551020";
+chr1	Cufflinks	exon	3211677	3211774	1000	.	.	gene_id "CUFF.71"; transcript_id "CUFF.71.1"; exon_number "1"; FPKM "8.6216877142"; frac "1.000000"; conf_lo "0.000000"; conf_hi "20.814595"; cov "0.551020";
+chr1	Cufflinks	transcript	3220199	3220253	1000	.	.	gene_id "CUFF.73"; transcript_id "CUFF.73.1"; FPKM "15.3622799272"; frac "1.000000"; conf_lo "0.000000"; conf_hi "37.087825"; cov "0.981818";
+chr1	Cufflinks	exon	3220199	3220253	1000	.	.	gene_id "CUFF.73"; transcript_id "CUFF.73.1"; exon_number "1"; FPKM "15.3622799272"; frac "1.000000"; conf_lo "0.000000"; conf_hi "37.087825"; cov "0.981818";
+chr1	Cufflinks	transcript	3220641	3220667	1000	.	.	gene_id "CUFF.75"; transcript_id "CUFF.75.1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	exon	3220641	3220667	1000	.	.	gene_id "CUFF.75"; transcript_id "CUFF.75.1"; exon_number "1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	transcript	3240464	3240515	1000	.	.	gene_id "CUFF.77"; transcript_id "CUFF.77.1"; FPKM "16.2485653076"; frac "1.000000"; conf_lo "0.000000"; conf_hi "39.227507"; cov "1.038462";
+chr1	Cufflinks	exon	3240464	3240515	1000	.	.	gene_id "CUFF.77"; transcript_id "CUFF.77.1"; exon_number "1"; FPKM "16.2485653076"; frac "1.000000"; conf_lo "0.000000"; conf_hi "39.227507"; cov "1.038462";
+chr1	Cufflinks	transcript	3277601	3277627	1000	.	.	gene_id "CUFF.79"; transcript_id "CUFF.79.1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	exon	3277601	3277627	1000	.	.	gene_id "CUFF.79"; transcript_id "CUFF.79.1"; exon_number "1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	transcript	3285318	3285381	1000	.	.	gene_id "CUFF.81"; transcript_id "CUFF.81.1"; FPKM "13.2019593124"; frac "1.000000"; conf_lo "0.000000"; conf_hi "31.872349"; cov "0.843750";
+chr1	Cufflinks	exon	3285318	3285381	1000	.	.	gene_id "CUFF.81"; transcript_id "CUFF.81.1"; exon_number "1"; FPKM "13.2019593124"; frac "1.000000"; conf_lo "0.000000"; conf_hi "31.872349"; cov "0.843750";
+chr1	Cufflinks	transcript	3285858	3285953	1000	.	.	gene_id "CUFF.83"; transcript_id "CUFF.83.1"; FPKM "13.2019593124"; frac "1.000000"; conf_lo "0.000000"; conf_hi "28.446269"; cov "0.843750";
+chr1	Cufflinks	exon	3285858	3285953	1000	.	.	gene_id "CUFF.83"; transcript_id "CUFF.83.1"; exon_number "1"; FPKM "13.2019593124"; frac "1.000000"; conf_lo "0.000000"; conf_hi "28.446269"; cov "0.843750";
+chr1	Cufflinks	transcript	3289268	3289294	1000	.	.	gene_id "CUFF.85"; transcript_id "CUFF.85.1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	exon	3289268	3289294	1000	.	.	gene_id "CUFF.85"; transcript_id "CUFF.85.1"; exon_number "1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	transcript	3289466	3289514	1000	.	.	gene_id "CUFF.87"; transcript_id "CUFF.87.1"; FPKM "17.2433754285"; frac "1.000000"; conf_lo "0.000000"; conf_hi "41.629191"; cov "1.102041";
+chr1	Cufflinks	exon	3289466	3289514	1000	.	.	gene_id "CUFF.87"; transcript_id "CUFF.87.1"; exon_number "1"; FPKM "17.2433754285"; frac "1.000000"; conf_lo "0.000000"; conf_hi "41.629191"; cov "1.102041";
+chr1	Cufflinks	transcript	3300382	3300432	1000	.	.	gene_id "CUFF.89"; transcript_id "CUFF.89.1"; FPKM "16.5671646274"; frac "1.000000"; conf_lo "0.000000"; conf_hi "39.996674"; cov "1.058824";
+chr1	Cufflinks	exon	3300382	3300432	1000	.	.	gene_id "CUFF.89"; transcript_id "CUFF.89.1"; exon_number "1"; FPKM "16.5671646274"; frac "1.000000"; conf_lo "0.000000"; conf_hi "39.996674"; cov "1.058824";
+chr1	Cufflinks	transcript	3317446	3317472	1000	.	.	gene_id "CUFF.91"; transcript_id "CUFF.91.1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	exon	3317446	3317472	1000	.	.	gene_id "CUFF.91"; transcript_id "CUFF.91.1"; exon_number "1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	transcript	3365246	3365284	1000	.	.	gene_id "CUFF.93"; transcript_id "CUFF.93.1"; FPKM "21.6647537435"; frac "1.000000"; conf_lo "0.000000"; conf_hi "52.303342"; cov "1.384615";
+chr1	Cufflinks	exon	3365246	3365284	1000	.	.	gene_id "CUFF.93"; transcript_id "CUFF.93.1"; exon_number "1"; FPKM "21.6647537435"; frac "1.000000"; conf_lo "0.000000"; conf_hi "52.303342"; cov "1.384615";
+chr1	Cufflinks	transcript	3377607	3377633	1000	.	.	gene_id "CUFF.95"; transcript_id "CUFF.95.1"; FPKM "46.9402997776"; frac "1.000000"; conf_lo "0.000000"; conf_hi "101.142289"; cov "3.000000";
+chr1	Cufflinks	exon	3377607	3377633	1000	.	.	gene_id "CUFF.95"; transcript_id "CUFF.95.1"; exon_number "1"; FPKM "46.9402997776"; frac "1.000000"; conf_lo "0.000000"; conf_hi "101.142289"; cov "3.000000";
+chr1	Cufflinks	transcript	3381259	3381317	1000	.	.	gene_id "CUFF.97"; transcript_id "CUFF.97.1"; FPKM "21.4811541355"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.285454"; cov "1.372881";
+chr1	Cufflinks	exon	3381259	3381317	1000	.	.	gene_id "CUFF.97"; transcript_id "CUFF.97.1"; exon_number "1"; FPKM "21.4811541355"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.285454"; cov "1.372881";
+chr1	Cufflinks	transcript	3381404	3381474	1000	.	.	gene_id "CUFF.99"; transcript_id "CUFF.99.1"; FPKM "14.5676792413"; frac "1.000000"; conf_lo "0.000000"; conf_hi "35.169489"; cov "0.931034";
+chr1	Cufflinks	exon	3381404	3381474	1000	.	.	gene_id "CUFF.99"; transcript_id "CUFF.99.1"; exon_number "1"; FPKM "14.5676792413"; frac "1.000000"; conf_lo "0.000000"; conf_hi "35.169489"; cov "0.931034";
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data-orig/cuffcompare_in1_mult_liftover_unmapped.bed	Sat Aug 02 10:24:42 2014 -0400
@@ -0,0 +1,16 @@
+# Deleted in new
+chr1	Cufflinks	transcript	3111546	3111576	1000	.	.	gene_id "CUFF.3"; transcript_id "CUFF.3.1"; FPKM "27.2556579354"; frac "1.000000"; conf_lo "0.000000"; conf_hi "65.800979"; cov "1.741935";
+# Deleted in new
+chr1	Cufflinks	exon	3111546	3111576	1000	.	.	gene_id "CUFF.3"; transcript_id "CUFF.3.1"; exon_number "1"; FPKM "27.2556579354"; frac "1.000000"; conf_lo "0.000000"; conf_hi "65.800979"; cov "1.741935";
+# Partially deleted in new
+chr1	Cufflinks	transcript	3194186	3194226	1000	.	.	gene_id "CUFF.47"; transcript_id "CUFF.47.1"; FPKM "20.6079364877"; frac "1.000000"; conf_lo "0.000000"; conf_hi "49.751960"; cov "1.317073";
+# Partially deleted in new
+chr1	Cufflinks	exon	3194186	3194226	1000	.	.	gene_id "CUFF.47"; transcript_id "CUFF.47.1"; exon_number "1"; FPKM "20.6079364877"; frac "1.000000"; conf_lo "0.000000"; conf_hi "49.751960"; cov "1.317073";
+# Deleted in new
+chr1	Cufflinks	transcript	3277191	3277218	1000	.	.	gene_id "CUFF.61"; transcript_id "CUFF.61.1"; FPKM "45.2638604998"; frac "1.000000"; conf_lo "0.000000"; conf_hi "97.530065"; cov "2.892857";
+# Deleted in new
+chr1	Cufflinks	exon	3277191	3277218	1000	.	.	gene_id "CUFF.61"; transcript_id "CUFF.61.1"; exon_number "1"; FPKM "45.2638604998"; frac "1.000000"; conf_lo "0.000000"; conf_hi "97.530065"; cov "2.892857";
+# Deleted in new
+chr1	Cufflinks	transcript	3278237	3278263	1000	.	.	gene_id "CUFF.63"; transcript_id "CUFF.63.1"; FPKM "15.6467665925"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.940300"; cov "1.000000";
+# Deleted in new
+chr1	Cufflinks	exon	3278237	3278263	1000	.	.	gene_id "CUFF.63"; transcript_id "CUFF.63.1"; exon_number "1"; FPKM "15.6467665925"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.940300"; cov "1.000000";
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data-orig/cuffcompare_in2.gtf	Sat Aug 02 10:24:42 2014 -0400
@@ -0,0 +1,100 @@
+chr1	Cufflinks	transcript	3174766	3174792	1000	.	.	gene_id "CUFF.1"; transcript_id "CUFF.1.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000";
+chr1	Cufflinks	exon	3174766	3174792	1000	.	.	gene_id "CUFF.1"; transcript_id "CUFF.1.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000";
+chr1	Cufflinks	transcript	3187402	3187428	1000	.	.	gene_id "CUFF.3"; transcript_id "CUFF.3.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000";
+chr1	Cufflinks	exon	3187402	3187428	1000	.	.	gene_id "CUFF.3"; transcript_id "CUFF.3.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000";
+chr1	Cufflinks	transcript	3188522	3188548	1000	.	.	gene_id "CUFF.5"; transcript_id "CUFF.5.1"; FPKM "21.2266273824"; frac "1.000000"; conf_lo "0.000000"; conf_hi "59.889707"; cov "1.205672";
+chr1	Cufflinks	exon	3188522	3188548	1000	.	.	gene_id "CUFF.5"; transcript_id "CUFF.5.1"; exon_number "1"; FPKM "21.2266273824"; frac "1.000000"; conf_lo "0.000000"; conf_hi "59.889707"; cov "1.205672";
+chr1	Cufflinks	transcript	3190859	3191434	1000	.	.	gene_id "CUFF.7"; transcript_id "CUFF.7.1"; FPKM "29.7095235531"; frac "1.000000"; conf_lo "19.806349"; conf_hi "39.612698"; cov "1.687500";
+chr1	Cufflinks	exon	3190859	3191434	1000	.	.	gene_id "CUFF.7"; transcript_id "CUFF.7.1"; exon_number "1"; FPKM "29.7095235531"; frac "1.000000"; conf_lo "19.806349"; conf_hi "39.612698"; cov "1.687500";
+chr1	Cufflinks	transcript	3191513	3192077	1000	.	.	gene_id "CUFF.9"; transcript_id "CUFF.9.1"; FPKM "34.0729325807"; frac "1.000000"; conf_lo "23.364686"; conf_hi "44.781179"; cov "1.935341";
+chr1	Cufflinks	exon	3191513	3192077	1000	.	.	gene_id "CUFF.9"; transcript_id "CUFF.9.1"; exon_number "1"; FPKM "34.0729325807"; frac "1.000000"; conf_lo "23.364686"; conf_hi "44.781179"; cov "1.935341";
+chr1	Cufflinks	transcript	3189811	3190789	1000	.	.	gene_id "CUFF.11"; transcript_id "CUFF.11.1"; FPKM "32.5317765567"; frac "1.000000"; conf_lo "24.582998"; conf_hi "40.480555"; cov "1.847804";
+chr1	Cufflinks	exon	3189811	3190789	1000	.	.	gene_id "CUFF.11"; transcript_id "CUFF.11.1"; exon_number "1"; FPKM "32.5317765567"; frac "1.000000"; conf_lo "24.582998"; conf_hi "40.480555"; cov "1.847804";
+chr1	Cufflinks	transcript	3192251	3192336	1000	.	.	gene_id "CUFF.13"; transcript_id "CUFF.13.1"; FPKM "16.5820596576"; frac "1.000000"; conf_lo "0.000000"; conf_hi "35.729373"; cov "0.941860";
+chr1	Cufflinks	exon	3192251	3192336	1000	.	.	gene_id "CUFF.13"; transcript_id "CUFF.13.1"; exon_number "1"; FPKM "16.5820596576"; frac "1.000000"; conf_lo "0.000000"; conf_hi "35.729373"; cov "0.941860";
+chr1	Cufflinks	transcript	3192650	3192676	1000	.	.	gene_id "CUFF.15"; transcript_id "CUFF.15.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000";
+chr1	Cufflinks	exon	3192650	3192676	1000	.	.	gene_id "CUFF.15"; transcript_id "CUFF.15.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000";
+chr1	Cufflinks	transcript	3194707	3194733	1000	.	.	gene_id "CUFF.17"; transcript_id "CUFF.17.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000";
+chr1	Cufflinks	exon	3194707	3194733	1000	.	.	gene_id "CUFF.17"; transcript_id "CUFF.17.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000";
+chr1	Cufflinks	transcript	3197426	3197452	1000	.	.	gene_id "CUFF.19"; transcript_id "CUFF.19.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000";
+chr1	Cufflinks	exon	3197426	3197452	1000	.	.	gene_id "CUFF.19"; transcript_id "CUFF.19.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000";
+chr1	Cufflinks	transcript	3200431	3200457	1000	.	.	gene_id "CUFF.21"; transcript_id "CUFF.21.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000";
+chr1	Cufflinks	exon	3200431	3200457	1000	.	.	gene_id "CUFF.21"; transcript_id "CUFF.21.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000";
+chr1	Cufflinks	transcript	3200057	3200144	1000	.	.	gene_id "CUFF.23"; transcript_id "CUFF.23.1"; FPKM "16.2051946653"; frac "1.000000"; conf_lo "0.000000"; conf_hi "34.917342"; cov "0.920455";
+chr1	Cufflinks	exon	3200057	3200144	1000	.	.	gene_id "CUFF.23"; transcript_id "CUFF.23.1"; exon_number "1"; FPKM "16.2051946653"; frac "1.000000"; conf_lo "0.000000"; conf_hi "34.917342"; cov "0.920455";
+chr1	Cufflinks	transcript	3201161	3201187	1000	.	.	gene_id "CUFF.25"; transcript_id "CUFF.25.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000";
+chr1	Cufflinks	exon	3201161	3201187	1000	.	.	gene_id "CUFF.25"; transcript_id "CUFF.25.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000";
+chr1	Cufflinks	transcript	3201008	3201039	1000	.	.	gene_id "CUFF.26"; transcript_id "CUFF.26.1"; FPKM "29.7095235531"; frac "1.000000"; conf_lo "0.000000"; conf_hi "71.725135"; cov "1.687500";
+chr1	Cufflinks	exon	3201008	3201039	1000	.	.	gene_id "CUFF.26"; transcript_id "CUFF.26.1"; exon_number "1"; FPKM "29.7095235531"; frac "1.000000"; conf_lo "0.000000"; conf_hi "71.725135"; cov "1.687500";
+chr1	Cufflinks	transcript	3201597	3201666	1000	.	.	gene_id "CUFF.29"; transcript_id "CUFF.29.1"; FPKM "13.5814964814"; frac "1.000000"; conf_lo "0.000000"; conf_hi "32.788633"; cov "0.771429";
+chr1	Cufflinks	exon	3201597	3201666	1000	.	.	gene_id "CUFF.29"; transcript_id "CUFF.29.1"; exon_number "1"; FPKM "13.5814964814"; frac "1.000000"; conf_lo "0.000000"; conf_hi "32.788633"; cov "0.771429";
+chr1	Cufflinks	transcript	3201726	3201809	1000	.	.	gene_id "CUFF.31"; transcript_id "CUFF.31.1"; FPKM "22.6358274691"; frac "1.000000"; conf_lo "0.000000"; conf_hi "45.271655"; cov "1.285714";
+chr1	Cufflinks	exon	3201726	3201809	1000	.	.	gene_id "CUFF.31"; transcript_id "CUFF.31.1"; exon_number "1"; FPKM "22.6358274691"; frac "1.000000"; conf_lo "0.000000"; conf_hi "45.271655"; cov "1.285714";
+chr1	Cufflinks	transcript	3211522	3211561	1000	.	.	gene_id "CUFF.33"; transcript_id "CUFF.33.1"; FPKM "23.7676188425"; frac "1.000000"; conf_lo "0.000000"; conf_hi "57.380108"; cov "1.350000";
+chr1	Cufflinks	exon	3211522	3211561	1000	.	.	gene_id "CUFF.33"; transcript_id "CUFF.33.1"; exon_number "1"; FPKM "23.7676188425"; frac "1.000000"; conf_lo "0.000000"; conf_hi "57.380108"; cov "1.350000";
+chr1	Cufflinks	transcript	3212718	3212801	1000	.	.	gene_id "CUFF.35"; transcript_id "CUFF.35.1"; FPKM "11.3179137345"; frac "1.000000"; conf_lo "0.000000"; conf_hi "27.323861"; cov "0.642857";
+chr1	Cufflinks	exon	3212718	3212801	1000	.	.	gene_id "CUFF.35"; transcript_id "CUFF.35.1"; exon_number "1"; FPKM "11.3179137345"; frac "1.000000"; conf_lo "0.000000"; conf_hi "27.323861"; cov "0.642857";
+chr1	Cufflinks	transcript	3213119	3213242	1000	.	.	gene_id "CUFF.37"; transcript_id "CUFF.37.1"; FPKM "11.5004607302"; frac "1.000000"; conf_lo "0.000000"; conf_hi "24.780049"; cov "0.653226";
+chr1	Cufflinks	exon	3213119	3213242	1000	.	.	gene_id "CUFF.37"; transcript_id "CUFF.37.1"; exon_number "1"; FPKM "11.5004607302"; frac "1.000000"; conf_lo "0.000000"; conf_hi "24.780049"; cov "0.653226";
+chr1	Cufflinks	transcript	3240607	3240633	1000	.	.	gene_id "CUFF.39"; transcript_id "CUFF.39.1"; FPKM "52.8169307611"; frac "1.000000"; conf_lo "0.000000"; conf_hi "113.804669"; cov "3.000000";
+chr1	Cufflinks	exon	3240607	3240633	1000	.	.	gene_id "CUFF.39"; transcript_id "CUFF.39.1"; exon_number "1"; FPKM "52.8169307611"; frac "1.000000"; conf_lo "0.000000"; conf_hi "113.804669"; cov "3.000000";
+chr1	Cufflinks	transcript	3242480	3242512	1000	.	.	gene_id "CUFF.41"; transcript_id "CUFF.41.1"; FPKM "43.2138524409"; frac "1.000000"; conf_lo "0.000000"; conf_hi "93.112911"; cov "2.454545";
+chr1	Cufflinks	exon	3242480	3242512	1000	.	.	gene_id "CUFF.41"; transcript_id "CUFF.41.1"; exon_number "1"; FPKM "43.2138524409"; frac "1.000000"; conf_lo "0.000000"; conf_hi "93.112911"; cov "2.454545";
+chr1	Cufflinks	transcript	3242925	3243005	1000	.	.	gene_id "CUFF.43"; transcript_id "CUFF.43.1"; FPKM "23.4741914494"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.948383"; cov "1.333333";
+chr1	Cufflinks	exon	3242925	3243005	1000	.	.	gene_id "CUFF.43"; transcript_id "CUFF.43.1"; exon_number "1"; FPKM "23.4741914494"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.948383"; cov "1.333333";
+chr1	Cufflinks	transcript	3243109	3243154	1000	.	.	gene_id "CUFF.45"; transcript_id "CUFF.45.1"; FPKM "20.6674946457"; frac "1.000000"; conf_lo "0.000000"; conf_hi "49.895746"; cov "1.173913";
+chr1	Cufflinks	exon	3243109	3243154	1000	.	.	gene_id "CUFF.45"; transcript_id "CUFF.45.1"; exon_number "1"; FPKM "20.6674946457"; frac "1.000000"; conf_lo "0.000000"; conf_hi "49.895746"; cov "1.173913";
+chr1	Cufflinks	transcript	3254080	3254106	1000	.	.	gene_id "CUFF.47"; transcript_id "CUFF.47.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000";
+chr1	Cufflinks	exon	3254080	3254106	1000	.	.	gene_id "CUFF.47"; transcript_id "CUFF.47.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000";
+chr1	Cufflinks	transcript	3277156	3277182	1000	.	.	gene_id "CUFF.49"; transcript_id "CUFF.49.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000";
+chr1	Cufflinks	exon	3277156	3277182	1000	.	.	gene_id "CUFF.49"; transcript_id "CUFF.49.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000";
+chr1	Cufflinks	transcript	3277914	3278390	1000	.	.	gene_id "CUFF.51"; transcript_id "CUFF.51.1"; FPKM "14.9481879513"; frac "1.000000"; conf_lo "7.228977"; conf_hi "22.667399"; cov "0.849057";
+chr1	Cufflinks	exon	3277914	3278390	1000	.	.	gene_id "CUFF.51"; transcript_id "CUFF.51.1"; exon_number "1"; FPKM "14.9481879513"; frac "1.000000"; conf_lo "7.228977"; conf_hi "22.667399"; cov "0.849057";
+chr1	Cufflinks	transcript	3280118	3280144	1000	.	.	gene_id "CUFF.53"; transcript_id "CUFF.53.1"; FPKM "52.8169307611"; frac "1.000000"; conf_lo "0.000000"; conf_hi "113.804669"; cov "3.000000";
+chr1	Cufflinks	exon	3280118	3280144	1000	.	.	gene_id "CUFF.53"; transcript_id "CUFF.53.1"; exon_number "1"; FPKM "52.8169307611"; frac "1.000000"; conf_lo "0.000000"; conf_hi "113.804669"; cov "3.000000";
