# HG changeset patch
# User devteam
# Date 1444754258 14400
# Node ID 9ba750f285e3973ac02422d9d81fa4abc1da1646
# Parent 9a9e3e83889b5fdcf7f2ec03677ad997306b8d0e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
diff -r 9a9e3e83889b -r 9ba750f285e3 cuff_macros.xml
--- a/cuff_macros.xml Wed Nov 26 13:57:28 2014 -0500
+++ b/cuff_macros.xml Tue Oct 13 12:37:38 2015 -0400
@@ -10,8 +10,8 @@
-
-
+
+
@@ -88,4 +88,4 @@
#end for
getattr(inputs, "__len__", [].__len__)() >= 2
-
\ No newline at end of file
+
diff -r 9a9e3e83889b -r 9ba750f285e3 cuffdiff_wrapper.xml
--- a/cuffdiff_wrapper.xml Wed Nov 26 13:57:28 2014 -0500
+++ b/cuffdiff_wrapper.xml Tue Oct 13 12:37:38 2015 -0400
@@ -1,12 +1,16 @@
-
+
find significant changes in transcript expression, splicing, and promoter use
-
+
+ CUFFDIFF_SCRIPT_PATH
+ cufflinks
+ cummeRbund
+
cuff_macros.xml
cuffdiff 2>&1 | head -n 1
-
+
+
+
@@ -181,49 +192,74 @@
- (include_read_group_files == 'Yes')
+ (include_read_group_files == 'Yes') and not omit_tabular_output
- (include_read_group_files == 'Yes')
+ (include_read_group_files == 'Yes') and not omit_tabular_output
- (include_read_group_files == 'Yes')
+ (include_read_group_files == 'Yes') and not omit_tabular_output
- (include_read_group_files == 'Yes')
+ (include_read_group_files == 'Yes') and not omit_tabular_output
-
- (include_read_group_files == 'Yes')
+
+ (include_read_group_files == 'Yes') and not omit_tabular_output
-
- (include_read_group_files == 'Yes')
+
+ (include_read_group_files == 'Yes') and not omit_tabular_output
-
-
-
-
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+
+ not omit_tabular_output
+
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+ not omit_tabular_output
+
+
+ not omit_tabular_output
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+ not omit_tabular_output
+
+
+ not omit_tabular_output
+
- (include_count_files == 'Yes')
+ (include_count_files == 'Yes') and not omit_tabular_output
-
-
+
+ not omit_tabular_output
+
+
+ not omit_tabular_output
+
- (include_count_files == 'Yes')
+ (include_count_files == 'Yes') and not omit_tabular_output
-
-
+
+ not omit_tabular_output
+
+
+ not omit_tabular_output
+
- (include_count_files == 'Yes')
+ (include_count_files == 'Yes') and not omit_tabular_output
-
-
-
- (include_count_files == 'Yes')
+
+ not omit_tabular_output
+
+
+ not omit_tabular_output
+
+
+ (include_count_files == 'Yes') and not omit_tabular_output
+
+
+ generate_sqlite
@@ -232,7 +268,9 @@
-
+
+
+
@@ -254,17 +292,46 @@
-
-
-
-
-
-
-
-
-
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-
+
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@@ -272,8 +339,8 @@
Cuffdiff is part of Cufflinks_. Cuffdiff find significant changes in transcript expression, splicing, and promoter use. Please cite: Trapnell C, Williams BA, Pertea G, Mortazavi AM, Kwan G, van Baren MJ, Salzberg SL, Wold B, Pachter L. Transcript assembly and abundance estimation from RNA-Seq reveals thousands of new transcripts and switching among isoforms. Nature Biotechnology doi:10.1038/nbt.1621
-.. _Cufflinks: http://cufflinks.cbcb.umd.edu/
-
+.. _Cufflinks: http://cole-trapnell-lab.github.io/cufflinks/
+
------
**Know what you are doing**
@@ -282,7 +349,7 @@
There is no such thing (yet) as an automated gearshift in expression analysis. It is all like stick-shift driving in San Francisco. In other words, running this tool with default parameters will probably not give you meaningful results. A way to deal with this is to **understand** the parameters by carefully reading the `documentation`__ and experimenting. Fortunately, Galaxy makes experimenting easy.
-.. __: http://cufflinks.cbcb.umd.edu/manual.html#cuffdiff
+.. __: http://cole-trapnell-lab.github.io/cufflinks/cuffdiff/
------
diff -r 9a9e3e83889b -r 9ba750f285e3 cummeRbund.R
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/cummeRbund.R Tue Oct 13 12:37:38 2015 -0400
@@ -0,0 +1,2 @@
+library("cummeRbund")
+cuff <- readCufflinks(dir = ".", dbFile = 'cummeRbund.sqlite')
\ No newline at end of file
diff -r 9a9e3e83889b -r 9ba750f285e3 test-data/cds.diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cds.diff Tue Oct 13 12:37:38 2015 -0400
@@ -0,0 +1,1 @@
+test_id gene_id gene locus sample_1 sample_2 status value_1 value_2 sqrt(JS) test_stat p_value q_value significant
diff -r 9a9e3e83889b -r 9ba750f285e3 test-data/cds.exp_fpkm_tracking
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cds.exp_fpkm_tracking Tue Oct 13 12:37:38 2015 -0400
@@ -0,0 +1,1 @@
+test_id gene_id gene locus sample_1 sample_2 status value_1 value_2 log2(fold_change) test_stat p_value q_value significant
diff -r 9a9e3e83889b -r 9ba750f285e3 test-data/cds.fpkm_tracking
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cds.fpkm_tracking Tue Oct 13 12:37:38 2015 -0400
@@ -0,0 +1,1 @@
+tracking_id class_code nearest_ref_id gene_id gene_short_name tss_id locus length coverage
diff -r 9a9e3e83889b -r 9ba750f285e3 test-data/cuffcompare_out5.gtf
--- a/test-data/cuffcompare_out5.gtf Wed Nov 26 13:57:28 2014 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,90 +0,0 @@
-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";
diff -r 9a9e3e83889b -r 9ba750f285e3 test-data/cuffdiff_in1.gtf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cuffdiff_in1.gtf Tue Oct 13 12:37:38 2015 -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";
diff -r 9a9e3e83889b -r 9ba750f285e3 test-data/cuffdiff_out.sqlite
Binary file test-data/cuffdiff_out.sqlite has changed
diff -r 9a9e3e83889b -r 9ba750f285e3 test-data/cuffdiff_out1.txt
--- a/test-data/cuffdiff_out1.txt Wed Nov 26 13:57:28 2014 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,91 +0,0 @@
-test_id gene_id gene locus sample_1 sample_2 status value_1 value_2 log2(fold_change) test_stat p_value q_value significant
-TCONS_00000001 XLOC_000001 Xkr4 chr1:3204754-3204833 q1 q2 OK 0 9.45986e+06 inf -nan 0.01975 0.101571 no
-TCONS_00000002 XLOC_000002 - chr1:3111449-3111490 q1 q2 OK 0 2.43637e+08 inf -nan 0.12465 0.186975 no
-TCONS_00000003 XLOC_000003 - chr1:3111545-3111576 q1 q2 NOTEST 0 0 0 0 1 1 no
-TCONS_00000009 XLOC_000011 - chr1:3192441-3192494 q1 q2 OK 0 9.7002e+07 inf -nan 0.07975 0.186975 no
-TCONS_00000010 XLOC_000012 - chr1:3192550-3192629 q1 q2 OK 0 4.72993e+06 inf -nan 0.12465 0.186975 no
-TCONS_00000011 XLOC_000014 - chr1:3192731-3192811 q1 q2 NOTEST 0 0 0 0 1 1 no
-TCONS_00000012 XLOC_000015 - chr1:3192940-3193042 q1 q2 OK 0 6.86386e+06 inf -nan 0.0612 0.186975 no
-TCONS_00000013 XLOC_000016 - chr1:3194185-3194226 q1 q2 OK 0 2.43637e+08 inf -nan 0.12465 0.186975 no
-TCONS_00000014 XLOC_000017 - chr1:3194302-3194329 q1 q2 NOTEST 0 0 0 0 1 1 no
-TCONS_00000015 XLOC_000019 - chr1:3195083-3195110 q1 q2 NOTEST 0 0 0 0 1 1 no
-TCONS_00000016 XLOC_000020 - chr1:3195450-3195477 q1 q2 NOTEST 0 0 0 0 1 1 no
-TCONS_00000017 XLOC_000021 - chr1:3197089-3197116 q1 q2 NOTEST 0 0 0 0 1 1 no
-TCONS_00000018 XLOC_000022 - chr1:3197246-3197273 q1 q2 NOTEST 0 0 0 0 1 1 no
-TCONS_00000019 XLOC_000023 - chr1:3197346-3197373 q1 q2 NOTEST 0 0 0 0 1 1 no
-TCONS_00000020 XLOC_000025 - chr1:3200022-3200191 q1 q2 OK 826392 803108 -0.0412311 -0.0180163 0.8625 0.887143 no
-TCONS_00000021 XLOC_000026 - chr1:3200325-3200352 q1 q2 NOTEST 0 0 0 0 1 1 no
-TCONS_00000022 XLOC_000029 - chr1:3201077-3201481 q1 q2 OK 66791.3 324548 2.2807 1.1905 0.3026 0.380545 no
-TCONS_00000023 XLOC_000031 - chr1:3201672-3201699 q1 q2 NOTEST 0 0 0 0 1 1 no
-TCONS_00000024 XLOC_000034 Xkr4 chr1:3212213-3212292 q1 q2 OK 0 9.45986e+06 inf -nan 0.01975 0.101571 no
-TCONS_00000025 XLOC_000035 Xkr4 chr1:3212367-3212439 q1 q2 OK 0 2.80837e+07 inf -nan 0.0612 0.186975 no
-TCONS_00000026 XLOC_000037 Xkr4 chr1:3213095-3213242 q1 q2 OK 4.24463e+06 2.08209e+06 -1.0276 -0.36063 0.3844 0.435206 no
-TCONS_00000027 XLOC_000040 Xkr4 chr1:3242633-3242923 q1 q2 OK 48522.7 424400 3.12869 1.23747 0.38685 0.435206 no
-TCONS_00000028 XLOC_000042 Xkr4 chr1:3243018-3243079 q1 q2 OK 0 3.03053e+07 inf -nan 0.01975 0.101571 no
-TCONS_00000029 XLOC_000044 Xkr4 chr1:3243347-3243401 q1 q2 OK 0 5.79991e+07 inf -nan 0.01975 0.101571 no
-TCONS_00000030 XLOC_000046 Xkr4 chr1:3256974-3257011 q1 q2 OK 0 2.35423e+09 inf -nan 0.01975 0.101571 no
-TCONS_00000031 XLOC_000048 Xkr4 chr1:3277190-3277218 q1 q2 NOTEST 0 0 0 0 1 1 no
-TCONS_00000033 XLOC_000052 Xkr4 chr1:3280686-3280741 q1 q2 OK 0 2.61334e+07 inf -nan 0.12465 0.186975 no
-TCONS_00000034 XLOC_000057 Xkr4 chr1:3290488-3290553 q1 q2 OK 0 1.11503e+07 inf -nan 0.12465 0.186975 no
-TCONS_00000037 XLOC_000060 Xkr4 chr1:3299443-3299664 q1 q2 NOTEST 0 0 0 0 1 1 no
-TCONS_00000038 XLOC_000062 Xkr4 chr1:3300051-3300078 q1 q2 NOTEST 0 0 0 0 1 1 no
-TCONS_00000039 XLOC_000065 Xkr4 chr1:3318999-3319051 q1 q2 NOTEST 0 0 0 0 1 1 no
-TCONS_00000040 XLOC_000068 Xkr4 chr1:3355887-3356119 q1 q2 NOTEST 0 0 0 0 1 1 no
-TCONS_00000041 XLOC_000071 Xkr4 chr1:3363214-3363278 q1 q2 NOTEST 0 0 0 0 1 1 no
-TCONS_00000042 XLOC_000073 Xkr4 chr1:3363753-3363849 q1 q2 NOTEST 0 0 0 0 1 1 no
-TCONS_00000043 XLOC_000075 Xkr4 chr1:3367135-3367162 q1 q2 NOTEST 0 0 0 0 1 1 no
-TCONS_00000044 XLOC_000077 Xkr4 chr1:3367333-3367382 q1 q2 NOTEST 0 0 0 0 1 1 no
-TCONS_00000045 XLOC_000080 Xkr4 chr1:3377211-3377262 q1 q2 NOTEST 0 0 0 0 1 1 no
-TCONS_00000046 XLOC_000083 Xkr4 chr1:3391325-3391352 q1 q2 NOTEST 0 0 0 0 1 1 no
-TCONS_00000047 XLOC_000084 Xkr4 chr1:3435841-3435880 q1 q2 NOTEST 0 0 0 0 1 1 no
-TCONS_00000048 XLOC_000085 Xkr4 chr1:3447761-3447788 q1 q2 NOTEST 0 0 0 0 1 1 no
-TCONS_00000049 XLOC_000086 Xkr4 chr1:3450906-3450965 q1 q2 NOTEST 0 0 0 0 1 1 no
-TCONS_00000050 XLOC_000087 Xkr4 chr1:3451051-3451109 q1 q2 NOTEST 0 0 0 0 1 1 no
-TCONS_00000051 XLOC_000004 - chr1:3174765-3174792 q1 q2 NOTEST 0 0 0 0 1 1 no
-TCONS_00000052 XLOC_000005 - chr1:3187401-3187428 q1 q2 NOTEST 0 0 0 0 1 1 no
-TCONS_00000053 XLOC_000006 - chr1:3188521-3188548 q1 q2 NOTEST 0 0 0 0 1 1 no
-TCONS_00000054 XLOC_000007 - chr1:3189810-3190789 q1 q2 OK 358326 522345 0.543731 1.1445 0.1952 0.270969 no
-TCONS_00000055 XLOC_000008 - chr1:3190858-3191434 q1 q2 OK 408511 420354 0.0412311 0.0469899 0.96715 0.96715 no
-TCONS_00000056 XLOC_000009 - chr1:3191512-3192077 q1 q2 OK 433286 842157 0.958769 1.27887 0.20385 0.2718 no
-TCONS_00000057 XLOC_000010 - chr1:3192250-3192336 q1 q2 OK 3.44151e+06 3.34455e+06 -0.0412311 -0.014084 0.67715 0.716982 no
-TCONS_00000058 XLOC_000013 - chr1:3192649-3192676 q1 q2 NOTEST 0 0 0 0 1 1 no
-TCONS_00000059 XLOC_000018 - chr1:3194706-3194733 q1 q2 NOTEST 0 0 0 0 1 1 no
-TCONS_00000060 XLOC_000024 - chr1:3197425-3197452 q1 q2 NOTEST 0 0 0 0 1 1 no
-TCONS_00000062 XLOC_000027 - chr1:3200430-3200457 q1 q2 NOTEST 0 0 0 0 1 1 no
-TCONS_00000063 XLOC_000028 - chr1:3201007-3201039 q1 q2 NOTEST 0 0 0 0 1 1 no
-TCONS_00000065 XLOC_000030 - chr1:3201596-3201666 q1 q2 OK 1.6359e+07 0 -inf -nan 0.0148 0.101571 no
-TCONS_00000066 XLOC_000032 - chr1:3201725-3201809 q1 q2 OK 1.5136e+07 0 -inf -nan 0.06005 0.186975 no
-TCONS_00000067 XLOC_000033 Xkr4 chr1:3211521-3211561 q1 q2 NOTEST 0 0 0 0 1 1 no
-TCONS_00000068 XLOC_000036 Xkr4 chr1:3212717-3212801 q1 q2 OK 3.784e+06 0 -inf -nan 0.12165 0.186975 no
-TCONS_00000069 XLOC_000037 Xkr4 chr1:3213095-3213242 q1 q2 OK 863189 0 -inf -nan 0.1957 0.270969 no
-TCONS_00000070 XLOC_000038 Xkr4 chr1:3240606-3240633 q1 q2 NOTEST 0 0 0 0 1 1 no
-TCONS_00000071 XLOC_000039 Xkr4 chr1:3242479-3242512 q1 q2 NOTEST 0 0 0 0 1 1 no
-TCONS_00000072 XLOC_000041 Xkr4 chr1:3242924-3243005 q1 q2 NOTEST 0 0 0 0 1 1 no
-TCONS_00000073 XLOC_000043 Xkr4 chr1:3243108-3243154 q1 q2 OK 8.616e+07 0 -inf -nan 0.12165 0.186975 no
-TCONS_00000074 XLOC_000045 Xkr4 chr1:3254079-3254106 q1 q2 NOTEST 0 0 0 0 1 1 no
-TCONS_00000075 XLOC_000047 Xkr4 chr1:3277155-3277182 q1 q2 NOTEST 0 0 0 0 1 1 no
-TCONS_00000076 XLOC_000049 Xkr4 chr1:3277913-3278390 q1 q2 OK 228872 47662.2 -2.26362 -1.16262 0.30655 0.380545 no
-TCONS_00000077 XLOC_000050 Xkr4 chr1:3280117-3280144 q1 q2 NOTEST 0 0 0 0 1 1 no
-TCONS_00000078 XLOC_000051 Xkr4 chr1:3280498-3280525 q1 q2 NOTEST 0 0 0 0 1 1 no
-TCONS_00000079 XLOC_000053 Xkr4 chr1:3282504-3282531 q1 q2 NOTEST 0 0 0 0 1 1 no
-TCONS_00000080 XLOC_000054 Xkr4 chr1:3282650-3282677 q1 q2 NOTEST 0 0 0 0 1 1 no
-TCONS_00000081 XLOC_000055 Xkr4 chr1:3282760-3282832 q1 q2 NOTEST 0 0 0 0 1 1 no
-TCONS_00000082 XLOC_000056 Xkr4 chr1:3284966-3284993 q1 q2 NOTEST 0 0 0 0 1 1 no
-TCONS_00000083 XLOC_000058 Xkr4 chr1:3290798-3290859 q1 q2 OK 1.55919e+07 0 -inf -nan 0.12165 0.186975 no
-TCONS_00000084 XLOC_000059 Xkr4 chr1:3290919-3291273 q1 q2 OK 294879 85971.3 -1.7782 -0.902752 0.36915 0.435206 no
-TCONS_00000085 XLOC_000060 Xkr4 chr1:3299443-3299664 q1 q2 OK 807732 156995 -2.36316 -0.933704 0.4205 0.458727 no
-TCONS_00000086 XLOC_000061 Xkr4 chr1:3299691-3299733 q1 q2 NOTEST 0 0 0 0 1 1 no
-TCONS_00000087 XLOC_000063 Xkr4 chr1:3307748-3307775 q1 q2 NOTEST 0 0 0 0 1 1 no
-TCONS_00000088 XLOC_000064 Xkr4 chr1:3318620-3318647 q1 q2 NOTEST 0 0 0 0 1 1 no
-TCONS_00000089 XLOC_000066 Xkr4 chr1:3330527-3330554 q1 q2 NOTEST 0 0 0 0 1 1 no
-TCONS_00000090 XLOC_000067 Xkr4 chr1:3351240-3351311 q1 q2 OK 7.68169e+06 0 -inf -nan 0.12165 0.186975 no
-TCONS_00000091 XLOC_000068 Xkr4 chr1:3355887-3356119 q1 q2 OK 504790 0 -inf -nan 0.05945 0.186975 no
-TCONS_00000092 XLOC_000069 Xkr4 chr1:3356180-3356225 q1 q2 OK 1.02717e+08 0 -inf -nan 0.12165 0.186975 no
-TCONS_00000093 XLOC_000070 Xkr4 chr1:3363076-3363176 q1 q2 OK 3.81001e+06 0 -inf -nan 0.0148 0.101571 no