+chr1	Cufflinks	transcript	3280499	3280525	1000	.	.	gene_id "CUFF.55"; transcript_id "CUFF.55.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000";
+chr1	Cufflinks	exon	3280499	3280525	1000	.	.	gene_id "CUFF.55"; transcript_id "CUFF.55.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000";
+chr1	Cufflinks	transcript	3282505	3282531	1000	.	.	gene_id "CUFF.57"; transcript_id "CUFF.57.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000";
+chr1	Cufflinks	exon	3282505	3282531	1000	.	.	gene_id "CUFF.57"; transcript_id "CUFF.57.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000";
+chr1	Cufflinks	transcript	3282651	3282677	1000	.	.	gene_id "CUFF.59"; transcript_id "CUFF.59.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000";
+chr1	Cufflinks	exon	3282651	3282677	1000	.	.	gene_id "CUFF.59"; transcript_id "CUFF.59.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000";
+chr1	Cufflinks	transcript	3282761	3282832	1000	.	.	gene_id "CUFF.61"; transcript_id "CUFF.61.1"; FPKM "13.2042326903"; frac "1.000000"; conf_lo "0.000000"; conf_hi "31.877838"; cov "0.750000";
+chr1	Cufflinks	exon	3282761	3282832	1000	.	.	gene_id "CUFF.61"; transcript_id "CUFF.61.1"; exon_number "1"; FPKM "13.2042326903"; frac "1.000000"; conf_lo "0.000000"; conf_hi "31.877838"; cov "0.750000";
+chr1	Cufflinks	transcript	3284967	3284993	1000	.	.	gene_id "CUFF.63"; transcript_id "CUFF.63.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000";
+chr1	Cufflinks	exon	3284967	3284993	1000	.	.	gene_id "CUFF.63"; transcript_id "CUFF.63.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000";
+chr1	Cufflinks	transcript	3290799	3290859	1000	.	.	gene_id "CUFF.65"; transcript_id "CUFF.65.1"; FPKM "31.1706476623"; frac "1.000000"; conf_lo "0.000000"; conf_hi "62.341295"; cov "1.770492";
+chr1	Cufflinks	exon	3290799	3290859	1000	.	.	gene_id "CUFF.65"; transcript_id "CUFF.65.1"; exon_number "1"; FPKM "31.1706476623"; frac "1.000000"; conf_lo "0.000000"; conf_hi "62.341295"; cov "1.770492";
+chr1	Cufflinks	transcript	3299444	3299640	1000	.	.	gene_id "CUFF.67"; transcript_id "CUFF.67.1"; FPKM "15.6813507371"; frac "1.000000"; conf_lo "3.378764"; conf_hi "27.983938"; cov "0.890700";
+chr1	Cufflinks	exon	3299444	3299640	1000	.	.	gene_id "CUFF.67"; transcript_id "CUFF.67.1"; exon_number "1"; FPKM "15.6813507371"; frac "1.000000"; conf_lo "3.378764"; conf_hi "27.983938"; cov "0.890700";
+chr1	Cufflinks	transcript	3290920	3291273	1000	.	.	gene_id "CUFF.69"; transcript_id "CUFF.69.1"; FPKM "18.7992465421"; frac "1.000000"; conf_lo "8.750627"; conf_hi "28.847866"; cov "1.067797";
+chr1	Cufflinks	exon	3290920	3291273	1000	.	.	gene_id "CUFF.69"; transcript_id "CUFF.69.1"; exon_number "1"; FPKM "18.7992465421"; frac "1.000000"; conf_lo "8.750627"; conf_hi "28.847866"; cov "1.067797";
+chr1	Cufflinks	transcript	3299692	3299733	1000	.	.	gene_id "CUFF.71"; transcript_id "CUFF.71.1"; FPKM "22.6358274691"; frac "1.000000"; conf_lo "0.000000"; conf_hi "54.647722"; cov "1.285714";
+chr1	Cufflinks	exon	3299692	3299733	1000	.	.	gene_id "CUFF.71"; transcript_id "CUFF.71.1"; exon_number "1"; FPKM "22.6358274691"; frac "1.000000"; conf_lo "0.000000"; conf_hi "54.647722"; cov "1.285714";
+chr1	Cufflinks	transcript	3307749	3307775	1000	.	.	gene_id "CUFF.73"; transcript_id "CUFF.73.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000";
+chr1	Cufflinks	exon	3307749	3307775	1000	.	.	gene_id "CUFF.73"; transcript_id "CUFF.73.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000";
+chr1	Cufflinks	transcript	3318621	3318647	1000	.	.	gene_id "CUFF.75"; transcript_id "CUFF.75.1"; FPKM "52.8169307611"; frac "1.000000"; conf_lo "0.000000"; conf_hi "113.804669"; cov "3.000000";
+chr1	Cufflinks	exon	3318621	3318647	1000	.	.	gene_id "CUFF.75"; transcript_id "CUFF.75.1"; exon_number "1"; FPKM "52.8169307611"; frac "1.000000"; conf_lo "0.000000"; conf_hi "113.804669"; cov "3.000000";
+chr1	Cufflinks	transcript	3330528	3330554	1000	.	.	gene_id "CUFF.77"; transcript_id "CUFF.77.1"; FPKM "17.6056435870"; frac "1.000000"; conf_lo "0.000000"; conf_hi "52.816931"; cov "1.000000";
+chr1	Cufflinks	exon	3330528	3330554	1000	.	.	gene_id "CUFF.77"; transcript_id "CUFF.77.1"; exon_number "1"; FPKM "17.6056435870"; frac "1.000000"; conf_lo "0.000000"; conf_hi "52.816931"; cov "1.000000";
+chr1	Cufflinks	transcript	3351241	3351311	1000	.	.	gene_id "CUFF.79"; transcript_id "CUFF.79.1"; FPKM "13.3902077986"; frac "1.000000"; conf_lo "0.000000"; conf_hi "32.326821"; cov "0.760563";
+chr1	Cufflinks	exon	3351241	3351311	1000	.	.	gene_id "CUFF.79"; transcript_id "CUFF.79.1"; exon_number "1"; FPKM "13.3902077986"; frac "1.000000"; conf_lo "0.000000"; conf_hi "32.326821"; cov "0.760563";
+chr1	Cufflinks	transcript	3355908	3356119	1000	.	.	gene_id "CUFF.81"; transcript_id "CUFF.81.1"; FPKM "11.2111409634"; frac "1.000000"; conf_lo "1.183592"; conf_hi "21.238690"; cov "0.636792";
+chr1	Cufflinks	exon	3355908	3356119	1000	.	.	gene_id "CUFF.81"; transcript_id "CUFF.81.1"; exon_number "1"; FPKM "11.2111409634"; frac "1.000000"; conf_lo "1.183592"; conf_hi "21.238690"; cov "0.636792";
+chr1	Cufflinks	transcript	3356181	3356225	1000	.	.	gene_id "CUFF.83"; transcript_id "CUFF.83.1"; FPKM "21.1267723045"; frac "1.000000"; conf_lo "0.000000"; conf_hi "51.004540"; cov "1.200000";
+chr1	Cufflinks	exon	3356181	3356225	1000	.	.	gene_id "CUFF.83"; transcript_id "CUFF.83.1"; exon_number "1"; FPKM "21.1267723045"; frac "1.000000"; conf_lo "0.000000"; conf_hi "51.004540"; cov "1.200000";
+chr1	Cufflinks	transcript	3363077	3363176	1000	.	.	gene_id "CUFF.85"; transcript_id "CUFF.85.1"; FPKM "19.0140950740"; frac "1.000000"; conf_lo "0.000000"; conf_hi "38.028190"; cov "1.080000";
+chr1	Cufflinks	exon	3363077	3363176	1000	.	.	gene_id "CUFF.85"; transcript_id "CUFF.85.1"; exon_number "1"; FPKM "19.0140950740"; frac "1.000000"; conf_lo "0.000000"; conf_hi "38.028190"; cov "1.080000";
+chr1	Cufflinks	transcript	3363388	3363446	1000	.	.	gene_id "CUFF.87"; transcript_id "CUFF.87.1"; FPKM "24.1704598398"; frac "1.000000"; conf_lo "0.000000"; conf_hi "52.080103"; cov "1.372881";
+chr1	Cufflinks	exon	3363388	3363446	1000	.	.	gene_id "CUFF.87"; transcript_id "CUFF.87.1"; exon_number "1"; FPKM "24.1704598398"; frac "1.000000"; conf_lo "0.000000"; conf_hi "52.080103"; cov "1.372881";
+chr1	Cufflinks	transcript	3364872	3364919	1000	.	.	gene_id "CUFF.89"; transcript_id "CUFF.89.1"; FPKM "29.7095235531"; frac "1.000000"; conf_lo "0.000000"; conf_hi "64.015126"; cov "1.687500";
+chr1	Cufflinks	exon	3364872	3364919	1000	.	.	gene_id "CUFF.89"; transcript_id "CUFF.89.1"; exon_number "1"; FPKM "29.7095235531"; frac "1.000000"; conf_lo "0.000000"; conf_hi "64.015126"; cov "1.687500";
+chr1	Cufflinks	transcript	3367211	3367237	1000	.	.	gene_id "CUFF.91"; transcript_id "CUFF.91.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000";
+chr1	Cufflinks	exon	3367211	3367237	1000	.	.	gene_id "CUFF.91"; transcript_id "CUFF.91.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000";
+chr1	Cufflinks	transcript	3369581	3369607	1000	.	.	gene_id "CUFF.93"; transcript_id "CUFF.93.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000";
+chr1	Cufflinks	exon	3369581	3369607	1000	.	.	gene_id "CUFF.93"; transcript_id "CUFF.93.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000";
+chr1	Cufflinks	transcript	3375002	3375028	1000	.	.	gene_id "CUFF.95"; transcript_id "CUFF.95.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000";
+chr1	Cufflinks	exon	3375002	3375028	1000	.	.	gene_id "CUFF.95"; transcript_id "CUFF.95.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000";
+chr1	Cufflinks	transcript	3379889	3379915	1000	.	.	gene_id "CUFF.97"; transcript_id "CUFF.97.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000";
+chr1	Cufflinks	exon	3379889	3379915	1000	.	.	gene_id "CUFF.97"; transcript_id "CUFF.97.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000";
+chr1	Cufflinks	transcript	3386740	3386836	1000	.	.	gene_id "CUFF.99"; transcript_id "CUFF.99.1"; FPKM "19.6021598701"; frac "1.000000"; conf_lo "0.000000"; conf_hi "39.204320"; cov "1.113402";
+chr1	Cufflinks	exon	3386740	3386836	1000	.	.	gene_id "CUFF.99"; transcript_id "CUFF.99.1"; exon_number "1"; FPKM "19.6021598701"; frac "1.000000"; conf_lo "0.000000"; conf_hi "39.204320"; cov "1.113402";
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data-orig/cuffcompare_in3.gtf	Sat Aug 02 10:24:42 2014 -0400
@@ -0,0 +1,100 @@
+chr1	mm9_refFlat	stop_codon	3206103	3206105	0.000000	-	.	gene_id "Xkr4"; transcript_id "Xkr4"; 
+chr1	mm9_refFlat	CDS	3206106	3207049	0.000000	-	2	gene_id "Xkr4"; transcript_id "Xkr4"; 
+chr1	mm9_refFlat	exon	3204563	3207049	0.000000	-	.	gene_id "Xkr4"; transcript_id "Xkr4"; 
+chr1	mm9_refFlat	CDS	3411783	3411982	0.000000	-	1	gene_id "Xkr4"; transcript_id "Xkr4"; 
+chr1	mm9_refFlat	exon	3411783	3411982	0.000000	-	.	gene_id "Xkr4"; transcript_id "Xkr4"; 
+chr1	mm9_refFlat	CDS	3660633	3661429	0.000000	-	0	gene_id "Xkr4"; transcript_id "Xkr4"; 
+chr1	mm9_refFlat	start_codon	3661427	3661429	0.000000	-	.	gene_id "Xkr4"; transcript_id "Xkr4"; 
+chr1	mm9_refFlat	exon	3660633	3661579	0.000000	-	.	gene_id "Xkr4"; transcript_id "Xkr4"; 
+chr1	mm9_refFlat	stop_codon	4334681	4334683	0.000000	-	.	gene_id "Rp1"; transcript_id "Rp1"; 
+chr1	mm9_refFlat	CDS	4334684	4340172	0.000000	-	2	gene_id "Rp1"; transcript_id "Rp1"; 
+chr1	mm9_refFlat	exon	4334224	4340172	0.000000	-	.	gene_id "Rp1"; transcript_id "Rp1"; 
+chr1	mm9_refFlat	CDS	4341991	4342162	0.000000	-	0	gene_id "Rp1"; transcript_id "Rp1"; 
+chr1	mm9_refFlat	exon	4341991	4342162	0.000000	-	.	gene_id "Rp1"; transcript_id "Rp1"; 
+chr1	mm9_refFlat	CDS	4342283	4342906	0.000000	-	0	gene_id "Rp1"; transcript_id "Rp1"; 
+chr1	mm9_refFlat	start_codon	4342904	4342906	0.000000	-	.	gene_id "Rp1"; transcript_id "Rp1"; 
+chr1	mm9_refFlat	exon	4342283	4342918	0.000000	-	.	gene_id "Rp1"; transcript_id "Rp1"; 
+chr1	mm9_refFlat	exon	4350281	4350473	0.000000	-	.	gene_id "Rp1"; transcript_id "Rp1"; 
+chr1	mm9_refFlat	stop_codon	4481797	4481799	0.000000	-	.	gene_id "Sox17"; transcript_id "Sox17"; 
+chr1	mm9_refFlat	CDS	4481800	4482749	0.000000	-	2	gene_id "Sox17"; transcript_id "Sox17"; 
+chr1	mm9_refFlat	exon	4481009	4482749	0.000000	-	.	gene_id "Sox17"; transcript_id "Sox17"; 
+chr1	mm9_refFlat	CDS	4483181	4483487	0.000000	-	0	gene_id "Sox17"; transcript_id "Sox17"; 
+chr1	mm9_refFlat	start_codon	4483485	4483487	0.000000	-	.	gene_id "Sox17"; transcript_id "Sox17"; 
+chr1	mm9_refFlat	exon	4483181	4483547	0.000000	-	.	gene_id "Sox17"; transcript_id "Sox17"; 
+chr1	mm9_refFlat	exon	4483853	4483944	0.000000	-	.	gene_id "Sox17"; transcript_id "Sox17"; 
+chr1	mm9_refFlat	exon	4485217	4486023	0.000000	-	.	gene_id "Sox17"; transcript_id "Sox17"; 
+chr1	mm9_refFlat	exon	4486372	4486494	0.000000	-	.	gene_id "Sox17"; transcript_id "Sox17"; 
+chr1	mm9_refFlat	stop_codon	4766545	4766547	0.000000	-	.	gene_id "Mrpl15"; transcript_id "Mrpl15"; 
+chr1	mm9_refFlat	CDS	4766548	4766882	0.000000	-	2	gene_id "Mrpl15"; transcript_id "Mrpl15"; 
+chr1	mm9_refFlat	exon	4763279	4766882	0.000000	-	.	gene_id "Mrpl15"; transcript_id "Mrpl15"; 
+chr1	mm9_refFlat	CDS	4767606	4767729	0.000000	-	0	gene_id "Mrpl15"; transcript_id "Mrpl15"; 
+chr1	mm9_refFlat	exon	4767606	4767729	0.000000	-	.	gene_id "Mrpl15"; transcript_id "Mrpl15"; 
+chr1	mm9_refFlat	CDS	4772649	4772814	0.000000	-	1	gene_id "Mrpl15"; transcript_id "Mrpl15"; 
+chr1	mm9_refFlat	exon	4772649	4772814	0.000000	-	.	gene_id "Mrpl15"; transcript_id "Mrpl15"; 
+chr1	mm9_refFlat	CDS	4774032	4774186	0.000000	-	0	gene_id "Mrpl15"; transcript_id "Mrpl15"; 
+chr1	mm9_refFlat	exon	4774032	4774186	0.000000	-	.	gene_id "Mrpl15"; transcript_id "Mrpl15"; 
+chr1	mm9_refFlat	CDS	4775654	4775758	0.000000	-	0	gene_id "Mrpl15"; transcript_id "Mrpl15"; 
+chr1	mm9_refFlat	start_codon	4775756	4775758	0.000000	-	.	gene_id "Mrpl15"; transcript_id "Mrpl15"; 
+chr1	mm9_refFlat	exon	4775654	4775807	0.000000	-	.	gene_id "Mrpl15"; transcript_id "Mrpl15"; 
+chr1	mm9_refFlat	stop_codon	4764533	4764535	0.000000	-	.	gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; 
+chr1	mm9_refFlat	CDS	4764536	4764597	0.000000	-	2	gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; 
+chr1	mm9_refFlat	exon	4763279	4764597	0.000000	-	.	gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; 
+chr1	mm9_refFlat	CDS	4767606	4767729	0.000000	-	0	gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; 
+chr1	mm9_refFlat	exon	4767606	4767729	0.000000	-	.	gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; 
+chr1	mm9_refFlat	CDS	4772649	4772814	0.000000	-	1	gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; 
+chr1	mm9_refFlat	exon	4772649	4772814	0.000000	-	.	gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; 
+chr1	mm9_refFlat	CDS	4774032	4774186	0.000000	-	0	gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; 
+chr1	mm9_refFlat	exon	4774032	4774186	0.000000	-	.	gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; 
+chr1	mm9_refFlat	CDS	4775654	4775758	0.000000	-	0	gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; 
+chr1	mm9_refFlat	start_codon	4775756	4775758	0.000000	-	.	gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; 
+chr1	mm9_refFlat	exon	4775654	4775807	0.000000	-	.	gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; 
+chr1	mm9_refFlat	exon	4763279	4764597	0.000000	-	.	gene_id "Mrpl15"; transcript_id "Mrpl15_dup2"; 
+chr1	mm9_refFlat	exon	4767606	4767729	0.000000	-	.	gene_id "Mrpl15"; transcript_id "Mrpl15_dup2"; 
+chr1	mm9_refFlat	exon	4772649	4772814	0.000000	-	.	gene_id "Mrpl15"; transcript_id "Mrpl15_dup2"; 
+chr1	mm9_refFlat	exon	4775654	4775807	0.000000	-	.	gene_id "Mrpl15"; transcript_id "Mrpl15_dup2"; 
+chr1	mm9_refFlat	start_codon	4797995	4797997	0.000000	+	.	gene_id "Lypla1"; transcript_id "Lypla1"; 
+chr1	mm9_refFlat	CDS	4797995	4798063	0.000000	+	0	gene_id "Lypla1"; transcript_id "Lypla1"; 
+chr1	mm9_refFlat	exon	4797974	4798063	0.000000	+	.	gene_id "Lypla1"; transcript_id "Lypla1"; 
+chr1	mm9_refFlat	CDS	4798536	4798567	0.000000	+	0	gene_id "Lypla1"; transcript_id "Lypla1"; 
+chr1	mm9_refFlat	exon	4798536	4798567	0.000000	+	.	gene_id "Lypla1"; transcript_id "Lypla1"; 
+chr1	mm9_refFlat	CDS	4818665	4818730	0.000000	+	1	gene_id "Lypla1"; transcript_id "Lypla1"; 
+chr1	mm9_refFlat	exon	4818665	4818730	0.000000	+	.	gene_id "Lypla1"; transcript_id "Lypla1"; 
+chr1	mm9_refFlat	CDS	4820349	4820396	0.000000	+	1	gene_id "Lypla1"; transcript_id "Lypla1"; 
+chr1	mm9_refFlat	exon	4820349	4820396	0.000000	+	.	gene_id "Lypla1"; transcript_id "Lypla1"; 
+chr1	mm9_refFlat	CDS	4822392	4822462	0.000000	+	1	gene_id "Lypla1"; transcript_id "Lypla1"; 
+chr1	mm9_refFlat	exon	4822392	4822462	0.000000	+	.	gene_id "Lypla1"; transcript_id "Lypla1"; 
+chr1	mm9_refFlat	CDS	4827082	4827155	0.000000	+	2	gene_id "Lypla1"; transcript_id "Lypla1"; 
+chr1	mm9_refFlat	exon	4827082	4827155	0.000000	+	.	gene_id "Lypla1"; transcript_id "Lypla1"; 
+chr1	mm9_refFlat	CDS	4829468	4829569	0.000000	+	0	gene_id "Lypla1"; transcript_id "Lypla1"; 
+chr1	mm9_refFlat	exon	4829468	4829569	0.000000	+	.	gene_id "Lypla1"; transcript_id "Lypla1"; 
+chr1	mm9_refFlat	CDS	4831037	4831213	0.000000	+	0	gene_id "Lypla1"; transcript_id "Lypla1"; 
+chr1	mm9_refFlat	exon	4831037	4831213	0.000000	+	.	gene_id "Lypla1"; transcript_id "Lypla1"; 
+chr1	mm9_refFlat	CDS	4835044	4835094	0.000000	+	0	gene_id "Lypla1"; transcript_id "Lypla1"; 
+chr1	mm9_refFlat	stop_codon	4835095	4835097	0.000000	+	.	gene_id "Lypla1"; transcript_id "Lypla1"; 
+chr1	mm9_refFlat	exon	4835044	4836816	0.000000	+	.	gene_id "Lypla1"; transcript_id "Lypla1"; 
+chr1	mm9_refFlat	start_codon	4847995	4847997	0.000000	+	.	gene_id "Tcea1"; transcript_id "Tcea1"; 
+chr1	mm9_refFlat	CDS	4847995	4848057	0.000000	+	0	gene_id "Tcea1"; transcript_id "Tcea1"; 
+chr1	mm9_refFlat	exon	4847775	4848057	0.000000	+	.	gene_id "Tcea1"; transcript_id "Tcea1"; 
+chr1	mm9_refFlat	CDS	4857551	4857613	0.000000	+	0	gene_id "Tcea1"; transcript_id "Tcea1"; 
+chr1	mm9_refFlat	exon	4857551	4857613	0.000000	+	.	gene_id "Tcea1"; transcript_id "Tcea1"; 
+chr1	mm9_refFlat	CDS	4868108	4868213	0.000000	+	0	gene_id "Tcea1"; transcript_id "Tcea1"; 
+chr1	mm9_refFlat	exon	4868108	4868213	0.000000	+	.	gene_id "Tcea1"; transcript_id "Tcea1"; 
+chr1	mm9_refFlat	CDS	4876825	4876912	0.000000	+	2	gene_id "Tcea1"; transcript_id "Tcea1"; 
+chr1	mm9_refFlat	exon	4876825	4876912	0.000000	+	.	gene_id "Tcea1"; transcript_id "Tcea1"; 
+chr1	mm9_refFlat	CDS	4879538	4879683	0.000000	+	1	gene_id "Tcea1"; transcript_id "Tcea1"; 
+chr1	mm9_refFlat	exon	4879538	4879683	0.000000	+	.	gene_id "Tcea1"; transcript_id "Tcea1"; 
+chr1	mm9_refFlat	CDS	4880821	4880877	0.000000	+	2	gene_id "Tcea1"; transcript_id "Tcea1"; 
+chr1	mm9_refFlat	exon	4880821	4880877	0.000000	+	.	gene_id "Tcea1"; transcript_id "Tcea1"; 
+chr1	mm9_refFlat	CDS	4881996	4882150	0.000000	+	2	gene_id "Tcea1"; transcript_id "Tcea1"; 
+chr1	mm9_refFlat	exon	4881996	4882150	0.000000	+	.	gene_id "Tcea1"; transcript_id "Tcea1"; 
+chr1	mm9_refFlat	CDS	4883498	4883644	0.000000	+	0	gene_id "Tcea1"; transcript_id "Tcea1"; 
+chr1	mm9_refFlat	exon	4883498	4883644	0.000000	+	.	gene_id "Tcea1"; transcript_id "Tcea1"; 
+chr1	mm9_refFlat	CDS	4885015	4885086	0.000000	+	0	gene_id "Tcea1"; transcript_id "Tcea1"; 
+chr1	mm9_refFlat	exon	4885015	4885086	0.000000	+	.	gene_id "Tcea1"; transcript_id "Tcea1"; 
+chr1	mm9_refFlat	CDS	4886437	4886442	0.000000	+	0	gene_id "Tcea1"; transcript_id "Tcea1"; 
+chr1	mm9_refFlat	stop_codon	4886443	4886445	0.000000	+	.	gene_id "Tcea1"; transcript_id "Tcea1"; 
+chr1	mm9_refFlat	exon	4886437	4887987	0.000000	+	.	gene_id "Tcea1"; transcript_id "Tcea1"; 
+chr1	mm9_refFlat	start_codon	4847995	4847997	0.000000	+	.	gene_id "Tcea1"; transcript_id "Tcea1_dup1"; 
+chr1	mm9_refFlat	CDS	4847995	4848057	0.000000	+	0	gene_id "Tcea1"; transcript_id "Tcea1_dup1"; 
+chr1	mm9_refFlat	exon	4847775	4848057	0.000000	+	.	gene_id "Tcea1"; transcript_id "Tcea1_dup1"; 
+chr1	mm9_refFlat	CDS	4857551	4857613	0.000000	+	0	gene_id "Tcea1"; transcript_id "Tcea1_dup1"; 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data-orig/cuffcompare_out1.tmap	Sat Aug 02 10:24:42 2014 -0400
@@ -0,0 +1,51 @@
+ref_gene_id	ref_id	class_code	cuff_gene_id	cuff_id	FMI	FPKM	FPKM_conf_lo	FPKM_conf_hi	cov	len	major_iso_id	ref_match_len
+-	-	u	CUFF.1	CUFF.1.1	100	20.607936	0.000000	49.751960	1.317073	41	CUFF.1.1	-
+-	-	u	CUFF.3	CUFF.3.1	100	27.255658	0.000000	65.800979	1.741935	31	CUFF.3.1	-
+-	-	u	CUFF.5	CUFF.5.1	100	31.293533	0.000000	75.549272	2.000000	27	CUFF.5.1	-
+-	-	u	CUFF.7	CUFF.7.1	100	9.999117	0.000000	19.998234	0.639053	169	CUFF.7.1	-
+-	-	u	CUFF.9	CUFF.9.1	100	17.776896	9.153835	26.399957	1.136139	404	CUFF.9.1	-
+-	-	u	CUFF.11	CUFF.11.1	100	31.293533	0.000000	75.549272	2.000000	27	CUFF.11.1	-
+Xkr4	Xkr4	c	CUFF.13	CUFF.13.1	100	10.695258	0.000000	25.820637	0.683544	79	CUFF.13.1	3634
+Xkr4	Xkr4	i	CUFF.15	CUFF.15.1	100	10.695258	0.000000	25.820637	0.683544	79	CUFF.15.1	3634
+Xkr4	Xkr4	i	CUFF.17	CUFF.17.1	100	8.710571	0.000000	21.029179	0.556701	97	CUFF.17.1	3634
+Xkr4	Xkr4	i	CUFF.19	CUFF.19.1	100	29.337687	3.097262	55.578113	1.875000	72	CUFF.19.1	3634
+Xkr4	Xkr4	i	CUFF.21	CUFF.21.1	100	13.851236	0.000000	33.439842	0.885246	61	CUFF.21.1	3634
+Xkr4	Xkr4	i	CUFF.23	CUFF.23.1	100	23.470150	0.000000	50.571145	1.500000	54	CUFF.23.1	3634
+Xkr4	Xkr4	i	CUFF.25	CUFF.25.1	100	14.567679	5.354270	23.781089	0.931034	290	CUFF.25.1	3634
+Xkr4	Xkr4	i	CUFF.27	CUFF.27.1	100	34.253732	0.000000	73.806535	2.189189	37	CUFF.27.1	3634
+-	-	u	CUFF.29	CUFF.29.1	100	107.103219	71.402146	142.804292	6.845070	142	CUFF.29.1	-
+-	-	u	CUFF.31	CUFF.31.1	100	122.650461	40.883487	204.417435	7.838710	31	CUFF.31.1	-
+-	-	u	CUFF.33	CUFF.33.1	100	109.527366	26.732460	192.322273	7.000000	27	CUFF.33.1	-
+-	-	u	CUFF.35	CUFF.35.1	100	96.747183	61.420107	132.074259	6.183206	131	CUFF.35.1	-
+-	-	u	CUFF.37	CUFF.37.1	100	104.085013	53.596365	154.573660	6.652174	69	CUFF.37.1	-
+-	-	u	CUFF.39	CUFF.39.1	100	23.912983	0.000000	51.525317	1.528302	53	CUFF.39.1	-
+-	-	u	CUFF.41	CUFF.41.1	100	10.695258	0.000000	25.820637	0.683544	79	CUFF.41.1	-
+-	-	u	CUFF.43	CUFF.43.1	100	10.561567	0.000000	25.497879	0.675000	80	CUFF.43.1	-
+-	-	u	CUFF.45	CUFF.45.1	100	20.708956	2.186303	39.231609	1.323529	102	CUFF.45.1	-
+-	-	u	CUFF.47	CUFF.47.1	100	20.607936	0.000000	49.751960	1.317073	41	CUFF.47.1	-
+-	-	u	CUFF.49	CUFF.49.1	100	15.646767	0.000000	46.940300	1.000000	27	CUFF.49.1	-
+-	-	u	CUFF.51	CUFF.51.1	100	31.293533	0.000000	75.549272	2.000000	27	CUFF.51.1	-
+-	-	u	CUFF.53	CUFF.53.1	100	31.293533	0.000000	75.549272	2.000000	27	CUFF.53.1	-
+-	-	u	CUFF.55	CUFF.55.1	100	31.293533	0.000000	75.549272	2.000000	27	CUFF.55.1	-
+-	-	u	CUFF.57	CUFF.57.1	100	15.646767	0.000000	46.940300	1.000000	27	CUFF.57.1	-
+-	-	u	CUFF.59	CUFF.59.1	100	15.646767	0.000000	46.940300	1.000000	27	CUFF.59.1	-
+Xkr4	Xkr4	i	CUFF.61	CUFF.61.1	100	45.263860	0.000000	97.530065	2.892857	28	CUFF.61.1	3634
+Xkr4	Xkr4	i	CUFF.63	CUFF.63.1	100	15.646767	0.000000	46.940300	1.000000	27	CUFF.63.1	3634
+Xkr4	Xkr4	i	CUFF.65	CUFF.65.1	100	15.362280	0.000000	37.087825	0.981818	55	CUFF.65.1	3634
+Xkr4	Xkr4	i	CUFF.67	CUFF.67.1	100	12.998852	0.000000	31.382005	0.830769	65	CUFF.67.1	3634
+Xkr4	Xkr4	i	CUFF.69	CUFF.69.1	100	10.058636	0.000000	24.283695	0.642857	84	CUFF.69.1	3634
+Xkr4	Xkr4	i	CUFF.71	CUFF.71.1	100	8.621688	0.000000	20.814595	0.551020	98	CUFF.71.1	3634
+Xkr4	Xkr4	i	CUFF.73	CUFF.73.1	100	15.362280	0.000000	37.087825	0.981818	55	CUFF.73.1	3634
+Xkr4	Xkr4	i	CUFF.75	CUFF.75.1	100	31.293533	0.000000	75.549272	2.000000	27	CUFF.75.1	3634
+Xkr4	Xkr4	i	CUFF.77	CUFF.77.1	100	16.248565	0.000000	39.227507	1.038462	52	CUFF.77.1	3634
+Xkr4	Xkr4	i	CUFF.79	CUFF.79.1	100	31.293533	0.000000	75.549272	2.000000	27	CUFF.79.1	3634
+Xkr4	Xkr4	i	CUFF.81	CUFF.81.1	100	13.201959	0.000000	31.872349	0.843750	64	CUFF.81.1	3634
+Xkr4	Xkr4	i	CUFF.83	CUFF.83.1	100	13.201959	0.000000	28.446269	0.843750	96	CUFF.83.1	3634
+Xkr4	Xkr4	i	CUFF.85	CUFF.85.1	100	31.293533	0.000000	75.549272	2.000000	27	CUFF.85.1	3634
+Xkr4	Xkr4	i	CUFF.87	CUFF.87.1	100	17.243375	0.000000	41.629191	1.102041	49	CUFF.87.1	3634
+Xkr4	Xkr4	i	CUFF.89	CUFF.89.1	100	16.567165	0.000000	39.996674	1.058824	51	CUFF.89.1	3634
+Xkr4	Xkr4	i	CUFF.91	CUFF.91.1	100	31.293533	0.000000	75.549272	2.000000	27	CUFF.91.1	3634
+Xkr4	Xkr4	i	CUFF.93	CUFF.93.1	100	21.664754	0.000000	52.303342	1.384615	39	CUFF.93.1	3634
+Xkr4	Xkr4	i	CUFF.95	CUFF.95.1	100	46.940300	0.000000	101.142289	3.000000	27	CUFF.95.1	3634
+Xkr4	Xkr4	i	CUFF.97	CUFF.97.1	100	21.481154	0.000000	46.285454	1.372881	59	CUFF.97.1	3634
+Xkr4	Xkr4	i	CUFF.99	CUFF.99.1	100	14.567679	0.000000	35.169489	0.931034	58	CUFF.99.1	3634
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data-orig/cuffcompare_out2.refmap	Sat Aug 02 10:24:42 2014 -0400
@@ -0,0 +1,2 @@
+ref_gene_id	ref_id	class_code	cuff_id_list
+Xkr4	Xkr4	c	CUFF.13|CUFF.13.1
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data-orig/cuffcompare_out3.tmap	Sat Aug 02 10:24:42 2014 -0400
@@ -0,0 +1,51 @@
+ref_gene_id	ref_id	class_code	cuff_gene_id	cuff_id	FMI	FPKM	FPKM_conf_lo	FPKM_conf_hi	cov	len	major_iso_id	ref_match_len
+-	-	u	CUFF.1	CUFF.1.1	100	35.211287	0.000000	85.007567	2.000000	27	CUFF.1.1	-
+-	-	u	CUFF.3	CUFF.3.1	100	35.211287	0.000000	85.007567	2.000000	27	CUFF.3.1	-
+-	-	u	CUFF.5	CUFF.5.1	100	21.226627	0.000000	59.889707	1.205672	27	CUFF.5.1	-
+-	-	u	CUFF.7	CUFF.7.1	100	29.709524	19.806349	39.612698	1.687500	576	CUFF.7.1	-
+-	-	u	CUFF.9	CUFF.9.1	100	34.072933	23.364686	44.781179	1.935341	565	CUFF.9.1	-
+-	-	u	CUFF.11	CUFF.11.1	100	32.531777	24.582998	40.480555	1.847804	979	CUFF.11.1	-
+-	-	u	CUFF.13	CUFF.13.1	100	16.582060	0.000000	35.729373	0.941860	86	CUFF.13.1	-
+-	-	u	CUFF.15	CUFF.15.1	100	35.211287	0.000000	85.007567	2.000000	27	CUFF.15.1	-
+-	-	u	CUFF.17	CUFF.17.1	100	35.211287	0.000000	85.007567	2.000000	27	CUFF.17.1	-
+-	-	u	CUFF.19	CUFF.19.1	100	35.211287	0.000000	85.007567	2.000000	27	CUFF.19.1	-
+-	-	u	CUFF.21	CUFF.21.1	100	35.211287	0.000000	85.007567	2.000000	27	CUFF.21.1	-
+-	-	u	CUFF.23	CUFF.23.1	100	16.205195	0.000000	34.917342	0.920455	88	CUFF.23.1	-
+-	-	u	CUFF.25	CUFF.25.1	100	35.211287	0.000000	85.007567	2.000000	27	CUFF.25.1	-
+-	-	u	CUFF.26	CUFF.26.1	100	29.709524	0.000000	71.725135	1.687500	32	CUFF.26.1	-
+-	-	u	CUFF.29	CUFF.29.1	100	13.581496	0.000000	32.788633	0.771429	70	CUFF.29.1	-
+-	-	u	CUFF.31	CUFF.31.1	100	22.635827	0.000000	45.271655	1.285714	84	CUFF.31.1	-
+Xkr4	Xkr4	i	CUFF.33	CUFF.33.1	100	23.767619	0.000000	57.380108	1.350000	40	CUFF.33.1	3634
+Xkr4	Xkr4	i	CUFF.35	CUFF.35.1	100	11.317914	0.000000	27.323861	0.642857	84	CUFF.35.1	3634
+Xkr4	Xkr4	i	CUFF.37	CUFF.37.1	100	11.500461	0.000000	24.780049	0.653226	124	CUFF.37.1	3634
+Xkr4	Xkr4	i	CUFF.39	CUFF.39.1	100	52.816931	0.000000	113.804669	3.000000	27	CUFF.39.1	3634
+Xkr4	Xkr4	i	CUFF.41	CUFF.41.1	100	43.213852	0.000000	93.112911	2.454545	33	CUFF.41.1	3634
+Xkr4	Xkr4	i	CUFF.43	CUFF.43.1	100	23.474191	0.000000	46.948383	1.333333	81	CUFF.43.1	3634
+Xkr4	Xkr4	i	CUFF.45	CUFF.45.1	100	20.667495	0.000000	49.895746	1.173913	46	CUFF.45.1	3634
+Xkr4	Xkr4	i	CUFF.47	CUFF.47.1	100	35.211287	0.000000	85.007567	2.000000	27	CUFF.47.1	3634
+Xkr4	Xkr4	i	CUFF.49	CUFF.49.1	100	35.211287	0.000000	85.007567	2.000000	27	CUFF.49.1	3634
+Xkr4	Xkr4	i	CUFF.51	CUFF.51.1	100	14.948188	7.228977	22.667399	0.849057	477	CUFF.51.1	3634
+Xkr4	Xkr4	i	CUFF.53	CUFF.53.1	100	52.816931	0.000000	113.804669	3.000000	27	CUFF.53.1	3634
+Xkr4	Xkr4	i	CUFF.55	CUFF.55.1	100	35.211287	0.000000	85.007567	2.000000	27	CUFF.55.1	3634
+Xkr4	Xkr4	i	CUFF.57	CUFF.57.1	100	35.211287	0.000000	85.007567	2.000000	27	CUFF.57.1	3634
+Xkr4	Xkr4	i	CUFF.59	CUFF.59.1	100	35.211287	0.000000	85.007567	2.000000	27	CUFF.59.1	3634
+Xkr4	Xkr4	i	CUFF.61	CUFF.61.1	100	13.204233	0.000000	31.877838	0.750000	72	CUFF.61.1	3634
+Xkr4	Xkr4	i	CUFF.63	CUFF.63.1	100	35.211287	0.000000	85.007567	2.000000	27	CUFF.63.1	3634
+Xkr4	Xkr4	i	CUFF.65	CUFF.65.1	100	31.170648	0.000000	62.341295	1.770492	61	CUFF.65.1	3634
+Xkr4	Xkr4	i	CUFF.67	CUFF.67.1	100	15.681351	3.378764	27.983938	0.890700	197	CUFF.67.1	3634
+Xkr4	Xkr4	i	CUFF.69	CUFF.69.1	100	18.799247	8.750627	28.847866	1.067797	354	CUFF.69.1	3634
+Xkr4	Xkr4	i	CUFF.71	CUFF.71.1	100	22.635827	0.000000	54.647722	1.285714	42	CUFF.71.1	3634
+Xkr4	Xkr4	i	CUFF.73	CUFF.73.1	100	35.211287	0.000000	85.007567	2.000000	27	CUFF.73.1	3634
+Xkr4	Xkr4	i	CUFF.75	CUFF.75.1	100	52.816931	0.000000	113.804669	3.000000	27	CUFF.75.1	3634
+Xkr4	Xkr4	i	CUFF.77	CUFF.77.1	100	17.605644	0.000000	52.816931	1.000000	27	CUFF.77.1	3634
+Xkr4	Xkr4	i	CUFF.79	CUFF.79.1	100	13.390208	0.000000	32.326821	0.760563	71	CUFF.79.1	3634
+Xkr4	Xkr4	i	CUFF.81	CUFF.81.1	100	11.211141	1.183592	21.238690	0.636792	212	CUFF.81.1	3634
+Xkr4	Xkr4	i	CUFF.83	CUFF.83.1	100	21.126772	0.000000	51.004540	1.200000	45	CUFF.83.1	3634
+Xkr4	Xkr4	i	CUFF.85	CUFF.85.1	100	19.014095	0.000000	38.028190	1.080000	100	CUFF.85.1	3634
+Xkr4	Xkr4	i	CUFF.87	CUFF.87.1	100	24.170460	0.000000	52.080103	1.372881	59	CUFF.87.1	3634
+Xkr4	Xkr4	i	CUFF.89	CUFF.89.1	100	29.709524	0.000000	64.015126	1.687500	48	CUFF.89.1	3634
+Xkr4	Xkr4	i	CUFF.91	CUFF.91.1	100	35.211287	0.000000	85.007567	2.000000	27	CUFF.91.1	3634
+Xkr4	Xkr4	i	CUFF.93	CUFF.93.1	100	35.211287	0.000000	85.007567	2.000000	27	CUFF.93.1	3634
+Xkr4	Xkr4	i	CUFF.95	CUFF.95.1	100	35.211287	0.000000	85.007567	2.000000	27	CUFF.95.1	3634
+Xkr4	Xkr4	i	CUFF.97	CUFF.97.1	100	35.211287	0.000000	85.007567	2.000000	27	CUFF.97.1	3634
+Xkr4	Xkr4	i	CUFF.99	CUFF.99.1	100	19.602160	0.000000	39.204320	1.113402	97	CUFF.99.1	3634
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data-orig/cuffcompare_out4.refmap	Sat Aug 02 10:24:42 2014 -0400
@@ -0,0 +1,1 @@
+ref_gene_id	ref_id	class_code	cuff_id_list
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data-orig/cuffcompare_out5.gtf	Sat Aug 02 10:24:42 2014 -0400
@@ -0,0 +1,90 @@
+chr1	Cufflinks	exon	3204755	3204833	.	-	.	gene_id "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.13.1"; nearest_ref "Xkr4"; class_code "c"; tss_id "TSS1";
+chr1	Cufflinks	exon	3111450	3111490	.	.	.	gene_id "XLOC_000002"; transcript_id "TCONS_00000002"; exon_number "1"; oId "CUFF.1.1"; class_code "u"; tss_id "TSS2";
+chr1	Cufflinks	exon	3111546	3111576	.	.	.	gene_id "XLOC_000003"; transcript_id "TCONS_00000003"; exon_number "1"; oId "CUFF.3.1"; class_code "u"; tss_id "TSS3";
+chr1	Cufflinks	exon	3174766	3174792	.	.	.	gene_id "XLOC_000004"; transcript_id "TCONS_00000051"; exon_number "1"; oId "CUFF.1.1"; class_code "u"; tss_id "TSS4";
+chr1	Cufflinks	exon	3187402	3187428	.	.	.	gene_id "XLOC_000005"; transcript_id "TCONS_00000052"; exon_number "1"; oId "CUFF.3.1"; class_code "u"; tss_id "TSS5";
+chr1	Cufflinks	exon	3188522	3188548	.	.	.	gene_id "XLOC_000006"; transcript_id "TCONS_00000053"; exon_number "1"; oId "CUFF.5.1"; class_code "u"; tss_id "TSS6";
+chr1	Cufflinks	exon	3189811	3190789	.	.	.	gene_id "XLOC_000007"; transcript_id "TCONS_00000054"; exon_number "1"; oId "CUFF.11.1"; class_code "u"; tss_id "TSS7";
+chr1	Cufflinks	exon	3190859	3191434	.	.	.	gene_id "XLOC_000008"; transcript_id "TCONS_00000055"; exon_number "1"; oId "CUFF.7.1"; class_code "u"; tss_id "TSS10";
+chr1	Cufflinks	exon	3191513	3192077	.	.	.	gene_id "XLOC_000009"; transcript_id "TCONS_00000056"; exon_number "1"; oId "CUFF.9.1"; class_code "u"; tss_id "TSS11";
+chr1	Cufflinks	exon	3192251	3192336	.	.	.	gene_id "XLOC_000010"; transcript_id "TCONS_00000057"; exon_number "1"; oId "CUFF.13.1"; class_code "u"; tss_id "TSS13";
+chr1	Cufflinks	exon	3192442	3192494	.	.	.	gene_id "XLOC_000011"; transcript_id "TCONS_00000009"; exon_number "1"; oId "CUFF.39.1"; class_code "u"; tss_id "TSS14";
+chr1	Cufflinks	exon	3192551	3192629	.	.	.	gene_id "XLOC_000012"; transcript_id "TCONS_00000010"; exon_number "1"; oId "CUFF.41.1"; class_code "u"; tss_id "TSS15";
+chr1	Cufflinks	exon	3192650	3192676	.	.	.	gene_id "XLOC_000013"; transcript_id "TCONS_00000058"; exon_number "1"; oId "CUFF.15.1"; class_code "u"; tss_id "TSS16";
+chr1	Cufflinks	exon	3192732	3192811	.	.	.	gene_id "XLOC_000014"; transcript_id "TCONS_00000011"; exon_number "1"; oId "CUFF.43.1"; class_code "u"; tss_id "TSS17";
+chr1	Cufflinks	exon	3192941	3193042	.	.	.	gene_id "XLOC_000015"; transcript_id "TCONS_00000012"; exon_number "1"; oId "CUFF.45.1"; class_code "u"; tss_id "TSS18";
+chr1	Cufflinks	exon	3194186	3194226	.	.	.	gene_id "XLOC_000016"; transcript_id "TCONS_00000013"; exon_number "1"; oId "CUFF.47.1"; class_code "u"; tss_id "TSS19";
+chr1	Cufflinks	exon	3194303	3194329	.	.	.	gene_id "XLOC_000017"; transcript_id "TCONS_00000014"; exon_number "1"; oId "CUFF.49.1"; class_code "u"; tss_id "TSS20";
+chr1	Cufflinks	exon	3194707	3194733	.	.	.	gene_id "XLOC_000018"; transcript_id "TCONS_00000059"; exon_number "1"; oId "CUFF.17.1"; class_code "u"; tss_id "TSS21";
+chr1	Cufflinks	exon	3195084	3195110	.	.	.	gene_id "XLOC_000019"; transcript_id "TCONS_00000015"; exon_number "1"; oId "CUFF.51.1"; class_code "u"; tss_id "TSS22";
+chr1	Cufflinks	exon	3195451	3195477	.	.	.	gene_id "XLOC_000020"; transcript_id "TCONS_00000016"; exon_number "1"; oId "CUFF.53.1"; class_code "u"; tss_id "TSS23";
+chr1	Cufflinks	exon	3197090	3197116	.	.	.	gene_id "XLOC_000021"; transcript_id "TCONS_00000017"; exon_number "1"; oId "CUFF.55.1"; class_code "u"; tss_id "TSS24";
+chr1	Cufflinks	exon	3197247	3197273	.	.	.	gene_id "XLOC_000022"; transcript_id "TCONS_00000018"; exon_number "1"; oId "CUFF.57.1"; class_code "u"; tss_id "TSS25";
+chr1	Cufflinks	exon	3197347	3197373	.	.	.	gene_id "XLOC_000023"; transcript_id "TCONS_00000019"; exon_number "1"; oId "CUFF.59.1"; class_code "u"; tss_id "TSS26";
+chr1	Cufflinks	exon	3197426	3197452	.	.	.	gene_id "XLOC_000024"; transcript_id "TCONS_00000060"; exon_number "1"; oId "CUFF.19.1"; class_code "u"; tss_id "TSS27";
+chr1	Cufflinks	exon	3200023	3200191	.	.	.	gene_id "XLOC_000025"; transcript_id "TCONS_00000020"; exon_number "1"; oId "CUFF.7.1"; class_code "u"; tss_id "TSS28";
+chr1	Cufflinks	exon	3200326	3200352	.	.	.	gene_id "XLOC_000026"; transcript_id "TCONS_00000021"; exon_number "1"; oId "CUFF.5.1"; class_code "u"; tss_id "TSS29";
+chr1	Cufflinks	exon	3200431	3200457	.	.	.	gene_id "XLOC_000027"; transcript_id "TCONS_00000062"; exon_number "1"; oId "CUFF.21.1"; class_code "u"; tss_id "TSS30";
+chr1	Cufflinks	exon	3201008	3201039	.	.	.	gene_id "XLOC_000028"; transcript_id "TCONS_00000063"; exon_number "1"; oId "CUFF.26.1"; class_code "u"; tss_id "TSS31";
+chr1	Cufflinks	exon	3201078	3201481	.	.	.	gene_id "XLOC_000029"; transcript_id "TCONS_00000022"; exon_number "1"; oId "CUFF.9.1"; class_code "u"; tss_id "TSS32";
+chr1	Cufflinks	exon	3201597	3201666	.	.	.	gene_id "XLOC_000030"; transcript_id "TCONS_00000065"; exon_number "1"; oId "CUFF.29.1"; class_code "u"; tss_id "TSS33";
+chr1	Cufflinks	exon	3201673	3201699	.	.	.	gene_id "XLOC_000031"; transcript_id "TCONS_00000023"; exon_number "1"; oId "CUFF.11.1"; class_code "u"; tss_id "TSS34";
+chr1	Cufflinks	exon	3201726	3201809	.	.	.	gene_id "XLOC_000032"; transcript_id "TCONS_00000066"; exon_number "1"; oId "CUFF.31.1"; class_code "u"; tss_id "TSS35";
+chr1	Cufflinks	exon	3211522	3211561	.	.	.	gene_id "XLOC_000033"; transcript_id "TCONS_00000067"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.33.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS36";
+chr1	Cufflinks	exon	3212214	3212292	.	.	.	gene_id "XLOC_000034"; transcript_id "TCONS_00000024"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.15.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS37";
+chr1	Cufflinks	exon	3212368	3212439	.	.	.	gene_id "XLOC_000035"; transcript_id "TCONS_00000025"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.19.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS38";
+chr1	Cufflinks	exon	3212718	3212801	.	.	.	gene_id "XLOC_000036"; transcript_id "TCONS_00000068"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.35.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS39";
+chr1	Cufflinks	exon	3213096	3213192	.	.	.	gene_id "XLOC_000037"; transcript_id "TCONS_00000026"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.17.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS40";
+chr1	Cufflinks	exon	3213119	3213242	.	.	.	gene_id "XLOC_000037"; transcript_id "TCONS_00000069"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.37.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS40";