-TCONS_00000094 XLOC_000072 Xkr4 chr1:3363387-3363446 q1 q2 OK 5.53654e+07 0 -inf -nan 0.0773 0.186975 no
-TCONS_00000095 XLOC_000074 Xkr4 chr1:3364871-3364919 q1 q2 OK 6.28966e+07 0 -inf -nan 0.12165 0.186975 no
-TCONS_00000096 XLOC_000076 Xkr4 chr1:3367210-3367237 q1 q2 NOTEST 0 0 0 0 1 1 no
-TCONS_00000097 XLOC_000078 Xkr4 chr1:3369580-3369607 q1 q2 NOTEST 0 0 0 0 1 1 no
-TCONS_00000098 XLOC_000079 Xkr4 chr1:3375001-3375028 q1 q2 NOTEST 0 0 0 0 1 1 no
-TCONS_00000099 XLOC_000081 Xkr4 chr1:3379888-3379915 q1 q2 NOTEST 0 0 0 0 1 1 no
-TCONS_00000100 XLOC_000082 Xkr4 chr1:3386739-3386836 q1 q2 NOTEST 0 0 0 0 1 1 no
diff -r 9a9e3e83889b -r 9ba750f285e3 test-data/cuffdiff_out10.txt
--- a/test-data/cuffdiff_out10.txt Wed Nov 26 13:57:28 2014 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,88 +0,0 @@
-test_id gene_id gene locus sample_1 sample_2 status value_1 value_2 sqrt(JS) test_stat p_value q_value significant
-XLOC_000001 XLOC_000001 Xkr4 chr1:3204754-3204833 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000002 XLOC_000002 - chr1:3111449-3111490 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000003 XLOC_000003 - chr1:3111545-3111576 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000004 XLOC_000004 - chr1:3174765-3174792 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000005 XLOC_000005 - chr1:3187401-3187428 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000006 XLOC_000006 - chr1:3188521-3188548 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000007 XLOC_000007 - chr1:3189810-3190789 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000008 XLOC_000008 - chr1:3190858-3191434 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000009 XLOC_000009 - chr1:3191512-3192077 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000010 XLOC_000010 - chr1:3192250-3192336 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000011 XLOC_000011 - chr1:3192441-3192494 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000012 XLOC_000012 - chr1:3192550-3192629 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000013 XLOC_000013 - chr1:3192649-3192676 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000014 XLOC_000014 - chr1:3192731-3192811 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000015 XLOC_000015 - chr1:3192940-3193042 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000016 XLOC_000016 - chr1:3194185-3194226 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000017 XLOC_000017 - chr1:3194302-3194329 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000018 XLOC_000018 - chr1:3194706-3194733 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000019 XLOC_000019 - chr1:3195083-3195110 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000020 XLOC_000020 - chr1:3195450-3195477 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000021 XLOC_000021 - chr1:3197089-3197116 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000022 XLOC_000022 - chr1:3197246-3197273 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000023 XLOC_000023 - chr1:3197346-3197373 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000024 XLOC_000024 - chr1:3197425-3197452 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000025 XLOC_000025 - chr1:3200022-3200191 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000026 XLOC_000026 - chr1:3200325-3200352 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000027 XLOC_000027 - chr1:3200430-3200457 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000028 XLOC_000028 - chr1:3201007-3201039 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000029 XLOC_000029 - chr1:3201077-3201481 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000030 XLOC_000030 - chr1:3201596-3201666 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000031 XLOC_000031 - chr1:3201672-3201699 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000032 XLOC_000032 - chr1:3201725-3201809 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000033 XLOC_000033 Xkr4 chr1:3211521-3211561 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000034 XLOC_000034 Xkr4 chr1:3212213-3212292 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000035 XLOC_000035 Xkr4 chr1:3212367-3212439 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000036 XLOC_000036 Xkr4 chr1:3212717-3212801 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000037 XLOC_000037 Xkr4 chr1:3213095-3213242 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000038 XLOC_000038 Xkr4 chr1:3240606-3240633 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000039 XLOC_000039 Xkr4 chr1:3242479-3242512 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000040 XLOC_000040 Xkr4 chr1:3242633-3242923 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000041 XLOC_000041 Xkr4 chr1:3242924-3243005 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000042 XLOC_000042 Xkr4 chr1:3243018-3243079 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000043 XLOC_000043 Xkr4 chr1:3243108-3243154 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000044 XLOC_000044 Xkr4 chr1:3243347-3243401 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000045 XLOC_000045 Xkr4 chr1:3254079-3254106 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000046 XLOC_000046 Xkr4 chr1:3256974-3257011 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000047 XLOC_000047 Xkr4 chr1:3277155-3277182 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000048 XLOC_000048 Xkr4 chr1:3277190-3277218 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000049 XLOC_000049 Xkr4 chr1:3277913-3278390 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000050 XLOC_000050 Xkr4 chr1:3280117-3280144 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000051 XLOC_000051 Xkr4 chr1:3280498-3280525 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000052 XLOC_000052 Xkr4 chr1:3280686-3280741 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000053 XLOC_000053 Xkr4 chr1:3282504-3282531 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000054 XLOC_000054 Xkr4 chr1:3282650-3282677 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000055 XLOC_000055 Xkr4 chr1:3282760-3282832 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000056 XLOC_000056 Xkr4 chr1:3284966-3284993 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000057 XLOC_000057 Xkr4 chr1:3290488-3290553 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000058 XLOC_000058 Xkr4 chr1:3290798-3290859 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000059 XLOC_000059 Xkr4 chr1:3290919-3291273 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000060 XLOC_000060 Xkr4 chr1:3299443-3299664 