+chr1	Cufflinks	exon	3240607	3240633	.	.	.	gene_id "XLOC_000038"; transcript_id "TCONS_00000070"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.39.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS41";
+chr1	Cufflinks	exon	3242480	3242512	.	.	.	gene_id "XLOC_000039"; transcript_id "TCONS_00000071"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.41.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS42";
+chr1	Cufflinks	exon	3242634	3242923	.	.	.	gene_id "XLOC_000040"; transcript_id "TCONS_00000027"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.25.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS43";
+chr1	Cufflinks	exon	3242925	3243005	.	.	.	gene_id "XLOC_000041"; transcript_id "TCONS_00000072"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.43.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS44";
+chr1	Cufflinks	exon	3243019	3243079	.	.	.	gene_id "XLOC_000042"; transcript_id "TCONS_00000028"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.21.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS45";
+chr1	Cufflinks	exon	3243109	3243154	.	.	.	gene_id "XLOC_000043"; transcript_id "TCONS_00000073"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.45.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS46";
+chr1	Cufflinks	exon	3243348	3243401	.	.	.	gene_id "XLOC_000044"; transcript_id "TCONS_00000029"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.23.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS47";
+chr1	Cufflinks	exon	3254080	3254106	.	.	.	gene_id "XLOC_000045"; transcript_id "TCONS_00000074"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.47.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS48";
+chr1	Cufflinks	exon	3256975	3257011	.	.	.	gene_id "XLOC_000046"; transcript_id "TCONS_00000030"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.27.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS49";
+chr1	Cufflinks	exon	3277156	3277182	.	.	.	gene_id "XLOC_000047"; transcript_id "TCONS_00000075"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.49.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS50";
+chr1	Cufflinks	exon	3277191	3277218	.	.	.	gene_id "XLOC_000048"; transcript_id "TCONS_00000031"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.61.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS51";
+chr1	Cufflinks	exon	3277914	3278390	.	.	.	gene_id "XLOC_000049"; transcript_id "TCONS_00000076"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.51.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS52";
+chr1	Cufflinks	exon	3280118	3280144	.	.	.	gene_id "XLOC_000050"; transcript_id "TCONS_00000077"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.53.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS54";
+chr1	Cufflinks	exon	3280499	3280525	.	.	.	gene_id "XLOC_000051"; transcript_id "TCONS_00000078"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.55.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS55";
+chr1	Cufflinks	exon	3280687	3280741	.	.	.	gene_id "XLOC_000052"; transcript_id "TCONS_00000033"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.65.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS56";
+chr1	Cufflinks	exon	3282505	3282531	.	.	.	gene_id "XLOC_000053"; transcript_id "TCONS_00000079"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.57.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS57";
+chr1	Cufflinks	exon	3282651	3282677	.	.	.	gene_id "XLOC_000054"; transcript_id "TCONS_00000080"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.59.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS58";
+chr1	Cufflinks	exon	3282761	3282832	.	.	.	gene_id "XLOC_000055"; transcript_id "TCONS_00000081"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.61.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS59";
+chr1	Cufflinks	exon	3284967	3284993	.	.	.	gene_id "XLOC_000056"; transcript_id "TCONS_00000082"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.63.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS60";
+chr1	Cufflinks	exon	3290489	3290553	.	.	.	gene_id "XLOC_000057"; transcript_id "TCONS_00000034"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.67.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS61";
+chr1	Cufflinks	exon	3290799	3290859	.	.	.	gene_id "XLOC_000058"; transcript_id "TCONS_00000083"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.65.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS62";
+chr1	Cufflinks	exon	3290920	3291273	.	.	.	gene_id "XLOC_000059"; transcript_id "TCONS_00000084"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.69.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS63";
+chr1	Cufflinks	exon	3299444	3299640	.	.	.	gene_id "XLOC_000060"; transcript_id "TCONS_00000085"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.67.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS65";
+chr1	Cufflinks	exon	3299610	3299664	.	.	.	gene_id "XLOC_000060"; transcript_id "TCONS_00000037"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.73.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS66";
+chr1	Cufflinks	exon	3299692	3299733	.	.	.	gene_id "XLOC_000061"; transcript_id "TCONS_00000086"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.71.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS67";
+chr1	Cufflinks	exon	3300052	3300078	.	.	.	gene_id "XLOC_000062"; transcript_id "TCONS_00000038"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.75.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS68";
+chr1	Cufflinks	exon	3307749	3307775	.	.	.	gene_id "XLOC_000063"; transcript_id "TCONS_00000087"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.73.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS69";
+chr1	Cufflinks	exon	3318621	3318647	.	.	.	gene_id "XLOC_000064"; transcript_id "TCONS_00000088"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.75.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS70";
+chr1	Cufflinks	exon	3319000	3319051	.	.	.	gene_id "XLOC_000065"; transcript_id "TCONS_00000039"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.77.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS71";
+chr1	Cufflinks	exon	3330528	3330554	.	.	.	gene_id "XLOC_000066"; transcript_id "TCONS_00000089"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.77.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS72";
+chr1	Cufflinks	exon	3351241	3351311	.	.	.	gene_id "XLOC_000067"; transcript_id "TCONS_00000090"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.79.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS73";
+chr1	Cufflinks	exon	3355888	3355914	.	.	.	gene_id "XLOC_000068"; transcript_id "TCONS_00000040"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.79.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS74";
+chr1	Cufflinks	exon	3355908	3356119	.	.	.	gene_id "XLOC_000068"; transcript_id "TCONS_00000091"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.81.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS74";
+chr1	Cufflinks	exon	3356181	3356225	.	.	.	gene_id "XLOC_000069"; transcript_id "TCONS_00000092"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.83.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS75";
+chr1	Cufflinks	exon	3363077	3363176	.	.	.	gene_id "XLOC_000070"; transcript_id "TCONS_00000093"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.85.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS76";
+chr1	Cufflinks	exon	3363215	3363278	.	.	.	gene_id "XLOC_000071"; transcript_id "TCONS_00000041"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.81.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS77";
+chr1	Cufflinks	exon	3363388	3363446	.	.	.	gene_id "XLOC_000072"; transcript_id "TCONS_00000094"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.87.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS78";
+chr1	Cufflinks	exon	3363754	3363849	.	.	.	gene_id "XLOC_000073"; transcript_id "TCONS_00000042"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.83.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS79";
+chr1	Cufflinks	exon	3364872	3364919	.	.	.	gene_id "XLOC_000074"; transcript_id "TCONS_00000095"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.89.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS80";
+chr1	Cufflinks	exon	3367136	3367162	.	.	.	gene_id "XLOC_000075"; transcript_id "TCONS_00000043"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.85.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS81";
+chr1	Cufflinks	exon	3367211	3367237	.	.	.	gene_id "XLOC_000076"; transcript_id "TCONS_00000096"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.91.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS82";
+chr1	Cufflinks	exon	3367334	3367382	.	.	.	gene_id "XLOC_000077"; transcript_id "TCONS_00000044"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.87.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS83";
+chr1	Cufflinks	exon	3369581	3369607	.	.	.	gene_id "XLOC_000078"; transcript_id "TCONS_00000097"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.93.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS84";
+chr1	Cufflinks	exon	3375002	3375028	.	.	.	gene_id "XLOC_000079"; transcript_id "TCONS_00000098"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.95.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS85";
+chr1	Cufflinks	exon	3377212	3377262	.	.	.	gene_id "XLOC_000080"; transcript_id "TCONS_00000045"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.89.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS86";
+chr1	Cufflinks	exon	3379889	3379915	.	.	.	gene_id "XLOC_000081"; transcript_id "TCONS_00000099"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.97.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS87";
+chr1	Cufflinks	exon	3386740	3386836	.	.	.	gene_id "XLOC_000082"; transcript_id "TCONS_00000100"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.99.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS88";
+chr1	Cufflinks	exon	3391326	3391352	.	.	.	gene_id "XLOC_000083"; transcript_id "TCONS_00000046"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.91.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS89";
+chr1	Cufflinks	exon	3435842	3435880	.	.	.	gene_id "XLOC_000084"; transcript_id "TCONS_00000047"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.93.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS90";
+chr1	Cufflinks	exon	3447762	3447788	.	.	.	gene_id "XLOC_000085"; transcript_id "TCONS_00000048"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.95.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS91";
+chr1	Cufflinks	exon	3450907	3450965	.	.	.	gene_id "XLOC_000086"; transcript_id "TCONS_00000049"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.97.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS92";
+chr1	Cufflinks	exon	3451052	3451109	.	.	.	gene_id "XLOC_000087"; transcript_id "TCONS_00000050"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.99.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS93";
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data-orig/cuffcompare_out6.tracking	Sat Aug 02 10:24:42 2014 -0400
@@ -0,0 +1,100 @@
+TCONS_00000001	XLOC_000001	Xkr4|Xkr4	c	q1:CUFF.13|CUFF.13.1|100|10.695258|0.000000|25.820637|0.683544|-	-
+TCONS_00000002	XLOC_000002	-	u	q1:CUFF.1|CUFF.1.1|100|20.607936|0.000000|49.751960|1.317073|-	-
+TCONS_00000003	XLOC_000003	-	u	q1:CUFF.3|CUFF.3.1|100|27.255658|0.000000|65.800979|1.741935|-	-
+TCONS_00000004	XLOC_000007	-	u	q1:CUFF.29|CUFF.29.1|100|107.103219|71.402146|142.804292|6.845070|-	-
+TCONS_00000005	XLOC_000007	-	u	q1:CUFF.31|CUFF.31.1|100|122.650461|40.883487|204.417435|7.838710|-	-
+TCONS_00000006	XLOC_000007	-	u	q1:CUFF.33|CUFF.33.1|100|109.527366|26.732460|192.322273|7.000000|-	-
+TCONS_00000007	XLOC_000009	-	u	q1:CUFF.35|CUFF.35.1|100|96.747183|61.420107|132.074259|6.183206|-	-
+TCONS_00000008	XLOC_000009	-	u	q1:CUFF.37|CUFF.37.1|100|104.085013|53.596365|154.573660|6.652174|-	-
+TCONS_00000009	XLOC_000011	-	u	q1:CUFF.39|CUFF.39.1|100|23.912983|0.000000|51.525317|1.528302|-	-
+TCONS_00000010	XLOC_000012	-	u	q1:CUFF.41|CUFF.41.1|100|10.695258|0.000000|25.820637|0.683544|-	-
+TCONS_00000011	XLOC_000014	-	u	q1:CUFF.43|CUFF.43.1|100|10.561567|0.000000|25.497879|0.675000|-	-
+TCONS_00000012	XLOC_000015	-	u	q1:CUFF.45|CUFF.45.1|100|20.708956|2.186303|39.231609|1.323529|-	-
+TCONS_00000013	XLOC_000016	-	u	q1:CUFF.47|CUFF.47.1|100|20.607936|0.000000|49.751960|1.317073|-	-
+TCONS_00000014	XLOC_000017	-	u	q1:CUFF.49|CUFF.49.1|100|15.646767|0.000000|46.940300|1.000000|-	-
+TCONS_00000015	XLOC_000019	-	u	q1:CUFF.51|CUFF.51.1|100|31.293533|0.000000|75.549272|2.000000|-	-
+TCONS_00000016	XLOC_000020	-	u	q1:CUFF.53|CUFF.53.1|100|31.293533|0.000000|75.549272|2.000000|-	-
+TCONS_00000017	XLOC_000021	-	u	q1:CUFF.55|CUFF.55.1|100|31.293533|0.000000|75.549272|2.000000|-	-
+TCONS_00000018	XLOC_000022	-	u	q1:CUFF.57|CUFF.57.1|100|15.646767|0.000000|46.940300|1.000000|-	-
+TCONS_00000019	XLOC_000023	-	u	q1:CUFF.59|CUFF.59.1|100|15.646767|0.000000|46.940300|1.000000|-	-
+TCONS_00000020	XLOC_000025	-	u	q1:CUFF.7|CUFF.7.1|100|9.999117|0.000000|19.998234|0.639053|-	-
+TCONS_00000021	XLOC_000026	-	u	q1:CUFF.5|CUFF.5.1|100|31.293533|0.000000|75.549272|2.000000|-	-
+TCONS_00000022	XLOC_000029	-	u	q1:CUFF.9|CUFF.9.1|100|17.776896|9.153835|26.399957|1.136139|-	-
+TCONS_00000023	XLOC_000031	-	u	q1:CUFF.11|CUFF.11.1|100|31.293533|0.000000|75.549272|2.000000|-	-
+TCONS_00000024	XLOC_000034	Xkr4|Xkr4	i	q1:CUFF.15|CUFF.15.1|100|10.695258|0.000000|25.820637|0.683544|-	-
+TCONS_00000025	XLOC_000035	Xkr4|Xkr4	i	q1:CUFF.19|CUFF.19.1|100|29.337687|3.097262|55.578113|1.875000|-	-
+TCONS_00000026	XLOC_000037	Xkr4|Xkr4	i	q1:CUFF.17|CUFF.17.1|100|8.710571|0.000000|21.029179|0.556701|-	-
+TCONS_00000027	XLOC_000040	Xkr4|Xkr4	i	q1:CUFF.25|CUFF.25.1|100|14.567679|5.354270|23.781089|0.931034|-	-
+TCONS_00000028	XLOC_000042	Xkr4|Xkr4	i	q1:CUFF.21|CUFF.21.1|100|13.851236|0.000000|33.439842|0.885246|-	-
+TCONS_00000029	XLOC_000044	Xkr4|Xkr4	i	q1:CUFF.23|CUFF.23.1|100|23.470150|0.000000|50.571145|1.500000|-	-
+TCONS_00000030	XLOC_000046	Xkr4|Xkr4	i	q1:CUFF.27|CUFF.27.1|100|34.253732|0.000000|73.806535|2.189189|-	-
+TCONS_00000031	XLOC_000048	Xkr4|Xkr4	i	q1:CUFF.61|CUFF.61.1|100|45.263860|0.000000|97.530065|2.892857|-	-
+TCONS_00000032	XLOC_000049	Xkr4|Xkr4	i	q1:CUFF.63|CUFF.63.1|100|15.646767|0.000000|46.940300|1.000000|-	-
+TCONS_00000033	XLOC_000052	Xkr4|Xkr4	i	q1:CUFF.65|CUFF.65.1|100|15.362280|0.000000|37.087825|0.981818|-	-
+TCONS_00000034	XLOC_000057	Xkr4|Xkr4	i	q1:CUFF.67|CUFF.67.1|100|12.998852|0.000000|31.382005|0.830769|-	-
+TCONS_00000035	XLOC_000059	Xkr4|Xkr4	i	q1:CUFF.69|CUFF.69.1|100|10.058636|0.000000|24.283695|0.642857|-	-
+TCONS_00000036	XLOC_000059	Xkr4|Xkr4	i	q1:CUFF.71|CUFF.71.1|100|8.621688|0.000000|20.814595|0.551020|-	-
+TCONS_00000037	XLOC_000060	Xkr4|Xkr4	i	q1:CUFF.73|CUFF.73.1|100|15.362280|0.000000|37.087825|0.981818|-	-
+TCONS_00000038	XLOC_000062	Xkr4|Xkr4	i	q1:CUFF.75|CUFF.75.1|100|31.293533|0.000000|75.549272|2.000000|-	-
+TCONS_00000039	XLOC_000065	Xkr4|Xkr4	i	q1:CUFF.77|CUFF.77.1|100|16.248565|0.000000|39.227507|1.038462|-	-
+TCONS_00000040	XLOC_000068	Xkr4|Xkr4	i	q1:CUFF.79|CUFF.79.1|100|31.293533|0.000000|75.549272|2.000000|-	-
+TCONS_00000041	XLOC_000071	Xkr4|Xkr4	i	q1:CUFF.81|CUFF.81.1|100|13.201959|0.000000|31.872349|0.843750|-	-
+TCONS_00000042	XLOC_000073	Xkr4|Xkr4	i	q1:CUFF.83|CUFF.83.1|100|13.201959|0.000000|28.446269|0.843750|-	-
+TCONS_00000043	XLOC_000075	Xkr4|Xkr4	i	q1:CUFF.85|CUFF.85.1|100|31.293533|0.000000|75.549272|2.000000|-	-
+TCONS_00000044	XLOC_000077	Xkr4|Xkr4	i	q1:CUFF.87|CUFF.87.1|100|17.243375|0.000000|41.629191|1.102041|-	-
+TCONS_00000045	XLOC_000080	Xkr4|Xkr4	i	q1:CUFF.89|CUFF.89.1|100|16.567165|0.000000|39.996674|1.058824|-	-
+TCONS_00000046	XLOC_000083	Xkr4|Xkr4	i	q1:CUFF.91|CUFF.91.1|100|31.293533|0.000000|75.549272|2.000000|-	-
+TCONS_00000047	XLOC_000084	Xkr4|Xkr4	i	q1:CUFF.93|CUFF.93.1|100|21.664754|0.000000|52.303342|1.384615|-	-
+TCONS_00000048	XLOC_000085	Xkr4|Xkr4	i	q1:CUFF.95|CUFF.95.1|100|46.940300|0.000000|101.142289|3.000000|-	-
+TCONS_00000049	XLOC_000086	Xkr4|Xkr4	i	q1:CUFF.97|CUFF.97.1|100|21.481154|0.000000|46.285454|1.372881|-	-
+TCONS_00000050	XLOC_000087	Xkr4|Xkr4	i	q1:CUFF.99|CUFF.99.1|100|14.567679|0.000000|35.169489|0.931034|-	-
+TCONS_00000051	XLOC_000004	-	u	-	q2:CUFF.1|CUFF.1.1|100|35.211287|0.000000|85.007567|2.000000|-
+TCONS_00000052	XLOC_000005	-	u	-	q2:CUFF.3|CUFF.3.1|100|35.211287|0.000000|85.007567|2.000000|-
+TCONS_00000053	XLOC_000006	-	u	-	q2:CUFF.5|CUFF.5.1|100|21.226627|0.000000|59.889707|1.205672|-
+TCONS_00000054	XLOC_000007	-	u	-	q2:CUFF.11|CUFF.11.1|100|32.531777|24.582998|40.480555|1.847804|-
+TCONS_00000055	XLOC_000008	-	u	-	q2:CUFF.7|CUFF.7.1|100|29.709524|19.806349|39.612698|1.687500|-
+TCONS_00000056	XLOC_000009	-	u	-	q2:CUFF.9|CUFF.9.1|100|34.072933|23.364686|44.781179|1.935341|-
+TCONS_00000057	XLOC_000010	-	u	-	q2:CUFF.13|CUFF.13.1|100|16.582060|0.000000|35.729373|0.941860|-
+TCONS_00000058	XLOC_000013	-	u	-	q2:CUFF.15|CUFF.15.1|100|35.211287|0.000000|85.007567|2.000000|-
+TCONS_00000059	XLOC_000018	-	u	-	q2:CUFF.17|CUFF.17.1|100|35.211287|0.000000|85.007567|2.000000|-
+TCONS_00000060	XLOC_000024	-	u	-	q2:CUFF.19|CUFF.19.1|100|35.211287|0.000000|85.007567|2.000000|-