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000061 XLOC_000061 Xkr4 chr1:3299691-3299733 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000062 XLOC_000062 Xkr4 chr1:3300051-3300078 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000063 XLOC_000063 Xkr4 chr1:3307748-3307775 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000064 XLOC_000064 Xkr4 chr1:3318620-3318647 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000065 XLOC_000065 Xkr4 chr1:3318999-3319051 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000066 XLOC_000066 Xkr4 chr1:3330527-3330554 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000067 XLOC_000067 Xkr4 chr1:3351240-3351311 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000068 XLOC_000068 Xkr4 chr1:3355887-3356119 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000069 XLOC_000069 Xkr4 chr1:3356180-3356225 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000070 XLOC_000070 Xkr4 chr1:3363076-3363176 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000071 XLOC_000071 Xkr4 chr1:3363214-3363278 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000072 XLOC_000072 Xkr4 chr1:3363387-3363446 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000073 XLOC_000073 Xkr4 chr1:3363753-3363849 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000074 XLOC_000074 Xkr4 chr1:3364871-3364919 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000075 XLOC_000075 Xkr4 chr1:3367135-3367162 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000076 XLOC_000076 Xkr4 chr1:3367210-3367237 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000077 XLOC_000077 Xkr4 chr1:3367333-3367382 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000078 XLOC_000078 Xkr4 chr1:3369580-3369607 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000079 XLOC_000079 Xkr4 chr1:3375001-3375028 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000080 XLOC_000080 Xkr4 chr1:3377211-3377262 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000081 XLOC_000081 Xkr4 chr1:3379888-3379915 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000082 XLOC_000082 Xkr4 chr1:3386739-3386836 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000083 XLOC_000083 Xkr4 chr1:3391325-3391352 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000084 XLOC_000084 Xkr4 chr1:3435841-3435880 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000085 XLOC_000085 Xkr4 chr1:3447761-3447788 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000086 XLOC_000086 Xkr4 chr1:3450906-3450965 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000087 XLOC_000087 Xkr4 chr1:3451051-3451109 q1 q2 NOTEST 0 0 0 0 1 1 no
diff -r 9a9e3e83889b -r 9ba750f285e3 test-data/cuffdiff_out11.txt
--- a/test-data/cuffdiff_out11.txt Wed Nov 26 13:57:28 2014 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-test_id gene_id gene locus sample_1 sample_2 status value_1 value_2 sqrt(JS) test_stat p_value q_value significant
diff -r 9a9e3e83889b -r 9ba750f285e3 test-data/cuffdiff_out2.txt
--- a/test-data/cuffdiff_out2.txt Wed Nov 26 13:57:28 2014 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,88 +0,0 @@
-test_id gene_id gene locus sample_1 sample_2 status value_1 value_2 log2(fold_change) test_stat p_value q_value significant
-XLOC_000001 XLOC_000001 Xkr4 chr1:3204754-3204833 q1 q2 OK 0 9.45986e+06 inf -nan 0.01975 0.09875 no
-XLOC_000002 XLOC_000002 - chr1:3111449-3111490 q1 q2 OK 0 2.43637e+08 inf -nan 0.12465 0.181781 no
-XLOC_000003 XLOC_000003 - chr1:3111545-3111576 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000004 XLOC_000004 - chr1:3174765-3174792 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000005 XLOC_000005 - chr1:3187401-3187428 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000006 XLOC_000006 - chr1:3188521-3188548 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000007 XLOC_000007 - chr1:3189810-3190789 q1 q2 OK 358326 522345 0.543731 1.1445 0.1952 0.27328 no
-XLOC_000008 XLOC_000008 - chr1:3190858-3191434 q1 q2 OK 408511 420354 0.0412311 0.0469899 0.96715 0.96715 no
-XLOC_000009 XLOC_000009 - chr1:3191512-3192077 q1 q2 OK 433286 842157 0.958769 1.27887 0.20385 0.274413 no
-XLOC_000010 XLOC_000010 - chr1:3192250-3192336 q1 q2 OK 3.44151e+06 3.34455e+06 -0.0412311 -0.014084 0.67715 0.718189 no
-XLOC_000011 XLOC_000011 - chr1:3192441-3192494 q1 q2 OK 0 9.7002e+07 inf -nan 0.07975 0.181781 no
-XLOC_000012 XLOC_000012 - chr1:3192550-3192629 q1 q2 OK 0 4.72993e+06 inf -nan 0.12465 0.181781 no
-XLOC_000013 XLOC_000013 - chr1:3192649-3192676 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000014 XLOC_000014 - chr1:3192731-3192811 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000015 XLOC_000015 - chr1:3192940-3193042 q1 q2 OK 0 6.86386e+06 inf -nan 0.0612 0.181781 no
-XLOC_000016 XLOC_000016 - chr1:3194185-3194226 q1 q2 OK 0 2.43637e+08 inf -nan 0.12465 0.181781 no
-XLOC_000017 XLOC_000017 - chr1:3194302-3194329 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000018 XLOC_000018 - chr1:3194706-3194733 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000019 XLOC_000019 - chr1:3195083-3195110 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000020 XLOC_000020 - chr1:3195450-3195477 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000021 XLOC_000021 - chr1:3197089-3197116 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000022 XLOC_000022 - chr1:3197246-3197273 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000023 XLOC_000023 - chr1:3197346-3197373 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000024 XLOC_000024 - chr1:3197425-3197452 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000025 XLOC_000025 - chr1:3200022-3200191 q1 q2 OK 826392 803108 -0.0412311 -0.0180163 0.8625 0.887868 no
-XLOC_000026 XLOC_000026 - chr1:3200325-3200352 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000027 XLOC_000027 - chr1:3200430-3200457 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000028 XLOC_000028 - chr1:3201007-3201039 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000029 XLOC_000029 - chr1:3201077-3201481 q1 q2 OK 66791.3 324548 2.2807 1.1905 0.3026 0.383188 no
-XLOC_000030 XLOC_000030 - chr1:3201596-3201666 q1 q2 OK 1.6359e+07 0 -inf -nan 0.0148 0.09875 no
-XLOC_000031 XLOC_000031 - chr1:3201672-3201699 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000032 XLOC_000032 - chr1:3201725-3201809 q1 q2 OK 1.5136e+07 0 -inf -nan 0.06005 0.181781 no
-XLOC_000033 XLOC_000033 Xkr4 chr1:3211521-3211561 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000034 XLOC_000034 Xkr4 chr1:3212213-3212292 q1 q2 OK 0 9.45986e+06 inf -nan 0.01975 0.09875 no
-XLOC_000035 XLOC_000035 Xkr4 chr1:3212367-3212439 q1 q2 OK 0 2.80837e+07 inf -nan 0.0612 0.181781 no