+TCONS_00000061	XLOC_000025	-	u	-	q2:CUFF.23|CUFF.23.1|100|16.205195|0.000000|34.917342|0.920455|-
+TCONS_00000062	XLOC_000027	-	u	-	q2:CUFF.21|CUFF.21.1|100|35.211287|0.000000|85.007567|2.000000|-
+TCONS_00000063	XLOC_000028	-	u	-	q2:CUFF.26|CUFF.26.1|100|29.709524|0.000000|71.725135|1.687500|-
+TCONS_00000064	XLOC_000029	-	u	-	q2:CUFF.25|CUFF.25.1|100|35.211287|0.000000|85.007567|2.000000|-
+TCONS_00000065	XLOC_000030	-	u	-	q2:CUFF.29|CUFF.29.1|100|13.581496|0.000000|32.788633|0.771429|-
+TCONS_00000066	XLOC_000032	-	u	-	q2:CUFF.31|CUFF.31.1|100|22.635827|0.000000|45.271655|1.285714|-
+TCONS_00000067	XLOC_000033	Xkr4|Xkr4	i	-	q2:CUFF.33|CUFF.33.1|100|23.767619|0.000000|57.380108|1.350000|-
+TCONS_00000068	XLOC_000036	Xkr4|Xkr4	i	-	q2:CUFF.35|CUFF.35.1|100|11.317914|0.000000|27.323861|0.642857|-
+TCONS_00000069	XLOC_000037	Xkr4|Xkr4	i	-	q2:CUFF.37|CUFF.37.1|100|11.500461|0.000000|24.780049|0.653226|-
+TCONS_00000070	XLOC_000038	Xkr4|Xkr4	i	-	q2:CUFF.39|CUFF.39.1|100|52.816931|0.000000|113.804669|3.000000|-
+TCONS_00000071	XLOC_000039	Xkr4|Xkr4	i	-	q2:CUFF.41|CUFF.41.1|100|43.213852|0.000000|93.112911|2.454545|-
+TCONS_00000072	XLOC_000041	Xkr4|Xkr4	i	-	q2:CUFF.43|CUFF.43.1|100|23.474191|0.000000|46.948383|1.333333|-
+TCONS_00000073	XLOC_000043	Xkr4|Xkr4	i	-	q2:CUFF.45|CUFF.45.1|100|20.667495|0.000000|49.895746|1.173913|-
+TCONS_00000074	XLOC_000045	Xkr4|Xkr4	i	-	q2:CUFF.47|CUFF.47.1|100|35.211287|0.000000|85.007567|2.000000|-
+TCONS_00000075	XLOC_000047	Xkr4|Xkr4	i	-	q2:CUFF.49|CUFF.49.1|100|35.211287|0.000000|85.007567|2.000000|-
+TCONS_00000076	XLOC_000049	Xkr4|Xkr4	i	-	q2:CUFF.51|CUFF.51.1|100|14.948188|7.228977|22.667399|0.849057|-
+TCONS_00000077	XLOC_000050	Xkr4|Xkr4	i	-	q2:CUFF.53|CUFF.53.1|100|52.816931|0.000000|113.804669|3.000000|-
+TCONS_00000078	XLOC_000051	Xkr4|Xkr4	i	-	q2:CUFF.55|CUFF.55.1|100|35.211287|0.000000|85.007567|2.000000|-
+TCONS_00000079	XLOC_000053	Xkr4|Xkr4	i	-	q2:CUFF.57|CUFF.57.1|100|35.211287|0.000000|85.007567|2.000000|-
+TCONS_00000080	XLOC_000054	Xkr4|Xkr4	i	-	q2:CUFF.59|CUFF.59.1|100|35.211287|0.000000|85.007567|2.000000|-
+TCONS_00000081	XLOC_000055	Xkr4|Xkr4	i	-	q2:CUFF.61|CUFF.61.1|100|13.204233|0.000000|31.877838|0.750000|-
+TCONS_00000082	XLOC_000056	Xkr4|Xkr4	i	-	q2:CUFF.63|CUFF.63.1|100|35.211287|0.000000|85.007567|2.000000|-
+TCONS_00000083	XLOC_000058	Xkr4|Xkr4	i	-	q2:CUFF.65|CUFF.65.1|100|31.170648|0.000000|62.341295|1.770492|-
+TCONS_00000084	XLOC_000059	Xkr4|Xkr4	i	-	q2:CUFF.69|CUFF.69.1|100|18.799247|8.750627|28.847866|1.067797|-
+TCONS_00000085	XLOC_000060	Xkr4|Xkr4	i	-	q2:CUFF.67|CUFF.67.1|100|15.681351|3.378764|27.983938|0.890700|-
+TCONS_00000086	XLOC_000061	Xkr4|Xkr4	i	-	q2:CUFF.71|CUFF.71.1|100|22.635827|0.000000|54.647722|1.285714|-
+TCONS_00000087	XLOC_000063	Xkr4|Xkr4	i	-	q2:CUFF.73|CUFF.73.1|100|35.211287|0.000000|85.007567|2.000000|-
+TCONS_00000088	XLOC_000064	Xkr4|Xkr4	i	-	q2:CUFF.75|CUFF.75.1|100|52.816931|0.000000|113.804669|3.000000|-
+TCONS_00000089	XLOC_000066	Xkr4|Xkr4	i	-	q2:CUFF.77|CUFF.77.1|100|17.605644|0.000000|52.816931|1.000000|-
+TCONS_00000090	XLOC_000067	Xkr4|Xkr4	i	-	q2:CUFF.79|CUFF.79.1|100|13.390208|0.000000|32.326821|0.760563|-
+TCONS_00000091	XLOC_000068	Xkr4|Xkr4	i	-	q2:CUFF.81|CUFF.81.1|100|11.211141|1.183592|21.238690|0.636792|-
+TCONS_00000092	XLOC_000069	Xkr4|Xkr4	i	-	q2:CUFF.83|CUFF.83.1|100|21.126772|0.000000|51.004540|1.200000|-
+TCONS_00000093	XLOC_000070	Xkr4|Xkr4	i	-	q2:CUFF.85|CUFF.85.1|100|19.014095|0.000000|38.028190|1.080000|-
+TCONS_00000094	XLOC_000072	Xkr4|Xkr4	i	-	q2:CUFF.87|CUFF.87.1|100|24.170460|0.000000|52.080103|1.372881|-
+TCONS_00000095	XLOC_000074	Xkr4|Xkr4	i	-	q2:CUFF.89|CUFF.89.1|100|29.709524|0.000000|64.015126|1.687500|-
+TCONS_00000096	XLOC_000076	Xkr4|Xkr4	i	-	q2:CUFF.91|CUFF.91.1|100|35.211287|0.000000|85.007567|2.000000|-
+TCONS_00000097	XLOC_000078	Xkr4|Xkr4	i	-	q2:CUFF.93|CUFF.93.1|100|35.211287|0.000000|85.007567|2.000000|-
+TCONS_00000098	XLOC_000079	Xkr4|Xkr4	i	-	q2:CUFF.95|CUFF.95.1|100|35.211287|0.000000|85.007567|2.000000|-
+TCONS_00000099	XLOC_000081	Xkr4|Xkr4	i	-	q2:CUFF.97|CUFF.97.1|100|35.211287|0.000000|85.007567|2.000000|-
+TCONS_00000100	XLOC_000082	Xkr4|Xkr4	i	-	q2:CUFF.99|CUFF.99.1|100|19.602160|0.000000|39.204320|1.113402|-
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data-orig/cuffcompare_out7.txt	Sat Aug 02 10:24:42 2014 -0400
@@ -0,0 +1,33 @@
+# Cuffcompare v2.0.2 | Command line was:
+#cuffcompare -o cc_output -r /Users/jeremy/projects/galaxy-central/database/files/002/dataset_2770.dat -R ./input1 ./input2
+#
+
+#= Summary for dataset: ./input1 :
+#     Query mRNAs :      50 in      50 loci  (0 multi-exon transcripts)
+#            (0 multi-transcript loci, ~1.0 transcripts per locus)
+# Reference mRNAs :       1 in       1 loci  (1 multi-exon)
+# Corresponding super-loci:              1
+#--------------------|   Sn   |  Sp   |  fSn |  fSp  
+        Base level: 	  2.2	  2.3	  - 	  - 
+        Exon level: 	  0.0	  0.0	  0.0	  0.0
+      Intron level: 	  0.0	  nan	  0.0	  nan
+Intron chain level: 	  0.0	  nan	  0.0	  nan
+  Transcript level: 	  0.0	  0.0	  0.0	  0.0
+       Locus level: 	  0.0	  0.0	  0.0	  0.0
+
+Matching intron chains:       0
+         Matching loci:       0
+
+          Missed exons:       2/3	( 66.7%)
+           Novel exons:      49/50	( 98.0%)
+        Missed introns:       2/2	(100.0%)
+           Missed loci:       0/1	(  0.0%)
+            Novel loci:      49/50	( 98.0%)
+
+#= Summary for dataset: ./input2 :
+#     Query mRNAs :      50 in      50 loci  (0 multi-exon transcripts)
+#            (0 multi-transcript loci, ~1.0 transcripts per locus)
+# Reference mRNAs :       0 in       0 loci  (0 multi-exon)
+
+ Total union super-loci across all input datasets: 87 
+  (0 multi-transcript, ~1.1 transcripts per locus)
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data-orig/cuffmerge_out1.gtf	Sat Aug 02 10:24:42 2014 -0400
@@ -0,0 +1,74 @@
+chr1	Cufflinks	exon	4797974	4798063	.	+	.	gene_id "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "1"; gene_name "Lypla1"; oId "Lypla1"; nearest_ref "Lypla1"; class_code "="; tss_id "TSS1";
+chr1	Cufflinks	exon	4798536	4798567	.	+	.	gene_id "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "2"; gene_name "Lypla1"; oId "Lypla1"; nearest_ref "Lypla1"; class_code "="; tss_id "TSS1";
+chr1	Cufflinks	exon	4818665	4818730	.	+	.	gene_id "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "3"; gene_name "Lypla1"; oId "Lypla1"; nearest_ref "Lypla1"; class_code "="; tss_id "TSS1";
+chr1	Cufflinks	exon	4820349	4820396	.	+	.	gene_id "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "4"; gene_name "Lypla1"; oId "Lypla1"; nearest_ref "Lypla1"; class_code "="; tss_id "TSS1";
+chr1	Cufflinks	exon	4822392	4822462	.	+	.	gene_id "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "5"; gene_name "Lypla1"; oId "Lypla1"; nearest_ref "Lypla1"; class_code "="; tss_id "TSS1";
+chr1	Cufflinks	exon	4827082	4827155	.	+	.	gene_id "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "6"; gene_name "Lypla1"; oId "Lypla1"; nearest_ref "Lypla1"; class_code "="; tss_id "TSS1";
+chr1	Cufflinks	exon	4829468	4829569	.	+	.	gene_id "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "7"; gene_name "Lypla1"; oId "Lypla1"; nearest_ref "Lypla1"; class_code "="; tss_id "TSS1";
+chr1	Cufflinks	exon	4831037	4831213	.	+	.	gene_id "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "8"; gene_name "Lypla1"; oId "Lypla1"; nearest_ref "Lypla1"; class_code "="; tss_id "TSS1";
+chr1	Cufflinks	exon	4835044	4836816	.	+	.	gene_id "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "9"; gene_name "Lypla1"; oId "Lypla1"; nearest_ref "Lypla1"; class_code "="; tss_id "TSS1";
+chr1	Cufflinks	exon	4847775	4848057	.	+	.	gene_id "XLOC_000002"; transcript_id "TCONS_00000002"; exon_number "1"; gene_name "Tcea1"; oId "Tcea1_dup1"; contained_in "TCONS_00000003"; nearest_ref "Tcea1_dup1"; class_code "="; tss_id "TSS2";
+chr1	Cufflinks	exon	4857551	4857613	.	+	.	gene_id "XLOC_000002"; transcript_id "TCONS_00000002"; exon_number "2"; gene_name "Tcea1"; oId "Tcea1_dup1"; contained_in "TCONS_00000003"; nearest_ref "Tcea1_dup1"; class_code "="; tss_id "TSS2";
+chr1	Cufflinks	exon	4847775	4848057	.	+	.	gene_id "XLOC_000002"; transcript_id "TCONS_00000003"; exon_number "1"; gene_name "Tcea1"; oId "Tcea1"; nearest_ref "Tcea1"; class_code "="; tss_id "TSS2";
+chr1	Cufflinks	exon	4857551	4857613	.	+	.	gene_id "XLOC_000002"; transcript_id "TCONS_00000003"; exon_number "2"; gene_name "Tcea1"; oId "Tcea1"; nearest_ref "Tcea1"; class_code "="; tss_id "TSS2";
+chr1	Cufflinks	exon	4868108	4868213	.	+	.	gene_id "XLOC_000002"; transcript_id "TCONS_00000003"; exon_number "3"; gene_name "Tcea1"; oId "Tcea1"; nearest_ref "Tcea1"; class_code "="; tss_id "TSS2";
+chr1	Cufflinks	exon	4876825	4876912	.	+	.	gene_id "XLOC_000002"; transcript_id "TCONS_00000003"; exon_number "4"; gene_name "Tcea1"; oId "Tcea1"; nearest_ref "Tcea1"; class_code "="; tss_id "TSS2";
+chr1	Cufflinks	exon	4879538	4879683	.	+	.	gene_id "XLOC_000002"; transcript_id "TCONS_00000003"; exon_number "5"; gene_name "Tcea1"; oId "Tcea1"; nearest_ref "Tcea1"; class_code "="; tss_id "TSS2";
+chr1	Cufflinks	exon	4880821	4880877	.	+	.	gene_id "XLOC_000002"; transcript_id "TCONS_00000003"; exon_number "6"; gene_name "Tcea1"; oId "Tcea1"; nearest_ref "Tcea1"; class_code "="; tss_id "TSS2";
+chr1	Cufflinks	exon	4881996	4882150	.	+	.	gene_id "XLOC_000002"; transcript_id "TCONS_00000003"; exon_number "7"; gene_name "Tcea1"; oId "Tcea1"; nearest_ref "Tcea1"; class_code "="; tss_id "TSS2";
+chr1	Cufflinks	exon	4883498	4883644	.	+	.	gene_id "XLOC_000002"; transcript_id "TCONS_00000003"; exon_number "8"; gene_name "Tcea1"; oId "Tcea1"; nearest_ref "Tcea1"; class_code "="; tss_id "TSS2";
+chr1	Cufflinks	exon	4885015	4885086	.	+	.	gene_id "XLOC_000002"; transcript_id "TCONS_00000003"; exon_number "9"; gene_name "Tcea1"; oId "Tcea1"; nearest_ref "Tcea1"; class_code "="; tss_id "TSS2";
+chr1	Cufflinks	exon	4886437	4887987	.	+	.	gene_id "XLOC_000002"; transcript_id "TCONS_00000003"; exon_number "10"; gene_name "Tcea1"; oId "Tcea1"; nearest_ref "Tcea1"; class_code "="; tss_id "TSS2";
+chr1	Cufflinks	exon	3204563	3207049	.	-	.	gene_id "XLOC_000003"; transcript_id "TCONS_00000004"; exon_number "1"; gene_name "Xkr4"; oId "Xkr4"; nearest_ref "Xkr4"; class_code "="; tss_id "TSS3";
+chr1	Cufflinks	exon	3411783	3411982	.	-	.	gene_id "XLOC_000003"; transcript_id "TCONS_00000004"; exon_number "2"; gene_name "Xkr4"; oId "Xkr4"; nearest_ref "Xkr4"; class_code "="; tss_id "TSS3";
+chr1	Cufflinks	exon	3660633	3661579	.	-	.	gene_id "XLOC_000003"; transcript_id "TCONS_00000004"; exon_number "3"; gene_name "Xkr4"; oId "Xkr4"; nearest_ref "Xkr4"; class_code "="; tss_id "TSS3";
+chr1	Cufflinks	exon	4334224	4340172	.	-	.	gene_id "XLOC_000004"; transcript_id "TCONS_00000005"; exon_number "1"; gene_name "Rp1"; oId "Rp1"; nearest_ref "Rp1"; class_code "="; tss_id "TSS4";
+chr1	Cufflinks	exon	4341991	4342162	.	-	.	gene_id "XLOC_000004"; transcript_id "TCONS_00000005"; exon_number "2"; gene_name "Rp1"; oId "Rp1"; nearest_ref "Rp1"; class_code "="; tss_id "TSS4";
+chr1	Cufflinks	exon	4342283	4342918	.	-	.	gene_id "XLOC_000004"; transcript_id "TCONS_00000005"; exon_number "3"; gene_name "Rp1"; oId "Rp1"; nearest_ref "Rp1"; class_code "="; tss_id "TSS4";
+chr1	Cufflinks	exon	4350281	4350473	.	-	.	gene_id "XLOC_000004"; transcript_id "TCONS_00000005"; exon_number "4"; gene_name "Rp1"; oId "Rp1"; nearest_ref "Rp1"; class_code "="; tss_id "TSS4";
+chr1	Cufflinks	exon	4481009	4482749	.	-	.	gene_id "XLOC_000005"; transcript_id "TCONS_00000006"; exon_number "1"; gene_name "Sox17"; oId "Sox17"; nearest_ref "Sox17"; class_code "="; tss_id "TSS5";
+chr1	Cufflinks	exon	4483181	4483547	.	-	.	gene_id "XLOC_000005"; transcript_id "TCONS_00000006"; exon_number "2"; gene_name "Sox17"; oId "Sox17"; nearest_ref "Sox17"; class_code "="; tss_id "TSS5";
+chr1	Cufflinks	exon	4483853	4483944	.	-	.	gene_id "XLOC_000005"; transcript_id "TCONS_00000006"; exon_number "3"; gene_name "Sox17"; oId "Sox17"; nearest_ref "Sox17"; class_code "="; tss_id "TSS5";
+chr1	Cufflinks	exon	4485217	4486023	.	-	.	gene_id "XLOC_000005"; transcript_id "TCONS_00000006"; exon_number "4"; gene_name "Sox17"; oId "Sox17"; nearest_ref "Sox17"; class_code "="; tss_id "TSS5";
+chr1	Cufflinks	exon	4486372	4486494	.	-	.	gene_id "XLOC_000005"; transcript_id "TCONS_00000006"; exon_number "5"; gene_name "Sox17"; oId "Sox17"; nearest_ref "Sox17"; class_code "="; tss_id "TSS5";
+chr1	Cufflinks	exon	4763279	4764597	.	-	.	gene_id "XLOC_000006"; transcript_id "TCONS_00000009"; exon_number "1"; gene_name "Mrpl15"; oId "Mrpl15_dup2"; nearest_ref "Mrpl15_dup2"; class_code "="; tss_id "TSS6";
+chr1	Cufflinks	exon	4767606	4767729	.	-	.	gene_id "XLOC_000006"; transcript_id "TCONS_00000009"; exon_number "2"; gene_name "Mrpl15"; oId "Mrpl15_dup2"; nearest_ref "Mrpl15_dup2"; class_code "="; tss_id "TSS6";
+chr1	Cufflinks	exon	4772649	4772814	.	-	.	gene_id "XLOC_000006"; transcript_id "TCONS_00000009"; exon_number "3"; gene_name "Mrpl15"; oId "Mrpl15_dup2"; nearest_ref "Mrpl15_dup2"; class_code "="; tss_id "TSS6";
+chr1	Cufflinks	exon	4775654	4775807	.	-	.	gene_id "XLOC_000006"; transcript_id "TCONS_00000009"; exon_number "4"; gene_name "Mrpl15"; oId "Mrpl15_dup2"; nearest_ref "Mrpl15_dup2"; class_code "="; tss_id "TSS6";
+chr1	Cufflinks	exon	4763279	4764597	.	-	.	gene_id "XLOC_000006"; transcript_id "TCONS_00000008"; exon_number "1"; gene_name "Mrpl15"; oId "Mrpl15_dup1"; nearest_ref "Mrpl15_dup1"; class_code "="; tss_id "TSS6";
+chr1	Cufflinks	exon	4767606	4767729	.	-	.	gene_id "XLOC_000006"; transcript_id "TCONS_00000008"; exon_number "2"; gene_name "Mrpl15"; oId "Mrpl15_dup1"; nearest_ref "Mrpl15_dup1"; class_code "="; tss_id "TSS6";
+chr1	Cufflinks	exon	4772649	4772814	.	-	.	gene_id "XLOC_000006"; transcript_id "TCONS_00000008"; exon_number "3"; gene_name "Mrpl15"; oId "Mrpl15_dup1"; nearest_ref "Mrpl15_dup1"; class_code "="; tss_id "TSS6";
+chr1	Cufflinks	exon	4774032	4774186	.	-	.	gene_id "XLOC_000006"; transcript_id "TCONS_00000008"; exon_number "4"; gene_name "Mrpl15"; oId "Mrpl15_dup1"; nearest_ref "Mrpl15_dup1"; class_code "="; tss_id "TSS6";
+chr1	Cufflinks	exon	4775654	4775807	.	-	.	gene_id "XLOC_000006"; transcript_id "TCONS_00000008"; exon_number "5"; gene_name "Mrpl15"; oId "Mrpl15_dup1"; nearest_ref "Mrpl15_dup1"; class_code "="; tss_id "TSS6";
+chr1	Cufflinks	exon	4763279	4766882	.	-	.	gene_id "XLOC_000006"; transcript_id "TCONS_00000007"; exon_number "1"; gene_name "Mrpl15"; oId "Mrpl15"; nearest_ref "Mrpl15"; class_code "="; tss_id "TSS6";
+chr1	Cufflinks	exon	4767606	4767729	.	-	.	gene_id "XLOC_000006"; transcript_id "TCONS_00000007"; exon_number "2"; gene_name "Mrpl15"; oId "Mrpl15"; nearest_ref "Mrpl15"; class_code "="; tss_id "TSS6";
+chr1	Cufflinks	exon	4772649	4772814	.	-	.	gene_id "XLOC_000006"; transcript_id "TCONS_00000007"; exon_number "3"; gene_name "Mrpl15"; oId "Mrpl15"; nearest_ref "Mrpl15"; class_code "="; tss_id "TSS6";
+chr1	Cufflinks	exon	4774032	4774186	.	-	.	gene_id "XLOC_000006"; transcript_id "TCONS_00000007"; exon_number "4"; gene_name "Mrpl15"; oId "Mrpl15"; nearest_ref "Mrpl15"; class_code "="; tss_id "TSS6";
+chr1	Cufflinks	exon	4775654	4775807	.	-	.	gene_id "XLOC_000006"; transcript_id "TCONS_00000007"; exon_number "5"; gene_name "Mrpl15"; oId "Mrpl15"; nearest_ref "Mrpl15"; class_code "="; tss_id "TSS6";
+chr1	Cufflinks	exon	3111450	3111490	.	.	.	gene_id "XLOC_000007"; transcript_id "TCONS_00000010"; exon_number "1"; oId "CUFF.1.1"; class_code "u"; tss_id "TSS7";
+chr1	Cufflinks	exon	3111546	3111576	.	.	.	gene_id "XLOC_000008"; transcript_id "TCONS_00000011"; exon_number "1"; oId "CUFF.2.1"; class_code "u"; tss_id "TSS8";
+chr1	Cufflinks	exon	3174766	3174792	.	.	.	gene_id "XLOC_000009"; transcript_id "TCONS_00000012"; exon_number "1"; oId "CUFF.3.1"; class_code "u"; tss_id "TSS9";
+chr1	Cufflinks	exon	3187402	3187428	.	.	.	gene_id "XLOC_000010"; transcript_id "TCONS_00000013"; exon_number "1"; oId "CUFF.4.1"; class_code "u"; tss_id "TSS10";
+chr1	Cufflinks	exon	3188522	3188548	.	.	.	gene_id "XLOC_000011"; transcript_id "TCONS_00000014"; exon_number "1"; oId "CUFF.5.1"; class_code "u"; tss_id "TSS11";
+chr1	Cufflinks	exon	3189811	3190789	.	.	.	gene_id "XLOC_000012"; transcript_id "TCONS_00000015"; exon_number "1"; oId "CUFF.6.1"; class_code "u"; tss_id "TSS12";
+chr1	Cufflinks	exon	3190859	3191434	.	.	.	gene_id "XLOC_000013"; transcript_id "TCONS_00000016"; exon_number "1"; oId "CUFF.7.1"; class_code "u"; tss_id "TSS13";
+chr1	Cufflinks	exon	3191513	3192077	.	.	.	gene_id "XLOC_000014"; transcript_id "TCONS_00000017"; exon_number "1"; oId "CUFF.8.1"; class_code "u"; tss_id "TSS14";
+chr1	Cufflinks	exon	3192251	3192336	.	.	.	gene_id "XLOC_000015"; transcript_id "TCONS_00000018"; exon_number "1"; oId "CUFF.9.1"; class_code "u"; tss_id "TSS15";
+chr1	Cufflinks	exon	3192442	3192494	.	.	.	gene_id "XLOC_000016"; transcript_id "TCONS_00000019"; exon_number "1"; oId "CUFF.10.1"; class_code "u"; tss_id "TSS16";
+chr1	Cufflinks	exon	3192551	3192676	.	.	.	gene_id "XLOC_000017"; transcript_id "TCONS_00000020"; exon_number "1"; oId "CUFF.11.1"; class_code "u"; tss_id "TSS17";