-XLOC_000036 XLOC_000036 Xkr4 chr1:3212717-3212801 q1 q2 OK 3.784e+06 0 -inf -nan 0.12165 0.181781 no
-XLOC_000037 XLOC_000037 Xkr4 chr1:3213095-3213242 q1 q2 OK 5.10781e+06 2.08209e+06 -1.29467 -0.482193 0.5916 0.647062 no
-XLOC_000038 XLOC_000038 Xkr4 chr1:3240606-3240633 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000039 XLOC_000039 Xkr4 chr1:3242479-3242512 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000040 XLOC_000040 Xkr4 chr1:3242633-3242923 q1 q2 OK 48522.7 424400 3.12869 1.23747 0.38685 0.450823 no
-XLOC_000041 XLOC_000041 Xkr4 chr1:3242924-3243005 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000042 XLOC_000042 Xkr4 chr1:3243018-3243079 q1 q2 OK 0 3.03053e+07 inf -nan 0.01975 0.09875 no
-XLOC_000043 XLOC_000043 Xkr4 chr1:3243108-3243154 q1 q2 OK 8.616e+07 0 -inf -nan 0.12165 0.181781 no
-XLOC_000044 XLOC_000044 Xkr4 chr1:3243347-3243401 q1 q2 OK 0 5.79991e+07 inf -nan 0.01975 0.09875 no
-XLOC_000045 XLOC_000045 Xkr4 chr1:3254079-3254106 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000046 XLOC_000046 Xkr4 chr1:3256974-3257011 q1 q2 OK 0 2.35423e+09 inf -nan 0.01975 0.09875 no
-XLOC_000047 XLOC_000047 Xkr4 chr1:3277155-3277182 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000048 XLOC_000048 Xkr4 chr1:3277190-3277218 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000049 XLOC_000049 Xkr4 chr1:3277913-3278390 q1 q2 OK 228872 47662.2 -2.26362 -1.16262 0.30655 0.383188 no
-XLOC_000050 XLOC_000050 Xkr4 chr1:3280117-3280144 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000051 XLOC_000051 Xkr4 chr1:3280498-3280525 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000052 XLOC_000052 Xkr4 chr1:3280686-3280741 q1 q2 OK 0 2.61334e+07 inf -nan 0.12465 0.181781 no
-XLOC_000053 XLOC_000053 Xkr4 chr1:3282504-3282531 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000054 XLOC_000054 Xkr4 chr1:3282650-3282677 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000055 XLOC_000055 Xkr4 chr1:3282760-3282832 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000056 XLOC_000056 Xkr4 chr1:3284966-3284993 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000057 XLOC_000057 Xkr4 chr1:3290488-3290553 q1 q2 OK 0 1.11503e+07 inf -nan 0.12465 0.181781 no
-XLOC_000058 XLOC_000058 Xkr4 chr1:3290798-3290859 q1 q2 OK 1.55919e+07 0 -inf -nan 0.12165 0.181781 no
-XLOC_000059 XLOC_000059 Xkr4 chr1:3290919-3291273 q1 q2 OK 294879 85971.3 -1.7782 -0.902752 0.36915 0.445526 no
-XLOC_000060 XLOC_000060 Xkr4 chr1:3299443-3299664 q1 q2 OK 807732 156995 -2.36316 -0.89463 0.3993 0.450823 no
-XLOC_000061 XLOC_000061 Xkr4 chr1:3299691-3299733 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000062 XLOC_000062 Xkr4 chr1:3300051-3300078 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000063 XLOC_000063 Xkr4 chr1:3307748-3307775 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000064 XLOC_000064 Xkr4 chr1:3318620-3318647 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000065 XLOC_000065 Xkr4 chr1:3318999-3319051 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000066 XLOC_000066 Xkr4 chr1:3330527-3330554 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000067 XLOC_000067 Xkr4 chr1:3351240-3351311 q1 q2 OK 7.68169e+06 0 -inf -nan 0.12165 0.181781 no
-XLOC_000068 XLOC_000068 Xkr4 chr1:3355887-3356119 q1 q2 OK 504790 0 -inf -nan 0.04565 0.181781 no
-XLOC_000069 XLOC_000069 Xkr4 chr1:3356180-3356225 q1 q2 OK 1.02717e+08 0 -inf -nan 0.12165 0.181781 no
-XLOC_000070 XLOC_000070 Xkr4 chr1:3363076-3363176 q1 q2 OK 3.81001e+06 0 -inf -nan 0.0148 0.09875 no
-XLOC_000071 XLOC_000071 Xkr4 chr1:3363214-3363278 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000072 XLOC_000072 Xkr4 chr1:3363387-3363446 q1 q2 OK 5.53654e+07 0 -inf -nan 0.0773 0.181781 no
-XLOC_000073 XLOC_000073 Xkr4 chr1:3363753-3363849 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000074 XLOC_000074 Xkr4 chr1:3364871-3364919 q1 q2 OK 6.28966e+07 0 -inf -nan 0.12165 0.181781 no
-XLOC_000075 XLOC_000075 Xkr4 chr1:3367135-3367162 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000076 XLOC_000076 Xkr4 chr1:3367210-3367237 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000077 XLOC_000077 Xkr4 chr1:3367333-3367382 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000078 XLOC_000078 Xkr4 chr1:3369580-3369607 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000079 XLOC_000079 Xkr4 chr1:3375001-3375028 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000080 XLOC_000080 Xkr4 chr1:3377211-3377262 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000081 XLOC_000081 Xkr4 chr1:3379888-3379915 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000082 XLOC_000082 Xkr4 chr1:3386739-3386836 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000083 XLOC_000083 Xkr4 chr1:3391325-3391352 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000084 XLOC_000084 Xkr4 chr1:3435841-3435880 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000085 XLOC_000085 Xkr4 chr1:3447761-3447788 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000086 XLOC_000086 Xkr4 chr1:3450906-3450965 q1 q2 NOTEST 0 0 0 0 1 1 no
-XLOC_000087 XLOC_000087 Xkr4 chr1:3451051-3451109 q1 q2 NOTEST 0 0 0 0 1 1 no
diff -r 9a9e3e83889b -r 9ba750f285e3 test-data/cuffdiff_out3.txt
--- a/test-data/cuffdiff_out3.txt Wed Nov 26 13:57:28 2014 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,89 +0,0 @@
-test_id gene_id gene locus sample_1 sample_2 status value_1 value_2 log2(fold_change) test_stat p_value q_value significant
-TSS1 XLOC_000001 Xkr4 chr1:3204754-3204833 q1 q2 OK 0 9.45986e+06 inf -nan 0.01975 0.09875 no
-TSS10 XLOC_000008 - chr1:3190858-3191434 q1 q2 OK 408511 420354 0.0412311 0.0469899 0.96715 0.96715 no
-TSS11 XLOC_000009 - chr1:3191512-3192077 q1 q2 OK 433286 842157 0.958769 1.27887 0.20385 0.274413 no
-TSS13 XLOC_000010 - chr1:3192250-3192336 q1 q2 OK 3.44151e+06 3.34455e+06 -0.0412311 -0.014084 0.67715 0.718189 no
-TSS14 XLOC_000011 - chr1:3192441-3192494 q1 q2 OK 0 9.7002e+07 inf -nan 0.07975 0.181781 no
-TSS15 XLOC_000012 - chr1:3192550-3192629 q1 q2 OK 0 4.72993e+06 inf -nan 0.12465 0.181781 no
-TSS16 XLOC_000013 - chr1:3192649-3192676 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS17 XLOC_000014 - chr1:3192731-3192811 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS18 XLOC_000015 - chr1:3192940-3193042 q1 q2 OK 0 6.86386e+06 inf -nan 0.0612 0.181781 no
-TSS19 XLOC_000016 - chr1:3194185-3194226 q1 q2 OK 0 2.43637e+08 inf -nan 0.12465 0.181781 no
-TSS2 XLOC_000002 - chr1:3111449-3111490 q1 q2 OK 0 2.43637e+08 inf -nan 0.12465 0.181781 no