+chr1	Cufflinks	exon	3192732	3192811	.	.	.	gene_id "XLOC_000018"; transcript_id "TCONS_00000021"; exon_number "1"; oId "CUFF.12.1"; class_code "u"; tss_id "TSS18";
+chr1	Cufflinks	exon	3192941	3193042	.	.	.	gene_id "XLOC_000019"; transcript_id "TCONS_00000022"; exon_number "1"; oId "CUFF.13.1"; class_code "u"; tss_id "TSS19";
+chr1	Cufflinks	exon	3194186	3194226	.	.	.	gene_id "XLOC_000020"; transcript_id "TCONS_00000023"; exon_number "1"; oId "CUFF.14.1"; class_code "u"; tss_id "TSS20";
+chr1	Cufflinks	exon	3194303	3194329	.	.	.	gene_id "XLOC_000021"; transcript_id "TCONS_00000024"; exon_number "1"; oId "CUFF.15.1"; class_code "u"; tss_id "TSS21";
+chr1	Cufflinks	exon	3194707	3194733	.	.	.	gene_id "XLOC_000022"; transcript_id "TCONS_00000025"; exon_number "1"; oId "CUFF.16.1"; class_code "u"; tss_id "TSS22";
+chr1	Cufflinks	exon	3195084	3195110	.	.	.	gene_id "XLOC_000023"; transcript_id "TCONS_00000026"; exon_number "1"; oId "CUFF.17.1"; class_code "u"; tss_id "TSS23";
+chr1	Cufflinks	exon	3195451	3195477	.	.	.	gene_id "XLOC_000024"; transcript_id "TCONS_00000027"; exon_number "1"; oId "CUFF.18.1"; class_code "u"; tss_id "TSS24";
+chr1	Cufflinks	exon	3197090	3197116	.	.	.	gene_id "XLOC_000025"; transcript_id "TCONS_00000028"; exon_number "1"; oId "CUFF.19.1"; class_code "u"; tss_id "TSS25";
+chr1	Cufflinks	exon	3197247	3197273	.	.	.	gene_id "XLOC_000026"; transcript_id "TCONS_00000029"; exon_number "1"; oId "CUFF.20.1"; class_code "u"; tss_id "TSS26";
+chr1	Cufflinks	exon	3197347	3197373	.	.	.	gene_id "XLOC_000027"; transcript_id "TCONS_00000030"; exon_number "1"; oId "CUFF.21.1"; class_code "u"; tss_id "TSS27";
+chr1	Cufflinks	exon	3197426	3197452	.	.	.	gene_id "XLOC_000028"; transcript_id "TCONS_00000031"; exon_number "1"; oId "CUFF.22.1"; class_code "u"; tss_id "TSS28";
+chr1	Cufflinks	exon	3200023	3200191	.	.	.	gene_id "XLOC_000029"; transcript_id "TCONS_00000032"; exon_number "1"; oId "CUFF.23.1"; class_code "u"; tss_id "TSS29";
+chr1	Cufflinks	exon	3200326	3200352	.	.	.	gene_id "XLOC_000030"; transcript_id "TCONS_00000033"; exon_number "1"; oId "CUFF.24.1"; class_code "u"; tss_id "TSS30";
+chr1	Cufflinks	exon	3200431	3200457	.	.	.	gene_id "XLOC_000031"; transcript_id "TCONS_00000034"; exon_number "1"; oId "CUFF.25.1"; class_code "u"; tss_id "TSS31";
+chr1	Cufflinks	exon	3201008	3201481	.	.	.	gene_id "XLOC_000032"; transcript_id "TCONS_00000035"; exon_number "1"; oId "CUFF.26.1"; class_code "u"; tss_id "TSS32";
+chr1	Cufflinks	exon	3201597	3201809	.	.	.	gene_id "XLOC_000033"; transcript_id "TCONS_00000036"; exon_number "1"; oId "CUFF.27.1"; class_code "u"; tss_id "TSS33";
--- a/test-data/cuffcompare_out5.gtf	Fri Aug 01 11:01:51 2014 -0400
+++ b/test-data/cuffcompare_out5.gtf	Sat Aug 02 10:24:42 2014 -0400
@@ -22,67 +22,67 @@
 chr1	Cufflinks	exon	3197247	3197273	.	.	.	gene_id "XLOC_000022"; transcript_id "TCONS_00000018"; exon_number "1"; oId "CUFF.57.1"; class_code "u"; tss_id "TSS25";
 chr1	Cufflinks	exon	3197347	3197373	.	.	.	gene_id "XLOC_000023"; transcript_id "TCONS_00000019"; exon_number "1"; oId "CUFF.59.1"; class_code "u"; tss_id "TSS26";
 chr1	Cufflinks	exon	3197426	3197452	.	.	.	gene_id "XLOC_000024"; transcript_id "TCONS_00000060"; exon_number "1"; oId "CUFF.19.1"; class_code "u"; tss_id "TSS27";
-chr1	Cufflinks	exon	3200023	3200191	.	.	.	gene_id "XLOC_000025"; transcript_id "TCONS_00000020"; exon_number "1"; oId "CUFF.7.1"; class_code "u"; tss_id "TSS28";
+chr1	Cufflinks	exon	3200023	3200191	.	.	.	gene_id "XLOC_000025"; transcript_id "TCONS_00000020"; exon_number "1"; oId "CUFF.7.1"; class_code "."; tss_id "TSS28";
 chr1	Cufflinks	exon	3200326	3200352	.	.	.	gene_id "XLOC_000026"; transcript_id "TCONS_00000021"; exon_number "1"; oId "CUFF.5.1"; class_code "u"; tss_id "TSS29";
-chr1	Cufflinks	exon	3200431	3200457	.	.	.	gene_id "XLOC_000027"; transcript_id "TCONS_00000062"; exon_number "1"; oId "CUFF.21.1"; class_code "u"; tss_id "TSS30";
-chr1	Cufflinks	exon	3201008	3201039	.	.	.	gene_id "XLOC_000028"; transcript_id "TCONS_00000063"; exon_number "1"; oId "CUFF.26.1"; class_code "u"; tss_id "TSS31";
-chr1	Cufflinks	exon	3201078	3201481	.	.	.	gene_id "XLOC_000029"; transcript_id "TCONS_00000022"; exon_number "1"; oId "CUFF.9.1"; class_code "u"; tss_id "TSS32";
-chr1	Cufflinks	exon	3201597	3201666	.	.	.	gene_id "XLOC_000030"; transcript_id "TCONS_00000065"; exon_number "1"; oId "CUFF.29.1"; class_code "u"; tss_id "TSS33";
+chr1	Cufflinks	exon	3200431	3200457	.	.	.	gene_id "XLOC_000027"; transcript_id "TCONS_00000061"; exon_number "1"; oId "CUFF.21.1"; class_code "u"; tss_id "TSS30";
+chr1	Cufflinks	exon	3201008	3201039	.	.	.	gene_id "XLOC_000028"; transcript_id "TCONS_00000062"; exon_number "1"; oId "CUFF.26.1"; class_code "u"; tss_id "TSS31";
+chr1	Cufflinks	exon	3201078	3201481	.	.	.	gene_id "XLOC_000029"; transcript_id "TCONS_00000022"; exon_number "1"; oId "CUFF.9.1"; class_code "."; tss_id "TSS32";
+chr1	Cufflinks	exon	3201597	3201666	.	.	.	gene_id "XLOC_000030"; transcript_id "TCONS_00000063"; exon_number "1"; oId "CUFF.29.1"; class_code "u"; tss_id "TSS33";
 chr1	Cufflinks	exon	3201673	3201699	.	.	.	gene_id "XLOC_000031"; transcript_id "TCONS_00000023"; exon_number "1"; oId "CUFF.11.1"; class_code "u"; tss_id "TSS34";
-chr1	Cufflinks	exon	3201726	3201809	.	.	.	gene_id "XLOC_000032"; transcript_id "TCONS_00000066"; exon_number "1"; oId "CUFF.31.1"; class_code "u"; tss_id "TSS35";
-chr1	Cufflinks	exon	3211522	3211561	.	.	.	gene_id "XLOC_000033"; transcript_id "TCONS_00000067"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.33.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS36";
+chr1	Cufflinks	exon	3201726	3201809	.	.	.	gene_id "XLOC_000032"; transcript_id "TCONS_00000064"; exon_number "1"; oId "CUFF.31.1"; class_code "u"; tss_id "TSS35";
+chr1	Cufflinks	exon	3211522	3211561	.	.	.	gene_id "XLOC_000033"; transcript_id "TCONS_00000065"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.33.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS36";
 chr1	Cufflinks	exon	3212214	3212292	.	.	.	gene_id "XLOC_000034"; transcript_id "TCONS_00000024"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.15.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS37";
 chr1	Cufflinks	exon	3212368	3212439	.	.	.	gene_id "XLOC_000035"; transcript_id "TCONS_00000025"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.19.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS38";
-chr1	Cufflinks	exon	3212718	3212801	.	.	.	gene_id "XLOC_000036"; transcript_id "TCONS_00000068"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.35.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS39";
+chr1	Cufflinks	exon	3212718	3212801	.	.	.	gene_id "XLOC_000036"; transcript_id "TCONS_00000066"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.35.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS39";
 chr1	Cufflinks	exon	3213096	3213192	.	.	.	gene_id "XLOC_000037"; transcript_id "TCONS_00000026"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.17.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS40";
-chr1	Cufflinks	exon	3213119	3213242	.	.	.	gene_id "XLOC_000037"; transcript_id "TCONS_00000069"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.37.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS40";
-chr1	Cufflinks	exon	3240607	3240633	.	.	.	gene_id "XLOC_000038"; transcript_id "TCONS_00000070"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.39.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS41";
-chr1	Cufflinks	exon	3242480	3242512	.	.	.	gene_id "XLOC_000039"; transcript_id "TCONS_00000071"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.41.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS42";
+chr1	Cufflinks	exon	3213119	3213242	.	.	.	gene_id "XLOC_000037"; transcript_id "TCONS_00000067"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.37.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS40";
+chr1	Cufflinks	exon	3240607	3240633	.	.	.	gene_id "XLOC_000038"; transcript_id "TCONS_00000068"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.39.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS41";
+chr1	Cufflinks	exon	3242480	3242512	.	.	.	gene_id "XLOC_000039"; transcript_id "TCONS_00000069"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.41.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS42";
 chr1	Cufflinks	exon	3242634	3242923	.	.	.	gene_id "XLOC_000040"; transcript_id "TCONS_00000027"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.25.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS43";
-chr1	Cufflinks	exon	3242925	3243005	.	.	.	gene_id "XLOC_000041"; transcript_id "TCONS_00000072"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.43.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS44";
+chr1	Cufflinks	exon	3242925	3243005	.	.	.	gene_id "XLOC_000041"; transcript_id "TCONS_00000070"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.43.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS44";
 chr1	Cufflinks	exon	3243019	3243079	.	.	.	gene_id "XLOC_000042"; transcript_id "TCONS_00000028"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.21.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS45";
-chr1	Cufflinks	exon	3243109	3243154	.	.	.	gene_id "XLOC_000043"; transcript_id "TCONS_00000073"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.45.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS46";
+chr1	Cufflinks	exon	3243109	3243154	.	.	.	gene_id "XLOC_000043"; transcript_id "TCONS_00000071"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.45.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS46";
 chr1	Cufflinks	exon	3243348	3243401	.	.	.	gene_id "XLOC_000044"; transcript_id "TCONS_00000029"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.23.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS47";
-chr1	Cufflinks	exon	3254080	3254106	.	.	.	gene_id "XLOC_000045"; transcript_id "TCONS_00000074"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.47.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS48";
+chr1	Cufflinks	exon	3254080	3254106	.	.	.	gene_id "XLOC_000045"; transcript_id "TCONS_00000072"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.47.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS48";
 chr1	Cufflinks	exon	3256975	3257011	.	.	.	gene_id "XLOC_000046"; transcript_id "TCONS_00000030"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.27.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS49";
-chr1	Cufflinks	exon	3277156	3277182	.	.	.	gene_id "XLOC_000047"; transcript_id "TCONS_00000075"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.49.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS50";
+chr1	Cufflinks	exon	3277156	3277182	.	.	.	gene_id "XLOC_000047"; transcript_id "TCONS_00000073"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.49.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS50";
 chr1	Cufflinks	exon	3277191	3277218	.	.	.	gene_id "XLOC_000048"; transcript_id "TCONS_00000031"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.61.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS51";
-chr1	Cufflinks	exon	3277914	3278390	.	.	.	gene_id "XLOC_000049"; transcript_id "TCONS_00000076"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.51.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS52";
-chr1	Cufflinks	exon	3280118	3280144	.	.	.	gene_id "XLOC_000050"; transcript_id "TCONS_00000077"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.53.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS54";
-chr1	Cufflinks	exon	3280499	3280525	.	.	.	gene_id "XLOC_000051"; transcript_id "TCONS_00000078"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.55.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS55";
+chr1	Cufflinks	exon	3277914	3278390	.	.	.	gene_id "XLOC_000049"; transcript_id "TCONS_00000074"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.51.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS52";
+chr1	Cufflinks	exon	3280118	3280144	.	.	.	gene_id "XLOC_000050"; transcript_id "TCONS_00000075"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.53.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS54";
+chr1	Cufflinks	exon	3280499	3280525	.	.	.	gene_id "XLOC_000051"; transcript_id "TCONS_00000076"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.55.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS55";
 chr1	Cufflinks	exon	3280687	3280741	.	.	.	gene_id "XLOC_000052"; transcript_id "TCONS_00000033"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.65.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS56";
-chr1	Cufflinks	exon	3282505	3282531	.	.	.	gene_id "XLOC_000053"; transcript_id "TCONS_00000079"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.57.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS57";
-chr1	Cufflinks	exon	3282651	3282677	.	.	.	gene_id "XLOC_000054"; transcript_id "TCONS_00000080"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.59.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS58";
-chr1	Cufflinks	exon	3282761	3282832	.	.	.	gene_id "XLOC_000055"; transcript_id "TCONS_00000081"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.61.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS59";
-chr1	Cufflinks	exon	3284967	3284993	.	.	.	gene_id "XLOC_000056"; transcript_id "TCONS_00000082"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.63.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS60";
+chr1	Cufflinks	exon	3282505	3282531	.	.	.	gene_id "XLOC_000053"; transcript_id "TCONS_00000077"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.57.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS57";
+chr1	Cufflinks	exon	3282651	3282677	.	.	.	gene_id "XLOC_000054"; transcript_id "TCONS_00000078"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.59.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS58";
+chr1	Cufflinks	exon	3282761	3282832	.	.	.	gene_id "XLOC_000055"; transcript_id "TCONS_00000079"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.61.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS59";
+chr1	Cufflinks	exon	3284967	3284993	.	.	.	gene_id "XLOC_000056"; transcript_id "TCONS_00000080"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.63.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS60";
 chr1	Cufflinks	exon	3290489	3290553	.	.	.	gene_id "XLOC_000057"; transcript_id "TCONS_00000034"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.67.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS61";
-chr1	Cufflinks	exon	3290799	3290859	.	.	.	gene_id "XLOC_000058"; transcript_id "TCONS_00000083"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.65.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS62";
-chr1	Cufflinks	exon	3290920	3291273	.	.	.	gene_id "XLOC_000059"; transcript_id "TCONS_00000084"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.69.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS63";
-chr1	Cufflinks	exon	3299444	3299640	.	.	.	gene_id "XLOC_000060"; transcript_id "TCONS_00000085"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.67.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS65";
+chr1	Cufflinks	exon	3290799	3290859	.	.	.	gene_id "XLOC_000058"; transcript_id "TCONS_00000081"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.65.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS62";
+chr1	Cufflinks	exon	3290920	3291273	.	.	.	gene_id "XLOC_000059"; transcript_id "TCONS_00000082"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.69.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS63";
+chr1	Cufflinks	exon	3299444	3299640	.	.	.	gene_id "XLOC_000060"; transcript_id "TCONS_00000083"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.67.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS65";
 chr1	Cufflinks	exon	3299610	3299664	.	.	.	gene_id "XLOC_000060"; transcript_id "TCONS_00000037"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.73.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS66";
-chr1	Cufflinks	exon	3299692	3299733	.	.	.	gene_id "XLOC_000061"; transcript_id "TCONS_00000086"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.71.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS67";
+chr1	Cufflinks	exon	3299692	3299733	.	.	.	gene_id "XLOC_000061"; transcript_id "TCONS_00000084"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.71.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS67";
 chr1	Cufflinks	exon	3300052	3300078	.	.	.	gene_id "XLOC_000062"; transcript_id "TCONS_00000038"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.75.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS68";
-chr1	Cufflinks	exon	3307749	3307775	.	.	.	gene_id "XLOC_000063"; transcript_id "TCONS_00000087"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.73.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS69";
-chr1	Cufflinks	exon	3318621	3318647	.	.	.	gene_id "XLOC_000064"; transcript_id "TCONS_00000088"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.75.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS70";
+chr1	Cufflinks	exon	3307749	3307775	.	.	.	gene_id "XLOC_000063"; transcript_id "TCONS_00000085"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.73.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS69";