-TSS20 XLOC_000017 - chr1:3194302-3194329 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS21 XLOC_000018 - chr1:3194706-3194733 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS22 XLOC_000019 - chr1:3195083-3195110 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS23 XLOC_000020 - chr1:3195450-3195477 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS24 XLOC_000021 - chr1:3197089-3197116 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS25 XLOC_000022 - chr1:3197246-3197273 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS26 XLOC_000023 - chr1:3197346-3197373 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS27 XLOC_000024 - chr1:3197425-3197452 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS28 XLOC_000025 - chr1:3200022-3200191 q1 q2 OK 826392 803108 -0.0412311 -0.0180163 0.8625 0.887868 no
-TSS29 XLOC_000026 - chr1:3200325-3200352 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS3 XLOC_000003 - chr1:3111545-3111576 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS30 XLOC_000027 - chr1:3200430-3200457 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS31 XLOC_000028 - chr1:3201007-3201039 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS32 XLOC_000029 - chr1:3201077-3201481 q1 q2 OK 66791.3 324548 2.2807 1.1905 0.3026 0.383188 no
-TSS33 XLOC_000030 - chr1:3201596-3201666 q1 q2 OK 1.6359e+07 0 -inf -nan 0.0148 0.09875 no
-TSS34 XLOC_000031 - chr1:3201672-3201699 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS35 XLOC_000032 - chr1:3201725-3201809 q1 q2 OK 1.5136e+07 0 -inf -nan 0.06005 0.181781 no
-TSS36 XLOC_000033 Xkr4 chr1:3211521-3211561 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS37 XLOC_000034 Xkr4 chr1:3212213-3212292 q1 q2 OK 0 9.45986e+06 inf -nan 0.01975 0.09875 no
-TSS38 XLOC_000035 Xkr4 chr1:3212367-3212439 q1 q2 OK 0 2.80837e+07 inf -nan 0.0612 0.181781 no
-TSS39 XLOC_000036 Xkr4 chr1:3212717-3212801 q1 q2 OK 3.784e+06 0 -inf -nan 0.12165 0.181781 no
-TSS4 XLOC_000004 - chr1:3174765-3174792 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS40 XLOC_000037 Xkr4 chr1:3213095-3213242 q1 q2 OK 5.10781e+06 2.08209e+06 -1.29467 -0.482193 0.5916 0.647062 no
-TSS41 XLOC_000038 Xkr4 chr1:3240606-3240633 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS42 XLOC_000039 Xkr4 chr1:3242479-3242512 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS43 XLOC_000040 Xkr4 chr1:3242633-3242923 q1 q2 OK 48522.7 424400 3.12869 1.23747 0.38685 0.451325 no
-TSS44 XLOC_000041 Xkr4 chr1:3242924-3243005 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS45 XLOC_000042 Xkr4 chr1:3243018-3243079 q1 q2 OK 0 3.03053e+07 inf -nan 0.01975 0.09875 no
-TSS46 XLOC_000043 Xkr4 chr1:3243108-3243154 q1 q2 OK 8.616e+07 0 -inf -nan 0.12165 0.181781 no
-TSS47 XLOC_000044 Xkr4 chr1:3243347-3243401 q1 q2 OK 0 5.79991e+07 inf -nan 0.01975 0.09875 no
-TSS48 XLOC_000045 Xkr4 chr1:3254079-3254106 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS49 XLOC_000046 Xkr4 chr1:3256974-3257011 q1 q2 OK 0 2.35423e+09 inf -nan 0.01975 0.09875 no
-TSS5 XLOC_000005 - chr1:3187401-3187428 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS50 XLOC_000047 Xkr4 chr1:3277155-3277182 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS51 XLOC_000048 Xkr4 chr1:3277190-3277218 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS52 XLOC_000049 Xkr4 chr1:3277913-3278390 q1 q2 OK 228872 47662.2 -2.26362 -1.16262 0.30655 0.383188 no
-TSS54 XLOC_000050 Xkr4 chr1:3280117-3280144 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS55 XLOC_000051 Xkr4 chr1:3280498-3280525 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS56 XLOC_000052 Xkr4 chr1:3280686-3280741 q1 q2 OK 0 2.61334e+07 inf -nan 0.12465 0.181781 no
-TSS57 XLOC_000053 Xkr4 chr1:3282504-3282531 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS58 XLOC_000054 Xkr4 chr1:3282650-3282677 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS59 XLOC_000055 Xkr4 chr1:3282760-3282832 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS6 XLOC_000006 - chr1:3188521-3188548 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS60 XLOC_000056 Xkr4 chr1:3284966-3284993 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS61 XLOC_000057 Xkr4 chr1:3290488-3290553 q1 q2 OK 0 1.11503e+07 inf -nan 0.12465 0.181781 no
-TSS62 XLOC_000058 Xkr4 chr1:3290798-3290859 q1 q2 OK 1.55919e+07 0 -inf -nan 0.12165 0.181781 no
-TSS63 XLOC_000059 Xkr4 chr1:3290919-3291273 q1 q2 OK 294879 85971.3 -1.7782 -0.902752 0.36915 0.445526 no
-TSS65 XLOC_000060 Xkr4 chr1:3299443-3299664 q1 q2 OK 807732 156995 -2.36316 -0.933704 0.4205 0.474758 no
-TSS66 XLOC_000060 Xkr4 chr1:3299443-3299664 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS67 XLOC_000061 Xkr4 chr1:3299691-3299733 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS68 XLOC_000062 Xkr4 chr1:3300051-3300078 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS69 XLOC_000063 Xkr4 chr1:3307748-3307775 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS7 XLOC_000007 - chr1:3189810-3190789 q1 q2 OK 358326 522345 0.543731 1.1445 0.1952 0.27328 no
-TSS70 XLOC_000064 Xkr4 chr1:3318620-3318647 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS71 XLOC_000065 Xkr4 chr1:3318999-3319051 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS72 XLOC_000066 Xkr4 chr1:3330527-3330554 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS73 XLOC_000067 Xkr4 chr1:3351240-3351311 q1 q2 OK 7.68169e+06 0 -inf -nan 0.12165 0.181781 no
-TSS74 XLOC_000068 Xkr4 chr1:3355887-3356119 q1 q2 OK 504790 0 -inf -nan 0.04565 0.181781 no
-TSS75 XLOC_000069 Xkr4 chr1:3356180-3356225 q1 q2 OK 1.02717e+08 0 -inf -nan 0.12165 0.181781 no
-TSS76 XLOC_000070 Xkr4 chr1:3363076-3363176 q1 q2 OK 3.81001e+06 0 -inf -nan 0.0148 0.09875 no
-TSS77 XLOC_000071 Xkr4 chr1:3363214-3363278 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS78 XLOC_000072 Xkr4 chr1:3363387-3363446 q1 q2 OK 5.53654e+07 0 -inf -nan 0.0773 0.181781 no
-TSS79 XLOC_000073 Xkr4 chr1:3363753-3363849 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS80 XLOC_000074 Xkr4 chr1:3364871-3364919 q1 q2 OK 6.28966e+07 0 -inf -nan 0.12165 0.181781 no
-TSS81 XLOC_000075 Xkr4 chr1:3367135-3367162 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS82 XLOC_000076 Xkr4 chr1:3367210-3367237 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS83 XLOC_000077 Xkr4 chr1:3367333-3367382 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS84 XLOC_000078 Xkr4 chr1:3369580-3369607 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS85 XLOC_000079 Xkr4 chr1:3375001-3375028 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS86 XLOC_000080 Xkr4 chr1:3377211-3377262 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS87 XLOC_000081 Xkr4 chr1:3379888-3379915 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS88 XLOC_000082 Xkr4 chr1:3386739-3386836 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS89 XLOC_000083 Xkr4 chr1:3391325-3391352 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS90 XLOC_000084 Xkr4 chr1:3435841-3435880 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS91 XLOC_000085 Xkr4 chr1:3447761-3447788 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS92 XLOC_000086 Xkr4 chr1:3450906-3450965 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS93 XLOC_000087 Xkr4 chr1:3451051-3451109 q1 q2 NOTEST 0 0 0 0 1 1 no