+chr1	Cufflinks	exon	3318621	3318647	.	.	.	gene_id "XLOC_000064"; transcript_id "TCONS_00000086"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.75.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS70";
 chr1	Cufflinks	exon	3319000	3319051	.	.	.	gene_id "XLOC_000065"; transcript_id "TCONS_00000039"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.77.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS71";
-chr1	Cufflinks	exon	3330528	3330554	.	.	.	gene_id "XLOC_000066"; transcript_id "TCONS_00000089"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.77.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS72";
-chr1	Cufflinks	exon	3351241	3351311	.	.	.	gene_id "XLOC_000067"; transcript_id "TCONS_00000090"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.79.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS73";
+chr1	Cufflinks	exon	3330528	3330554	.	.	.	gene_id "XLOC_000066"; transcript_id "TCONS_00000087"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.77.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS72";
+chr1	Cufflinks	exon	3351241	3351311	.	.	.	gene_id "XLOC_000067"; transcript_id "TCONS_00000088"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.79.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS73";
 chr1	Cufflinks	exon	3355888	3355914	.	.	.	gene_id "XLOC_000068"; transcript_id "TCONS_00000040"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.79.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS74";
-chr1	Cufflinks	exon	3355908	3356119	.	.	.	gene_id "XLOC_000068"; transcript_id "TCONS_00000091"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.81.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS74";
-chr1	Cufflinks	exon	3356181	3356225	.	.	.	gene_id "XLOC_000069"; transcript_id "TCONS_00000092"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.83.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS75";
-chr1	Cufflinks	exon	3363077	3363176	.	.	.	gene_id "XLOC_000070"; transcript_id "TCONS_00000093"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.85.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS76";
+chr1	Cufflinks	exon	3355908	3356119	.	.	.	gene_id "XLOC_000068"; transcript_id "TCONS_00000089"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.81.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS74";
+chr1	Cufflinks	exon	3356181	3356225	.	.	.	gene_id "XLOC_000069"; transcript_id "TCONS_00000090"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.83.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS75";
+chr1	Cufflinks	exon	3363077	3363176	.	.	.	gene_id "XLOC_000070"; transcript_id "TCONS_00000091"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.85.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS76";
 chr1	Cufflinks	exon	3363215	3363278	.	.	.	gene_id "XLOC_000071"; transcript_id "TCONS_00000041"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.81.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS77";
-chr1	Cufflinks	exon	3363388	3363446	.	.	.	gene_id "XLOC_000072"; transcript_id "TCONS_00000094"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.87.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS78";
+chr1	Cufflinks	exon	3363388	3363446	.	.	.	gene_id "XLOC_000072"; transcript_id "TCONS_00000092"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.87.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS78";
 chr1	Cufflinks	exon	3363754	3363849	.	.	.	gene_id "XLOC_000073"; transcript_id "TCONS_00000042"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.83.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS79";
-chr1	Cufflinks	exon	3364872	3364919	.	.	.	gene_id "XLOC_000074"; transcript_id "TCONS_00000095"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.89.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS80";
+chr1	Cufflinks	exon	3364872	3364919	.	.	.	gene_id "XLOC_000074"; transcript_id "TCONS_00000093"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.89.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS80";
 chr1	Cufflinks	exon	3367136	3367162	.	.	.	gene_id "XLOC_000075"; transcript_id "TCONS_00000043"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.85.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS81";
-chr1	Cufflinks	exon	3367211	3367237	.	.	.	gene_id "XLOC_000076"; transcript_id "TCONS_00000096"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.91.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS82";
+chr1	Cufflinks	exon	3367211	3367237	.	.	.	gene_id "XLOC_000076"; transcript_id "TCONS_00000094"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.91.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS82";
 chr1	Cufflinks	exon	3367334	3367382	.	.	.	gene_id "XLOC_000077"; transcript_id "TCONS_00000044"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.87.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS83";
-chr1	Cufflinks	exon	3369581	3369607	.	.	.	gene_id "XLOC_000078"; transcript_id "TCONS_00000097"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.93.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS84";
-chr1	Cufflinks	exon	3375002	3375028	.	.	.	gene_id "XLOC_000079"; transcript_id "TCONS_00000098"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.95.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS85";
+chr1	Cufflinks	exon	3369581	3369607	.	.	.	gene_id "XLOC_000078"; transcript_id "TCONS_00000095"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.93.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS84";
+chr1	Cufflinks	exon	3375002	3375028	.	.	.	gene_id "XLOC_000079"; transcript_id "TCONS_00000096"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.95.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS85";
 chr1	Cufflinks	exon	3377212	3377262	.	.	.	gene_id "XLOC_000080"; transcript_id "TCONS_00000045"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.89.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS86";
-chr1	Cufflinks	exon	3379889	3379915	.	.	.	gene_id "XLOC_000081"; transcript_id "TCONS_00000099"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.97.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS87";
-chr1	Cufflinks	exon	3386740	3386836	.	.	.	gene_id "XLOC_000082"; transcript_id "TCONS_00000100"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.99.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS88";
+chr1	Cufflinks	exon	3379889	3379915	.	.	.	gene_id "XLOC_000081"; transcript_id "TCONS_00000097"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.97.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS87";
+chr1	Cufflinks	exon	3386740	3386836	.	.	.	gene_id "XLOC_000082"; transcript_id "TCONS_00000098"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.99.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS88";
 chr1	Cufflinks	exon	3391326	3391352	.	.	.	gene_id "XLOC_000083"; transcript_id "TCONS_00000046"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.91.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS89";
 chr1	Cufflinks	exon	3435842	3435880	.	.	.	gene_id "XLOC_000084"; transcript_id "TCONS_00000047"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.93.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS90";
 chr1	Cufflinks	exon	3447762	3447788	.	.	.	gene_id "XLOC_000085"; transcript_id "TCONS_00000048"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.95.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS91";
--- a/test-data/cuffcompare_out6.tracking	Fri Aug 01 11:01:51 2014 -0400
+++ b/test-data/cuffcompare_out6.tracking	Sat Aug 02 10:24:42 2014 -0400
@@ -17,9 +17,9 @@
 TCONS_00000017	XLOC_000021	-	u	q1:CUFF.55|CUFF.55.1|100|31.293533|0.000000|75.549272|2.000000|-	-
 TCONS_00000018	XLOC_000022	-	u	q1:CUFF.57|CUFF.57.1|100|15.646767|0.000000|46.940300|1.000000|-	-
 TCONS_00000019	XLOC_000023	-	u	q1:CUFF.59|CUFF.59.1|100|15.646767|0.000000|46.940300|1.000000|-	-
-TCONS_00000020	XLOC_000025	-	u	q1:CUFF.7|CUFF.7.1|100|9.999117|0.000000|19.998234|0.639053|-	-
+TCONS_00000020	XLOC_000025	-	.	q1:CUFF.7|CUFF.7.1|100|9.999117|0.000000|19.998234|0.639053|169	q2:CUFF.23|CUFF.23.1|100|16.205195|0.000000|34.917342|0.920455|88
 TCONS_00000021	XLOC_000026	-	u	q1:CUFF.5|CUFF.5.1|100|31.293533|0.000000|75.549272|2.000000|-	-
-TCONS_00000022	XLOC_000029	-	u	q1:CUFF.9|CUFF.9.1|100|17.776896|9.153835|26.399957|1.136139|-	-
+TCONS_00000022	XLOC_000029	-	.	q1:CUFF.9|CUFF.9.1|100|17.776896|9.153835|26.399957|1.136139|404	q2:CUFF.25|CUFF.25.1|100|35.211287|0.000000|85.007567|2.000000|27
 TCONS_00000023	XLOC_000031	-	u	q1:CUFF.11|CUFF.11.1|100|31.293533|0.000000|75.549272|2.000000|-	-
 TCONS_00000024	XLOC_000034	Xkr4|Xkr4	i	q1:CUFF.15|CUFF.15.1|100|10.695258|0.000000|25.820637|0.683544|-	-
 TCONS_00000025	XLOC_000035	Xkr4|Xkr4	i	q1:CUFF.19|CUFF.19.1|100|29.337687|3.097262|55.578113|1.875000|-	-
@@ -58,43 +58,41 @@
 TCONS_00000058	XLOC_000013	-	u	-	q2:CUFF.15|CUFF.15.1|100|35.211287|0.000000|85.007567|2.000000|-
 TCONS_00000059	XLOC_000018	-	u	-	q2:CUFF.17|CUFF.17.1|100|35.211287|0.000000|85.007567|2.000000|-
 TCONS_00000060	XLOC_000024	-	u	-	q2:CUFF.19|CUFF.19.1|100|35.211287|0.000000|85.007567|2.000000|-
-TCONS_00000061	XLOC_000025	-	u	-	q2:CUFF.23|CUFF.23.1|100|16.205195|0.000000|34.917342|0.920455|-
-TCONS_00000062	XLOC_000027	-	u	-	q2:CUFF.21|CUFF.21.1|100|35.211287|0.000000|85.007567|2.000000|-
-TCONS_00000063	XLOC_000028	-	u	-	q2:CUFF.26|CUFF.26.1|100|29.709524|0.000000|71.725135|1.687500|-
-TCONS_00000064	XLOC_000029	-	u	-	q2:CUFF.25|CUFF.25.1|100|35.211287|0.000000|85.007567|2.000000|-
-TCONS_00000065	XLOC_000030	-	u	-	q2:CUFF.29|CUFF.29.1|100|13.581496|0.000000|32.788633|0.771429|-
-TCONS_00000066	XLOC_000032	-	u	-	q2:CUFF.31|CUFF.31.1|100|22.635827|0.000000|45.271655|1.285714|-
-TCONS_00000067	XLOC_000033	Xkr4|Xkr4	i	-	q2:CUFF.33|CUFF.33.1|100|23.767619|0.000000|57.380108|1.350000|-
-TCONS_00000068	XLOC_000036	Xkr4|Xkr4	i	-	q2:CUFF.35|CUFF.35.1|100|11.317914|0.000000|27.323861|0.642857|-
-TCONS_00000069	XLOC_000037	Xkr4|Xkr4	i	-	q2:CUFF.37|CUFF.37.1|100|11.500461|0.000000|24.780049|0.653226|-
-TCONS_00000070	XLOC_000038	Xkr4|Xkr4	i	-	q2:CUFF.39|CUFF.39.1|100|52.816931|0.000000|113.804669|3.000000|-
-TCONS_00000071	XLOC_000039	Xkr4|Xkr4	i	-	q2:CUFF.41|CUFF.41.1|100|43.213852|0.000000|93.112911|2.454545|-
-TCONS_00000072	XLOC_000041	Xkr4|Xkr4	i	-	q2:CUFF.43|CUFF.43.1|100|23.474191|0.000000|46.948383|1.333333|-
-TCONS_00000073	XLOC_000043	Xkr4|Xkr4	i	-	q2:CUFF.45|CUFF.45.1|100|20.667495|0.000000|49.895746|1.173913|-
-TCONS_00000074	XLOC_000045	Xkr4|Xkr4	i	-	q2:CUFF.47|CUFF.47.1|100|35.211287|0.000000|85.007567|2.000000|-
-TCONS_00000075	XLOC_000047	Xkr4|Xkr4	i	-	q2:CUFF.49|CUFF.49.1|100|35.211287|0.000000|85.007567|2.000000|-
-TCONS_00000076	XLOC_000049	Xkr4|Xkr4	i	-	q2:CUFF.51|CUFF.51.1|100|14.948188|7.228977|22.667399|0.849057|-
-TCONS_00000077	XLOC_000050	Xkr4|Xkr4	i	-	q2:CUFF.53|CUFF.53.1|100|52.816931|0.000000|113.804669|3.000000|-
-TCONS_00000078	XLOC_000051	Xkr4|Xkr4	i	-	q2:CUFF.55|CUFF.55.1|100|35.211287|0.000000|85.007567|2.000000|-
-TCONS_00000079	XLOC_000053	Xkr4|Xkr4	i	-	q2:CUFF.57|CUFF.57.1|100|35.211287|0.000000|85.007567|2.000000|-
-TCONS_00000080	XLOC_000054	Xkr4|Xkr4	i	-	q2:CUFF.59|CUFF.59.1|100|35.211287|0.000000|85.007567|2.000000|-
-TCONS_00000081	XLOC_000055	Xkr4|Xkr4	i	-	q2:CUFF.61|CUFF.61.1|100|13.204233|0.000000|31.877838|0.750000|-
-TCONS_00000082	XLOC_000056	Xkr4|Xkr4	i	-	q2:CUFF.63|CUFF.63.1|100|35.211287|0.000000|85.007567|2.000000|-
-TCONS_00000083	XLOC_000058	Xkr4|Xkr4	i	-	q2:CUFF.65|CUFF.65.1|100|31.170648|0.000000|62.341295|1.770492|-
-TCONS_00000084	XLOC_000059	Xkr4|Xkr4	i	-	q2:CUFF.69|CUFF.69.1|100|18.799247|8.750627|28.847866|1.067797|-
-TCONS_00000085	XLOC_000060	Xkr4|Xkr4	i	-	q2:CUFF.67|CUFF.67.1|100|15.681351|3.378764|27.983938|0.890700|-
-TCONS_00000086	XLOC_000061	Xkr4|Xkr4	i	-	q2:CUFF.71|CUFF.71.1|100|22.635827|0.000000|54.647722|1.285714|-
-TCONS_00000087	XLOC_000063	Xkr4|Xkr4	i	-	q2:CUFF.73|CUFF.73.1|100|35.211287|0.000000|85.007567|2.000000|-
-TCONS_00000088	XLOC_000064	Xkr4|Xkr4	i	-	q2:CUFF.75|CUFF.75.1|100|52.816931|0.000000|113.804669|3.000000|-
-TCONS_00000089	XLOC_000066	Xkr4|Xkr4	i	-	q2:CUFF.77|CUFF.77.1|100|17.605644|0.000000|52.816931|1.000000|-
-TCONS_00000090	XLOC_000067	Xkr4|Xkr4	i	-	q2:CUFF.79|CUFF.79.1|100|13.390208|0.000000|32.326821|0.760563|-
-TCONS_00000091	XLOC_000068	Xkr4|Xkr4	i	-	q2:CUFF.81|CUFF.81.1|100|11.211141|1.183592|21.238690|0.636792|-
-TCONS_00000092	XLOC_000069	Xkr4|Xkr4	i	-	q2:CUFF.83|CUFF.83.1|100|21.126772|0.000000|51.004540|1.200000|-
-TCONS_00000093	XLOC_000070	Xkr4|Xkr4	i	-	q2:CUFF.85|CUFF.85.1|100|19.014095|0.000000|38.028190|1.080000|-
-TCONS_00000094	XLOC_000072	Xkr4|Xkr4	i	-	q2:CUFF.87|CUFF.87.1|100|24.170460|0.000000|52.080103|1.372881|-
-TCONS_00000095	XLOC_000074	Xkr4|Xkr4	i	-	q2:CUFF.89|CUFF.89.1|100|29.709524|0.000000|64.015126|1.687500|-
-TCONS_00000096	XLOC_000076	Xkr4|Xkr4	i	-	q2:CUFF.91|CUFF.91.1|100|35.211287|0.000000|85.007567|2.000000|-
-TCONS_00000097	XLOC_000078	Xkr4|Xkr4	i	-	q2:CUFF.93|CUFF.93.1|100|35.211287|0.000000|85.007567|2.000000|-
-TCONS_00000098	XLOC_000079	Xkr4|Xkr4	i	-	q2:CUFF.95|CUFF.95.1|100|35.211287|0.000000|85.007567|2.000000|-
-TCONS_00000099	XLOC_000081	Xkr4|Xkr4	i	-	q2:CUFF.97|CUFF.97.1|100|35.211287|0.000000|85.007567|2.000000|-
-TCONS_00000100	XLOC_000082	Xkr4|Xkr4	i	-	q2:CUFF.99|CUFF.99.1|100|19.602160|0.000000|39.204320|1.113402|-
+TCONS_00000061	XLOC_000027	-	u	-	q2:CUFF.21|CUFF.21.1|100|35.211287|0.000000|85.007567|2.000000|-
+TCONS_00000062	XLOC_000028	-	u	-	q2:CUFF.26|CUFF.26.1|100|29.709524|0.000000|71.725135|1.687500|-
+TCONS_00000063	XLOC_000030	-	u	-	q2:CUFF.29|CUFF.29.1|100|13.581496|0.000000|32.788633|0.771429|-
+TCONS_00000064	XLOC_000032	-	u	-	q2:CUFF.31|CUFF.31.1|100|22.635827|0.000000|45.271655|1.285714|-
+TCONS_00000065	XLOC_000033	Xkr4|Xkr4	i	-	q2:CUFF.33|CUFF.33.1|100|23.767619|0.000000|57.380108|1.350000|-
+TCONS_00000066	XLOC_000036	Xkr4|Xkr4	i	-	q2:CUFF.35|CUFF.35.1|100|11.317914|0.000000|27.323861|0.642857|-
+TCONS_00000067	XLOC_000037	Xkr4|Xkr4	i	-	q2:CUFF.37|CUFF.37.1|100|11.500461|0.000000|24.780049|0.653226|-
+TCONS_00000068	XLOC_000038	Xkr4|Xkr4	i	-	q2:CUFF.39|CUFF.39.1|100|52.816931|0.000000|113.804669|3.000000|-
+TCONS_00000069	XLOC_000039	Xkr4|Xkr4	i	-	q2:CUFF.41|CUFF.41.1|100|43.213852|0.000000|93.112911|2.454545|-
+TCONS_00000070	XLOC_000041	Xkr4|Xkr4	i	-	q2:CUFF.43|CUFF.43.1|100|23.474191|0.000000|46.948383|1.333333|-
+TCONS_00000071	XLOC_000043	Xkr4|Xkr4	i	-	q2:CUFF.45|CUFF.45.1|100|20.667495|0.000000|49.895746|1.173913|-
+TCONS_00000072	XLOC_000045	Xkr4|Xkr4	i	-	q2:CUFF.47|CUFF.47.1|100|35.211287|0.000000|85.007567|2.000000|-
+TCONS_00000073	XLOC_000047	Xkr4|Xkr4	i	-	q2:CUFF.49|CUFF.49.1|100|35.211287|0.000000|85.007567|2.000000|-
+TCONS_00000074	XLOC_000049	Xkr4|Xkr4	i	-	q2:CUFF.51|CUFF.51.1|100|14.948188|7.228977|22.667399|0.849057|-
+TCONS_00000075	XLOC_000050	Xkr4|Xkr4	i	-	q2:CUFF.53|CUFF.53.1|100|52.816931|0.000000|113.804669|3.000000|-
+TCONS_00000076	XLOC_000051	Xkr4|Xkr4	i	-	q2:CUFF.55|CUFF.55.1|100|35.211287|0.000000|85.007567|2.000000|-
+TCONS_00000077	XLOC_000053	Xkr4|Xkr4	i	-	q2:CUFF.57|CUFF.57.1|100|35.211287|0.000000|85.007567|2.000000|-
+TCONS_00000078	XLOC_000054	Xkr4|Xkr4	i	-	q2:CUFF.59|CUFF.59.1|100|35.211287|0.000000|85.007567|2.000000|-
+TCONS_00000079	XLOC_000055	Xkr4|Xkr4	i	-	q2:CUFF.61|CUFF.61.1|100|13.204233|0.000000|31.877838|0.750000|-
+TCONS_00000080	XLOC_000056	Xkr4|Xkr4	i	-	q2:CUFF.63|CUFF.63.1|100|35.211287|0.000000|85.007567|2.000000|-
+TCONS_00000081	XLOC_000058	Xkr4|Xkr4	i	-	q2:CUFF.65|CUFF.65.1|100|31.170648|0.000000|62.341295|1.770492|-
+TCONS_00000082	XLOC_000059	Xkr4|Xkr4	i	-	q2:CUFF.69|CUFF.69.1|100|18.799247|8.750627|28.847866|1.067797|-
+TCONS_00000083	XLOC_000060	Xkr4|Xkr4	i	-	q2:CUFF.67|CUFF.67.1|100|15.681351|3.378764|27.983938|0.890700|-
+TCONS_00000084	XLOC_000061	Xkr4|Xkr4	i	-	q2:CUFF.71|CUFF.71.1|100|22.635827|0.000000|54.647722|1.285714|-
+TCONS_00000085	XLOC_000063	Xkr4|Xkr4	i	-	q2:CUFF.73|CUFF.73.1|100|35.211287|0.000000|85.007567|2.000000|-
+TCONS_00000086	XLOC_000064	Xkr4|Xkr4	i	-	q2:CUFF.75|CUFF.75.1|100|52.816931|0.000000|113.804669|3.000000|-
+TCONS_00000087	XLOC_000066	Xkr4|Xkr4	i	-	q2:CUFF.77|CUFF.77.1|100|17.605644|0.000000|52.816931|1.000000|-
+TCONS_00000088	XLOC_000067	Xkr4|Xkr4	i	-	q2:CUFF.79|CUFF.79.1|100|13.390208|0.000000|32.326821|0.760563|-
+TCONS_00000089	XLOC_000068	Xkr4|Xkr4	i	-	q2:CUFF.81|CUFF.81.1|100|11.211141|1.183592|21.238690|0.636792|-
+TCONS_00000090	XLOC_000069	Xkr4|Xkr4	i	-	q2:CUFF.83|CUFF.83.1|100|21.126772|0.000000|51.004540|1.200000|-
+TCONS_00000091	XLOC_000070	Xkr4|Xkr4	i	-	q2:CUFF.85|CUFF.85.1|100|19.014095|0.000000|38.028190|1.080000|-
+TCONS_00000092	XLOC_000072	Xkr4|Xkr4	i	-	q2:CUFF.87|CUFF.87.1|100|24.170460|0.000000|52.080103|1.372881|-
+TCONS_00000093	XLOC_000074	Xkr4|Xkr4	i	-	q2:CUFF.89|CUFF.89.1|100|29.709524|0.000000|64.015126|1.687500|-
+TCONS_00000094	XLOC_000076	Xkr4|Xkr4	i	-	q2:CUFF.91|CUFF.91.1|100|35.211287|0.000000|85.007567|2.000000|-
+TCONS_00000095	XLOC_000078	Xkr4|Xkr4	i	-	q2:CUFF.93|CUFF.93.1|100|35.211287|0.000000|85.007567|2.000000|-
+TCONS_00000096	XLOC_000079	Xkr4|Xkr4	i	-	q2:CUFF.95|CUFF.95.1|100|35.211287|0.000000|85.007567|2.000000|-