diff -r 9a9e3e83889b -r 9ba750f285e3 test-data/cuffdiff_out4.txt
--- a/test-data/cuffdiff_out4.txt Wed Nov 26 13:57:28 2014 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-test_id gene_id gene locus sample_1 sample_2 status value_1 value_2 log2(fold_change) test_stat p_value q_value significant
diff -r 9a9e3e83889b -r 9ba750f285e3 test-data/cuffdiff_out5.txt
--- a/test-data/cuffdiff_out5.txt Wed Nov 26 13:57:28 2014 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,91 +0,0 @@
-tracking_id class_code nearest_ref_id gene_id gene_short_name tss_id locus length coverage q1_FPKM q1_conf_lo q1_conf_hi q1_status q2_FPKM q2_conf_lo q2_conf_hi q2_status
-TCONS_00000001 c Xkr4 XLOC_000001 Xkr4 TSS1 chr1:3204754-3204833 79 - 0 0 0 OK 9.45986e+06 0 3.33035e+07 OK
-TCONS_00000002 - - XLOC_000002 - TSS2 chr1:3111449-3111490 41 - 0 0 0 OK 2.43637e+08 0 9.52723e+08 OK
-TCONS_00000003 - - XLOC_000003 - TSS3 chr1:3111545-3111576 31 - 0 0 0 OK 0 0 0 OK
-TCONS_00000009 - - XLOC_000011 - TSS14 chr1:3192441-3192494 53 - 0 0 0 OK 9.7002e+07 0 3.17699e+08 OK
-TCONS_00000010 - - XLOC_000012 - TSS15 chr1:3192550-3192629 79 - 0 0 0 OK 4.72993e+06 0 1.84961e+07 OK
-TCONS_00000011 - - XLOC_000014 - TSS17 chr1:3192731-3192811 80 - 0 0 0 OK 0 0 0 OK
-TCONS_00000012 - - XLOC_000015 - TSS18 chr1:3192940-3193042 102 - 0 0 0 OK 6.86386e+06 0 2.14243e+07 OK
-TCONS_00000013 - - XLOC_000016 - TSS19 chr1:3194185-3194226 41 - 0 0 0 OK 2.43637e+08 0 9.52723e+08 OK
-TCONS_00000014 - - XLOC_000017 - TSS20 chr1:3194302-3194329 27 - 0 0 0 OK 0 0 0 OK
-TCONS_00000015 - - XLOC_000019 - TSS22 chr1:3195083-3195110 27 - 0 0 0 OK 0 0 0 OK
-TCONS_00000016 - - XLOC_000020 - TSS23 chr1:3195450-3195477 27 - 0 0 0 OK 0 0 0 OK
-TCONS_00000017 - - XLOC_000021 - TSS24 chr1:3197089-3197116 27 - 0 0 0 OK 0 0 0 OK
-TCONS_00000018 - - XLOC_000022 - TSS25 chr1:3197246-3197273 27 - 0 0 0 OK 0 0 0 OK
-TCONS_00000019 - - XLOC_000023 - TSS26 chr1:3197346-3197373 27 - 0 0 0 OK 0 0 0 OK
-TCONS_00000020 - - XLOC_000025 - TSS28 chr1:3200022-3200191 169 - 826392 0 2.65361e+06 OK 803108 0 2.63033e+06 OK
-TCONS_00000021 - - XLOC_000026 - TSS29 chr1:3200325-3200352 27 - 0 0 0 OK 0 0 0 OK
-TCONS_00000022 - - XLOC_000029 - TSS32 chr1:3201077-3201481 404 - 66791.3 0 214473 OK 324548 0 802006 OK
-TCONS_00000023 - - XLOC_000031 - TSS34 chr1:3201672-3201699 27 - 0 0 0 OK 0 0 0 OK
-TCONS_00000024 i Xkr4 XLOC_000034 Xkr4 TSS37 chr1:3212213-3212292 79 - 0 0 0 OK 9.45986e+06 0 3.33035e+07 OK
-TCONS_00000025 i Xkr4 XLOC_000035 Xkr4 TSS38 chr1:3212367-3212439 72 - 0 0 0 OK 2.80837e+07 0 8.76584e+07 OK
-TCONS_00000026 i Xkr4 XLOC_000037 Xkr4 TSS40 chr1:3213095-3213242 97 - 4.24463e+06 0 1.55814e+07 OK 2.08209e+06 0 8.14187e+06 OK
-TCONS_00000027 i Xkr4 XLOC_000040 Xkr4 TSS43 chr1:3242633-3242923 290 - 48522.7 0 185766 OK 424400 0 1.30289e+06 OK
-TCONS_00000028 i Xkr4 XLOC_000042 Xkr4 TSS45 chr1:3243018-3243079 61 - 0 0 0 OK 3.03053e+07 0 1.0669e+08 OK
-TCONS_00000029 i Xkr4 XLOC_000044 Xkr4 TSS47 chr1:3243347-3243401 54 - 0 0 0 OK 5.79991e+07 0 2.04186e+08 OK
-TCONS_00000030 i Xkr4 XLOC_000046 Xkr4 TSS49 chr1:3256974-3257011 37 - 0 0 0 OK 2.35423e+09 0 8.28806e+09 OK
-TCONS_00000031 i Xkr4 XLOC_000048 Xkr4 TSS51 chr1:3277190-3277218 28 - 0 0 0 OK 0 0 0 OK
-TCONS_00000033 i Xkr4 XLOC_000052 Xkr4 TSS56 chr1:3280686-3280741 55 - 0 0 0 OK 2.61334e+07 0 1.02193e+08 OK
-TCONS_00000034 i Xkr4 XLOC_000057 Xkr4 TSS61 chr1:3290488-3290553 65 - 0 0 0 OK 1.11503e+07 0 4.36026e+07 OK
-TCONS_00000037 i Xkr4 XLOC_000060 Xkr4 TSS66 chr1:3299443-3299664 55 - 0 0 163195 OK 0 0 163195 OK
-TCONS_00000038 i Xkr4 XLOC_000062 Xkr4 TSS68 chr1:3300051-3300078 27 - 0 0 0 OK 0 0 0 OK
-TCONS_00000039 i Xkr4 XLOC_000065 Xkr4 TSS71 chr1:3318999-3319051 52 - 0 0 0 OK 0 0 0 OK
-TCONS_00000040 i Xkr4 XLOC_000068 Xkr4 TSS74 chr1:3355887-3356119 27 - 0 0 332434 OK 0 0 0 OK
-TCONS_00000041 i Xkr4 XLOC_000071 Xkr4 TSS77 chr1:3363214-3363278 64 - 0 0 0 OK 0 0 0 OK
-TCONS_00000042 i Xkr4 XLOC_000073 Xkr4 TSS79 chr1:3363753-3363849 96 - 0 0 0 OK 0 0 0 OK
-TCONS_00000043 i Xkr4 XLOC_000075 Xkr4 TSS81 chr1:3367135-3367162 27 - 0 0 0 OK 0 0 0 OK
-TCONS_00000044 i Xkr4 XLOC_000077 Xkr4 TSS83 chr1:3367333-3367382 49 - 0 0 0 OK 0 0 0 OK
-TCONS_00000045 i Xkr4 XLOC_000080 Xkr4 TSS86 chr1:3377211-3377262 51 - 0 0 0 OK 0 0 0 OK
-TCONS_00000046 i Xkr4 XLOC_000083 Xkr4 TSS89 chr1:3391325-3391352 27 - 0 0 0 OK 0 0 0 OK
-TCONS_00000047 i Xkr4 XLOC_000084 Xkr4 TSS90 chr1:3435841-3435880 39 - 0 0 0 OK 0 0 0 OK
-TCONS_00000048 i Xkr4 XLOC_000085 Xkr4 TSS91 chr1:3447761-3447788 27 - 0 0 0 OK 0 0 0 OK
-TCONS_00000049 i Xkr4 XLOC_000086 Xkr4 TSS92 chr1:3450906-3450965 59 - 0 0 0 OK 0 0 0 OK
-TCONS_00000050 i Xkr4 XLOC_000087 Xkr4 TSS93 chr1:3451051-3451109 58 - 0 0 0 OK 0 0 0 OK
-TCONS_00000051 - - XLOC_000004 - TSS4 chr1:3174765-3174792 27 - 0 0 0 OK 0 0 0 OK
-TCONS_00000052 - - XLOC_000005 - TSS5 chr1:3187401-3187428 27 - 0 0 0 OK 0 0 0 OK
-TCONS_00000053 - - XLOC_000006 - TSS6 chr1:3188521-3188548 27 - 0 0 0 OK 0 0 0 OK
-TCONS_00000054 - - XLOC_000007 - TSS7 chr1:3189810-3190789 979 - 358326 135086 581565 OK 522345 410780 633911 OK
-TCONS_00000055 - - XLOC_000008 - TSS10 chr1:3190858-3191434 576 - 408511 54526.1 762496 OK 420354 61509.1 779200 OK
-TCONS_00000056 - - XLOC_000009 - TSS11 chr1:3191512-3192077 565 - 433286 63552.3 803020 OK 842157 342520 1.34179e+06 OK
-TCONS_00000057 - - XLOC_000010 - TSS13 chr1:3192250-3192336 86 - 3.44151e+06 0 1.31756e+07 OK 3.34455e+06 0 1.30786e+07 OK
-TCONS_00000058 - - XLOC_000013 - TSS16 chr1:3192649-3192676 27 - 0 0 0 OK 0 0 0 OK
-TCONS_00000059 - - XLOC_000018 - TSS21 chr1:3194706-3194733 27 - 0 0 0 OK 0 0 0 OK
-TCONS_00000060 - - XLOC_000024 - TSS27 chr1:3197425-3197452 27 - 0 0 0 OK 0 0 0 OK
-TCONS_00000062 - - XLOC_000027 - TSS30 chr1:3200430-3200457 27 - 0 0 0 OK 0 0 0 OK
-TCONS_00000063 - - XLOC_000028 - TSS31 chr1:3201007-3201039 32 - 0 0 0 OK 0 0 0 OK
-TCONS_00000065 - - XLOC_000030 - TSS33 chr1:3201596-3201666 70 - 1.6359e+07 0 5.96409e+07 OK 0 0 0 OK
-TCONS_00000066 - - XLOC_000032 - TSS35 chr1:3201725-3201809 84 - 1.5136e+07 0 4.63396e+07 OK 0 0 0 OK