+TCONS_00000097	XLOC_000081	Xkr4|Xkr4	i	-	q2:CUFF.97|CUFF.97.1|100|35.211287|0.000000|85.007567|2.000000|-
+TCONS_00000098	XLOC_000082	Xkr4|Xkr4	i	-	q2:CUFF.99|CUFF.99.1|100|19.602160|0.000000|39.204320|1.113402|-
--- a/test-data/cuffcompare_out7.txt	Fri Aug 01 11:01:51 2014 -0400
+++ b/test-data/cuffcompare_out7.txt	Sat Aug 02 10:24:42 2014 -0400
@@ -1,33 +1,50 @@
-# Cuffcompare v2.0.2 | Command line was:
-#cuffcompare -o cc_output -r /Users/jeremy/projects/galaxy-central/database/files/002/dataset_2770.dat -R ./input1 ./input2
+# Cuffcompare v2.2.1 | Command line was:
+#cuffcompare -o cc_output -r /home/gvandeweyer/galaxy-dist/galaxy-dist/database/files/000/dataset_193.dat -e 100 -d 100 ./input1 ./input2
 #
 
 #= Summary for dataset: ./input1 :
 #     Query mRNAs :      50 in      50 loci  (0 multi-exon transcripts)
 #            (0 multi-transcript loci, ~1.0 transcripts per locus)
-# Reference mRNAs :       1 in       1 loci  (1 multi-exon)
-# Corresponding super-loci:              1
+# Reference mRNAs :       9 in       6 loci  (9 multi-exon)
+# Super-loci w/ reference transcripts:        1
 #--------------------|   Sn   |  Sp   |  fSn |  fSp  
-        Base level: 	  2.2	  2.3	  - 	  - 
+        Base level: 	  0.3	  2.3	  - 	  - 
         Exon level: 	  0.0	  0.0	  0.0	  0.0
-      Intron level: 	  0.0	  nan	  0.0	  nan
-Intron chain level: 	  0.0	  nan	  0.0	  nan
+      Intron level: 	  0.0	 -nan	  0.0	 -nan
+Intron chain level: 	  0.0	 -nan	  0.0	 -nan
   Transcript level: 	  0.0	  0.0	  0.0	  0.0
        Locus level: 	  0.0	  0.0	  0.0	  0.0
 
-Matching intron chains:       0
-         Matching loci:       0
+     Matching intron chains:       0
+              Matching loci:       0
 
-          Missed exons:       2/3	( 66.7%)
+          Missed exons:      36/37	( 97.3%)
            Novel exons:      49/50	( 98.0%)
-        Missed introns:       2/2	(100.0%)
-           Missed loci:       0/1	(  0.0%)
+        Missed introns:      32/32	(100.0%)
+           Missed loci:       5/6	( 83.3%)
             Novel loci:      49/50	( 98.0%)
 
 #= Summary for dataset: ./input2 :
 #     Query mRNAs :      50 in      50 loci  (0 multi-exon transcripts)
 #            (0 multi-transcript loci, ~1.0 transcripts per locus)
-# Reference mRNAs :       0 in       0 loci  (0 multi-exon)
+# Reference mRNAs :       8 in       5 loci  (8 multi-exon)
+# Super-loci w/ reference transcripts:        0
+#--------------------|   Sn   |  Sp   |  fSn |  fSp  
+        Base level: 	  0.0	  0.0	  - 	  - 
+        Exon level: 	  0.0	  0.0	  0.0	  0.0
+      Intron level: 	  0.0	 -nan	  0.0	 -nan
+Intron chain level: 	  0.0	 -nan	  0.0	 -nan
+  Transcript level: 	  0.0	  0.0	  0.0	  0.0
+       Locus level: 	  0.0	  0.0	  0.0	  0.0
+
+     Matching intron chains:       0
+              Matching loci:       0
+
+          Missed exons:      34/34	(100.0%)
+           Novel exons:      50/50	(100.0%)
+        Missed introns:      30/30	(100.0%)
+           Missed loci:       5/5	(100.0%)
+            Novel loci:      50/50	(100.0%)
 
  Total union super-loci across all input datasets: 87 
   (0 multi-transcript, ~1.1 transcripts per locus)
--- a/test-data/cuffmerge_out1.gtf	Fri Aug 01 11:01:51 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,74 +0,0 @@
-chr1	Cufflinks	exon	4797974	4798063	.	+	.	gene_id "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "1"; gene_name "Lypla1"; oId "Lypla1"; nearest_ref "Lypla1"; class_code "="; tss_id "TSS1";
-chr1	Cufflinks	exon	4798536	4798567	.	+	.	gene_id "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "2"; gene_name "Lypla1"; oId "Lypla1"; nearest_ref "Lypla1"; class_code "="; tss_id "TSS1";
-chr1	Cufflinks	exon	4818665	4818730	.	+	.	gene_id "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "3"; gene_name "Lypla1"; oId "Lypla1"; nearest_ref "Lypla1"; class_code "="; tss_id "TSS1";
-chr1	Cufflinks	exon	4820349	4820396	.	+	.	gene_id "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "4"; gene_name "Lypla1"; oId "Lypla1"; nearest_ref "Lypla1"; class_code "="; tss_id "TSS1";
-chr1	Cufflinks	exon	4822392	4822462	.	+	.	gene_id "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "5"; gene_name "Lypla1"; oId "Lypla1"; nearest_ref "Lypla1"; class_code "="; tss_id "TSS1";
-chr1	Cufflinks	exon	4827082	4827155	.	+	.	gene_id "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "6"; gene_name "Lypla1"; oId "Lypla1"; nearest_ref "Lypla1"; class_code "="; tss_id "TSS1";
-chr1	Cufflinks	exon	4829468	4829569	.	+	.	gene_id "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "7"; gene_name "Lypla1"; oId "Lypla1"; nearest_ref "Lypla1"; class_code "="; tss_id "TSS1";
-chr1	Cufflinks	exon	4831037	4831213	.	+	.	gene_id "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "8"; gene_name "Lypla1"; oId "Lypla1"; nearest_ref "Lypla1"; class_code "="; tss_id "TSS1";
-chr1	Cufflinks	exon	4835044	4836816	.	+	.	gene_id "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "9"; gene_name "Lypla1"; oId "Lypla1"; nearest_ref "Lypla1"; class_code "="; tss_id "TSS1";
-chr1	Cufflinks	exon	4847775	4848057	.	+	.	gene_id "XLOC_000002"; transcript_id "TCONS_00000002"; exon_number "1"; gene_name "Tcea1"; oId "Tcea1_dup1"; contained_in "TCONS_00000003"; nearest_ref "Tcea1_dup1"; class_code "="; tss_id "TSS2";
-chr1	Cufflinks	exon	4857551	4857613	.	+	.	gene_id "XLOC_000002"; transcript_id "TCONS_00000002"; exon_number "2"; gene_name "Tcea1"; oId "Tcea1_dup1"; contained_in "TCONS_00000003"; nearest_ref "Tcea1_dup1"; class_code "="; tss_id "TSS2";
-chr1	Cufflinks	exon	4847775	4848057	.	+	.	gene_id "XLOC_000002"; transcript_id "TCONS_00000003"; exon_number "1"; gene_name "Tcea1"; oId "Tcea1"; nearest_ref "Tcea1"; class_code "="; tss_id "TSS2";
-chr1	Cufflinks	exon	4857551	4857613	.	+	.	gene_id "XLOC_000002"; transcript_id "TCONS_00000003"; exon_number "2"; gene_name "Tcea1"; oId "Tcea1"; nearest_ref "Tcea1"; class_code "="; tss_id "TSS2";
-chr1	Cufflinks	exon	4868108	4868213	.	+	.	gene_id "XLOC_000002"; transcript_id "TCONS_00000003"; exon_number "3"; gene_name "Tcea1"; oId "Tcea1"; nearest_ref "Tcea1"; class_code "="; tss_id "TSS2";
-chr1	Cufflinks	exon	4876825	4876912	.	+	.	gene_id "XLOC_000002"; transcript_id "TCONS_00000003"; exon_number "4"; gene_name "Tcea1"; oId "Tcea1"; nearest_ref "Tcea1"; class_code "="; tss_id "TSS2";
-chr1	Cufflinks	exon	4879538	4879683	.	+	.	gene_id "XLOC_000002"; transcript_id "TCONS_00000003"; exon_number "5"; gene_name "Tcea1"; oId "Tcea1"; nearest_ref "Tcea1"; class_code "="; tss_id "TSS2";
-chr1	Cufflinks	exon	4880821	4880877	.	+	.	gene_id "XLOC_000002"; transcript_id "TCONS_00000003"; exon_number "6"; gene_name "Tcea1"; oId "Tcea1"; nearest_ref "Tcea1"; class_code "="; tss_id "TSS2";
-chr1	Cufflinks	exon	4881996	4882150	.	+	.	gene_id "XLOC_000002"; transcript_id "TCONS_00000003"; exon_number "7"; gene_name "Tcea1"; oId "Tcea1"; nearest_ref "Tcea1"; class_code "="; tss_id "TSS2";
-chr1	Cufflinks	exon	4883498	4883644	.	+	.	gene_id "XLOC_000002"; transcript_id "TCONS_00000003"; exon_number "8"; gene_name "Tcea1"; oId "Tcea1"; nearest_ref "Tcea1"; class_code "="; tss_id "TSS2";
-chr1	Cufflinks	exon	4885015	4885086	.	+	.	gene_id "XLOC_000002"; transcript_id "TCONS_00000003"; exon_number "9"; gene_name "Tcea1"; oId "Tcea1"; nearest_ref "Tcea1"; class_code "="; tss_id "TSS2";
-chr1	Cufflinks	exon	4886437	4887987	.	+	.	gene_id "XLOC_000002"; transcript_id "TCONS_00000003"; exon_number "10"; gene_name "Tcea1"; oId "Tcea1"; nearest_ref "Tcea1"; class_code "="; tss_id "TSS2";
-chr1	Cufflinks	exon	3204563	3207049	.	-	.	gene_id "XLOC_000003"; transcript_id "TCONS_00000004"; exon_number "1"; gene_name "Xkr4"; oId "Xkr4"; nearest_ref "Xkr4"; class_code "="; tss_id "TSS3";
-chr1	Cufflinks	exon	3411783	3411982	.	-	.	gene_id "XLOC_000003"; transcript_id "TCONS_00000004"; exon_number "2"; gene_name "Xkr4"; oId "Xkr4"; nearest_ref "Xkr4"; class_code "="; tss_id "TSS3";
-chr1	Cufflinks	exon	3660633	3661579	.	-	.	gene_id "XLOC_000003"; transcript_id "TCONS_00000004"; exon_number "3"; gene_name "Xkr4"; oId "Xkr4"; nearest_ref "Xkr4"; class_code "="; tss_id "TSS3";
-chr1	Cufflinks	exon	4334224	4340172	.	-	.	gene_id "XLOC_000004"; transcript_id "TCONS_00000005"; exon_number "1"; gene_name "Rp1"; oId "Rp1"; nearest_ref "Rp1"; class_code "="; tss_id "TSS4";
-chr1	Cufflinks	exon	4341991	4342162	.	-	.	gene_id "XLOC_000004"; transcript_id "TCONS_00000005"; exon_number "2"; gene_name "Rp1"; oId "Rp1"; nearest_ref "Rp1"; class_code "="; tss_id "TSS4";
-chr1	Cufflinks	exon	4342283	4342918	.	-	.	gene_id "XLOC_000004"; transcript_id "TCONS_00000005"; exon_number "3"; gene_name "Rp1"; oId "Rp1"; nearest_ref "Rp1"; class_code "="; tss_id "TSS4";
-chr1	Cufflinks	exon	4350281	4350473	.	-	.	gene_id "XLOC_000004"; transcript_id "TCONS_00000005"; exon_number "4"; gene_name "Rp1"; oId "Rp1"; nearest_ref "Rp1"; class_code "="; tss_id "TSS4";
-chr1	Cufflinks	exon	4481009	4482749	.	-	.	gene_id "XLOC_000005"; transcript_id "TCONS_00000006"; exon_number "1"; gene_name "Sox17"; oId "Sox17"; nearest_ref "Sox17"; class_code "="; tss_id "TSS5";
-chr1	Cufflinks	exon	4483181	4483547	.	-	.	gene_id "XLOC_000005"; transcript_id "TCONS_00000006"; exon_number "2"; gene_name "Sox17"; oId "Sox17"; nearest_ref "Sox17"; class_code "="; tss_id "TSS5";
-chr1	Cufflinks	exon	4483853	4483944	.	-	.	gene_id "XLOC_000005"; transcript_id "TCONS_00000006"; exon_number "3"; gene_name "Sox17"; oId "Sox17"; nearest_ref "Sox17"; class_code "="; tss_id "TSS5";
-chr1	Cufflinks	exon	4485217	4486023	.	-	.	gene_id "XLOC_000005"; transcript_id "TCONS_00000006"; exon_number "4"; gene_name "Sox17"; oId "Sox17"; nearest_ref "Sox17"; class_code "="; tss_id "TSS5";
-chr1	Cufflinks	exon	4486372	4486494	.	-	.	gene_id "XLOC_000005"; transcript_id "TCONS_00000006"; exon_number "5"; gene_name "Sox17"; oId "Sox17"; nearest_ref "Sox17"; class_code "="; tss_id "TSS5";
-chr1	Cufflinks	exon	4763279	4764597	.	-	.	gene_id "XLOC_000006"; transcript_id "TCONS_00000009"; exon_number "1"; gene_name "Mrpl15"; oId "Mrpl15_dup2"; nearest_ref "Mrpl15_dup2"; class_code "="; tss_id "TSS6";
-chr1	Cufflinks	exon	4767606	4767729	.	-	.	gene_id "XLOC_000006"; transcript_id "TCONS_00000009"; exon_number "2"; gene_name "Mrpl15"; oId "Mrpl15_dup2"; nearest_ref "Mrpl15_dup2"; class_code "="; tss_id "TSS6";
-chr1	Cufflinks	exon	4772649	4772814	.	-	.	gene_id "XLOC_000006"; transcript_id "TCONS_00000009"; exon_number "3"; gene_name "Mrpl15"; oId "Mrpl15_dup2"; nearest_ref "Mrpl15_dup2"; class_code "="; tss_id "TSS6";
-chr1	Cufflinks	exon	4775654	4775807	.	-	.	gene_id "XLOC_000006"; transcript_id "TCONS_00000009"; exon_number "4"; gene_name "Mrpl15"; oId "Mrpl15_dup2"; nearest_ref "Mrpl15_dup2"; class_code "="; tss_id "TSS6";
-chr1	Cufflinks	exon	4763279	4764597	.	-	.	gene_id "XLOC_000006"; transcript_id "TCONS_00000008"; exon_number "1"; gene_name "Mrpl15"; oId "Mrpl15_dup1"; nearest_ref "Mrpl15_dup1"; class_code "="; tss_id "TSS6";
-chr1	Cufflinks	exon	4767606	4767729	.	-	.	gene_id "XLOC_000006"; transcript_id "TCONS_00000008"; exon_number "2"; gene_name "Mrpl15"; oId "Mrpl15_dup1"; nearest_ref "Mrpl15_dup1"; class_code "="; tss_id "TSS6";
-chr1	Cufflinks	exon	4772649	4772814	.	-	.	gene_id "XLOC_000006"; transcript_id "TCONS_00000008"; exon_number "3"; gene_name "Mrpl15"; oId "Mrpl15_dup1"; nearest_ref "Mrpl15_dup1"; class_code "="; tss_id "TSS6";
-chr1	Cufflinks	exon	4774032	4774186	.	-	.	gene_id "XLOC_000006"; transcript_id "TCONS_00000008"; exon_number "4"; gene_name "Mrpl15"; oId "Mrpl15_dup1"; nearest_ref "Mrpl15_dup1"; class_code "="; tss_id "TSS6";
-chr1	Cufflinks	exon	4775654	4775807	.	-	.	gene_id "XLOC_000006"; transcript_id "TCONS_00000008"; exon_number "5"; gene_name "Mrpl15"; oId "Mrpl15_dup1"; nearest_ref "Mrpl15_dup1"; class_code "="; tss_id "TSS6";
-chr1	Cufflinks	exon	4763279	4766882	.	-	.	gene_id "XLOC_000006"; transcript_id "TCONS_00000007"; exon_number "1"; gene_name "Mrpl15"; oId "Mrpl15"; nearest_ref "Mrpl15"; class_code "="; tss_id "TSS6";
-chr1	Cufflinks	exon	4767606	4767729	.	-	.	gene_id "XLOC_000006"; transcript_id "TCONS_00000007"; exon_number "2"; gene_name "Mrpl15"; oId "Mrpl15"; nearest_ref "Mrpl15"; class_code "="; tss_id "TSS6";
-chr1	Cufflinks	exon	4772649	4772814	.	-	.	gene_id "XLOC_000006"; transcript_id "TCONS_00000007"; exon_number "3"; gene_name "Mrpl15"; oId "Mrpl15"; nearest_ref "Mrpl15"; class_code "="; tss_id "TSS6";
-chr1	Cufflinks	exon	4774032	4774186	.	-	.	gene_id "XLOC_000006"; transcript_id "TCONS_00000007"; exon_number "4"; gene_name "Mrpl15"; oId "Mrpl15"; nearest_ref "Mrpl15"; class_code "="; tss_id "TSS6";
-chr1	Cufflinks	exon	4775654	4775807	.	-	.	gene_id "XLOC_000006"; transcript_id "TCONS_00000007"; exon_number "5"; gene_name "Mrpl15"; oId "Mrpl15"; nearest_ref "Mrpl15"; class_code "="; tss_id "TSS6";
-chr1	Cufflinks	exon	3111450	3111490	.	.	.	gene_id "XLOC_000007"; transcript_id "TCONS_00000010"; exon_number "1"; oId "CUFF.1.1"; class_code "u"; tss_id "TSS7";
-chr1	Cufflinks	exon	3111546	3111576	.	.	.	gene_id "XLOC_000008"; transcript_id "TCONS_00000011"; exon_number "1"; oId "CUFF.2.1"; class_code "u"; tss_id "TSS8";
-chr1	Cufflinks	exon	3174766	3174792	.	.	.	gene_id "XLOC_000009"; transcript_id "TCONS_00000012"; exon_number "1"; oId "CUFF.3.1"; class_code "u"; tss_id "TSS9";
-chr1	Cufflinks	exon	3187402	3187428	.	.	.	gene_id "XLOC_000010"; transcript_id "TCONS_00000013"; exon_number "1"; oId "CUFF.4.1"; class_code "u"; tss_id "TSS10";
-chr1	Cufflinks	exon	3188522	3188548	.	.	.	gene_id "XLOC_000011"; transcript_id "TCONS_00000014"; exon_number "1"; oId "CUFF.5.1"; class_code "u"; tss_id "TSS11";
-chr1	Cufflinks	exon	3189811	3190789	.	.	.	gene_id "XLOC_000012"; transcript_id "TCONS_00000015"; exon_number "1"; oId "CUFF.6.1"; class_code "u"; tss_id "TSS12";
-chr1	Cufflinks	exon	3190859	3191434	.	.	.	gene_id "XLOC_000013"; transcript_id "TCONS_00000016"; exon_number "1"; oId "CUFF.7.1"; class_code "u"; tss_id "TSS13";
-chr1	Cufflinks	exon	3191513	3192077	.	.	.	gene_id "XLOC_000014"; transcript_id "TCONS_00000017"; exon_number "1"; oId "CUFF.8.1"; class_code "u"; tss_id "TSS14";
-chr1	Cufflinks	exon	3192251	3192336	.	.	.	gene_id "XLOC_000015"; transcript_id "TCONS_00000018"; exon_number "1"; oId "CUFF.9.1"; class_code "u"; tss_id "TSS15";
-chr1	Cufflinks	exon	3192442	3192494	.	.	.	gene_id "XLOC_000016"; transcript_id "TCONS_00000019"; exon_number "1"; oId "CUFF.10.1"; class_code "u"; tss_id "TSS16";
-chr1	Cufflinks	exon	3192551	3192676	.	.	.	gene_id "XLOC_000017"; transcript_id "TCONS_00000020"; exon_number "1"; oId "CUFF.11.1"; class_code "u"; tss_id "TSS17";
-chr1	Cufflinks	exon	3192732	3192811	.	.	.	gene_id "XLOC_000018"; transcript_id "TCONS_00000021"; exon_number "1"; oId "CUFF.12.1"; class_code "u"; tss_id "TSS18";
-chr1	Cufflinks	exon	3192941	3193042	.	.	.	gene_id "XLOC_000019"; transcript_id "TCONS_00000022"; exon_number "1"; oId "CUFF.13.1"; class_code "u"; tss_id "TSS19";
-chr1	Cufflinks	exon	3194186	3194226	.	.	.	gene_id "XLOC_000020"; transcript_id "TCONS_00000023"; exon_number "1"; oId "CUFF.14.1"; class_code "u"; tss_id "TSS20";
-chr1	Cufflinks	exon	3194303	3194329	.	.	.	gene_id "XLOC_000021"; transcript_id "TCONS_00000024"; exon_number "1"; oId "CUFF.15.1"; class_code "u"; tss_id "TSS21";
-chr1	Cufflinks	exon	3194707	3194733	.	.	.	gene_id "XLOC_000022"; transcript_id "TCONS_00000025"; exon_number "1"; oId "CUFF.16.1"; class_code "u"; tss_id "TSS22";
-chr1	Cufflinks	exon	3195084	3195110	.	.	.	gene_id "XLOC_000023"; transcript_id "TCONS_00000026"; exon_number "1"; oId "CUFF.17.1"; class_code "u"; tss_id "TSS23";
-chr1	Cufflinks	exon	3195451	3195477	.	.	.	gene_id "XLOC_000024"; transcript_id "TCONS_00000027"; exon_number "1"; oId "CUFF.18.1"; class_code "u"; tss_id "TSS24";
-chr1	Cufflinks	exon	3197090	3197116	.	.	.	gene_id "XLOC_000025"; transcript_id "TCONS_00000028"; exon_number "1"; oId "CUFF.19.1"; class_code "u"; tss_id "TSS25";
-chr1	Cufflinks	exon	3197247	3197273	.	.	.	gene_id "XLOC_000026"; transcript_id "TCONS_00000029"; exon_number "1"; oId "CUFF.20.1"; class_code "u"; tss_id "TSS26";
-chr1	Cufflinks	exon	3197347	3197373	.	.	.	gene_id "XLOC_000027"; transcript_id "TCONS_00000030"; exon_number "1"; oId "CUFF.21.1"; class_code "u"; tss_id "TSS27";
-chr1	Cufflinks	exon	3197426	3197452	.	.	.	gene_id "XLOC_000028"; transcript_id "TCONS_00000031"; exon_number "1"; oId "CUFF.22.1"; class_code "u"; tss_id "TSS28";
-chr1	Cufflinks	exon	3200023	3200191	.	.	.	gene_id "XLOC_000029"; transcript_id "TCONS_00000032"; exon_number "1"; oId "CUFF.23.1"; class_code "u"; tss_id "TSS29";
-chr1	Cufflinks	exon	3200326	3200352	.	.	.	gene_id "XLOC_000030"; transcript_id "TCONS_00000033"; exon_number "1"; oId "CUFF.24.1"; class_code "u"; tss_id "TSS30";
-chr1	Cufflinks	exon	3200431	3200457	.	.	.	gene_id "XLOC_000031"; transcript_id "TCONS_00000034"; exon_number "1"; oId "CUFF.25.1"; class_code "u"; tss_id "TSS31";
-chr1	Cufflinks	exon	3201008	3201481	.	.	.	gene_id "XLOC_000032"; transcript_id "TCONS_00000035"; exon_number "1"; oId "CUFF.26.1"; class_code "u"; tss_id "TSS32";
-chr1	Cufflinks	exon	3201597	3201809	.	.	.	gene_id "XLOC_000033"; transcript_id "TCONS_00000036"; exon_number "1"; oId "CUFF.27.1"; class_code "u"; tss_id "TSS33";