-TCONS_00000067 i Xkr4 XLOC_000033 Xkr4 TSS36 chr1:3211521-3211561 40 - 0 0 0 OK 0 0 0 OK
-TCONS_00000068 i Xkr4 XLOC_000036 Xkr4 TSS39 chr1:3212717-3212801 84 - 3.784e+06 0 1.44868e+07 OK 0 0 0 OK
-TCONS_00000069 i Xkr4 XLOC_000037 Xkr4 TSS40 chr1:3213095-3213242 124 - 863189 0 4.25222e+06 OK 0 0 72384.9 OK
-TCONS_00000070 i Xkr4 XLOC_000038 Xkr4 TSS41 chr1:3240606-3240633 27 - 0 0 0 OK 0 0 0 OK
-TCONS_00000071 i Xkr4 XLOC_000039 Xkr4 TSS42 chr1:3242479-3242512 33 - 0 0 0 OK 0 0 0 OK
-TCONS_00000072 i Xkr4 XLOC_000041 Xkr4 TSS44 chr1:3242924-3243005 81 - 0 0 0 OK 0 0 0 OK
-TCONS_00000073 i Xkr4 XLOC_000043 Xkr4 TSS46 chr1:3243108-3243154 46 - 8.616e+07 0 3.29857e+08 OK 0 0 0 OK
-TCONS_00000074 i Xkr4 XLOC_000045 Xkr4 TSS48 chr1:3254079-3254106 27 - 0 0 0 OK 0 0 0 OK
-TCONS_00000075 i Xkr4 XLOC_000047 Xkr4 TSS50 chr1:3277155-3277182 27 - 0 0 0 OK 0 0 0 OK
-TCONS_00000076 i Xkr4 XLOC_000049 Xkr4 TSS52 chr1:3277913-3278390 477 - 228872 0 561229 OK 47662.2 0 156103 OK
-TCONS_00000077 i Xkr4 XLOC_000050 Xkr4 TSS54 chr1:3280117-3280144 27 - 0 0 0 OK 0 0 0 OK
-TCONS_00000078 i Xkr4 XLOC_000051 Xkr4 TSS55 chr1:3280498-3280525 27 - 0 0 0 OK 0 0 0 OK
-TCONS_00000079 i Xkr4 XLOC_000053 Xkr4 TSS57 chr1:3282504-3282531 27 - 0 0 0 OK 0 0 0 OK
-TCONS_00000080 i Xkr4 XLOC_000054 Xkr4 TSS58 chr1:3282650-3282677 27 - 0 0 0 OK 0 0 0 OK
-TCONS_00000081 i Xkr4 XLOC_000055 Xkr4 TSS59 chr1:3282760-3282832 72 - 0 0 0 OK 0 0 0 OK
-TCONS_00000082 i Xkr4 XLOC_000056 Xkr4 TSS60 chr1:3284966-3284993 27 - 0 0 0 OK 0 0 0 OK
-TCONS_00000083 i Xkr4 XLOC_000058 Xkr4 TSS62 chr1:3290798-3290859 61 - 1.55919e+07 0 5.96926e+07 OK 0 0 0 OK
-TCONS_00000084 i Xkr4 XLOC_000059 Xkr4 TSS63 chr1:3290919-3291273 354 - 294879 0 740137 OK 85971.3 0 281572 OK
-TCONS_00000085 i Xkr4 XLOC_000060 Xkr4 TSS65 chr1:3299443-3299664 197 - 807732 0 2.39056e+06 OK 156995 0 613917 OK
-TCONS_00000086 i Xkr4 XLOC_000061 Xkr4 TSS67 chr1:3299691-3299733 42 - 0 0 0 OK 0 0 0 OK
-TCONS_00000087 i Xkr4 XLOC_000063 Xkr4 TSS69 chr1:3307748-3307775 27 - 0 0 0 OK 0 0 0 OK
-TCONS_00000088 i Xkr4 XLOC_000064 Xkr4 TSS70 chr1:3318620-3318647 27 - 0 0 0 OK 0 0 0 OK
-TCONS_00000089 i Xkr4 XLOC_000066 Xkr4 TSS72 chr1:3330527-3330554 27 - 0 0 0 OK 0 0 0 OK
-TCONS_00000090 i Xkr4 XLOC_000067 Xkr4 TSS73 chr1:3351240-3351311 71 - 7.68169e+06 0 2.94088e+07 OK 0 0 0 OK
-TCONS_00000091 i Xkr4 XLOC_000068 Xkr4 TSS74 chr1:3355887-3356119 212 - 504790 0 1.54544e+06 OK 0 0 0 OK
-TCONS_00000092 i Xkr4 XLOC_000069 Xkr4 TSS75 chr1:3356180-3356225 45 - 1.02717e+08 0 3.93246e+08 OK 0 0 0 OK
-TCONS_00000093 i Xkr4 XLOC_000070 Xkr4 TSS76 chr1:3363076-3363176 100 - 3.81001e+06 0 1.38903e+07 OK 0 0 0 OK
-TCONS_00000094 i Xkr4 XLOC_000072 Xkr4 TSS78 chr1:3363387-3363446 59 - 5.53654e+07 0 1.77783e+08 OK 0 0 0 OK
-TCONS_00000095 i Xkr4 XLOC_000074 Xkr4 TSS80 chr1:3364871-3364919 48 - 6.28966e+07 0 2.40795e+08 OK 0 0 0 OK
-TCONS_00000096 i Xkr4 XLOC_000076 Xkr4 TSS82 chr1:3367210-3367237 27 - 0 0 0 OK 0 0 0 OK
-TCONS_00000097 i Xkr4 XLOC_000078 Xkr4 TSS84 chr1:3369580-3369607 27 - 0 0 0 OK 0 0 0 OK
-TCONS_00000098 i Xkr4 XLOC_000079 Xkr4 TSS85 chr1:3375001-3375028 27 - 0 0 0 OK 0 0 0 OK
-TCONS_00000099 i Xkr4 XLOC_000081 Xkr4 TSS87 chr1:3379888-3379915 27 - 0 0 0 OK 0 0 0 OK
-TCONS_00000100 i Xkr4 XLOC_000082 Xkr4 TSS88 chr1:3386739-3386836 97 - 0 0 0 OK 0 0 0 OK
diff -r 9a9e3e83889b -r 9ba750f285e3 test-data/cuffdiff_out6.txt
--- a/test-data/cuffdiff_out6.txt Wed Nov 26 13:57:28 2014 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,88 +0,0 @@
-tracking_id class_code nearest_ref_id gene_id gene_short_name tss_id locus length coverage q1_FPKM q1_conf_lo q1_conf_hi q1_status q2_FPKM q2_conf_lo q2_conf_hi q2_status
-XLOC_000001 - - XLOC_000001 Xkr4 TSS1 chr1:3204754-3204833 - - 0 0 0 OK 9.45986e+06 0 3.33035e+07 OK
-XLOC_000002 - - XLOC_000002 - TSS2 chr1:3111449-3111490 - - 0 0 0 OK 2.43637e+08 0 9.52723e+08 OK
-XLOC_000003 - - XLOC_000003 - TSS3 chr1:3111545-3111576 - - 0 0 0 OK 0 0 0 OK
-XLOC_000004 - - XLOC_000004 - TSS4 chr1:3174765-3174792 - - 0 0 0 OK 0 0 0 OK
-XLOC_000005 - - XLOC_000005 - TSS5 chr1:3187401-3187428 - - 0 0 0 OK 0 0 0 OK
-XLOC_000006 - - XLOC_000006 - TSS6 chr1:3188521-3188548 - - 0 0 0 OK 0 0 0 OK
-XLOC_000007 - - XLOC_000007 - TSS7 chr1:3189810-3190789 - - 358326 135086 581565 OK 522345 410780 633911 OK
-XLOC_000008 - - XLOC_000008 - TSS10 chr1:3190858-3191434 - - 408511 54526.1 762496 OK 420354 61509.1 779200 OK
-XLOC_000009 - - XLOC_000009 - TSS11 chr1:3191512-3192077 - - 433286 63552.3 803020 OK 842157 342520 1.34179e+06 OK
-XLOC_000010 - - XLOC_000010 - TSS13 chr1:3192250-3192336 - - 3.44151e+06 0 1.31756e+07 OK 3.34455e+06 0 1.30786e+07 OK
-XLOC_000011 - - XLOC_000011 - TSS14 chr1:3192441-3192494 - - 0 0 0 OK 9.7002e+07 0 3.17699e+08 OK
-XLOC_000012 - - XLOC_000012 - TSS15 chr1:3192550-3192629 - - 0 0 0 OK 4.72993e+06 0 1.84961e+07 OK
-XLOC_000013 - - XLOC_000013 - TSS16 chr1:3192649-3192676 - - 0 0 0 OK 0 0 0 OK
-XLOC_000014 - - XLOC_000014 - TSS17 chr1:3192731-3192811 - - 0 0 0 OK 0 0 0 OK
-XLOC_000015 - - XLOC_000015 - TSS18 chr1:3192940-3193042 - - 0 0 0 OK 6.86386e+06 0 2.14243e+07 OK
-XLOC_000016 - - XLOC_000016 - TSS19 chr1:3194185-3194226 - - 0 0 0 OK 2.43637e+08 0 9.52723e+08 OK
-XLOC_000017 - - XLOC_000017 - TSS20 chr1:3194302-3194329 - - 0 0 0 OK 0 0 0 OK
-XLOC_000018 - - XLOC_000018 - TSS21 chr1:3194706-3194733 - - 0 0 0 OK 0 0 0 OK
-XLOC_000019 - - XLOC_000019 - TSS22 chr1:3195083-3195110 - - 0 0 0 OK 0 0 0 OK
-XLOC_000020 - - XLOC_000020 - TSS23 chr1:3195450-3195477 - - 0 0 0 OK 0 0 0 OK
-XLOC_000021 - - XLOC_000021 - TSS24 chr1:3197089-3197116 - - 0 0 0 OK 0 0 0 OK
-XLOC_000022 - - XLOC_000022 - TSS25 chr1:3197246-3197273 - - 0 0 0 OK 0 0 0 OK
-XLOC_000023 - - XLOC_000023 - TSS26 chr1:3197346-3197373 - - 0 0 0 OK 0 0 0 OK
-XLOC_000024 - - XLOC_000024 - TSS27 chr1:3197425-3197452 - - 0 0 0 OK 0 0 0 OK
-XLOC_000025 - - XLOC_000025 - TSS28 chr1:3200022-3200191 - - 826392 0 2.65361e+06 OK 803108 0 2.63033e+06 OK
-XLOC_000026 - - XLOC_000026 - TSS29 chr1:3200325-3200352 - - 0 0 0 OK 0 0 0 OK
-XLOC_000027 - - XLOC_000027 - TSS30 chr1:3200430-3200457 - - 0 0 0 OK 0 0 0 OK
-XLOC_000028 - - XLOC_000028 - TSS31 chr1:3201007-3201039 - - 0 0 0 OK 0 0 0 OK
-XLOC_000029 - - XLOC_000029 - TSS32 chr1:3201077-3201481 - - 66791.3 0 214473 OK 324548 0 802006 OK
-XLOC_000030 - - XLOC_000030 - TSS33 chr1:3201596-3201666 - - 1.6359e+07 0 5.96409e+07 OK 0 0 0 OK
-XLOC_000031 - - XLOC_000031 - TSS34 chr1:3201672-3201699 - - 0 0 0 OK 0 0 0 OK
-XLOC_000032 - - XLOC_000032 - TSS35 chr1:3201725-3201809 - - 1.5136e+07 0 4.63396e+07 OK 0 0 0 OK
-XLOC_000033 - - XLOC_000033 Xkr4 TSS36 chr1:3211521-3211561 - - 0 0 0 OK 0 0 0 OK
-XLOC_000034 - - XLOC_000034 Xkr4 TSS37 chr1:3212213-3212292 - - 0 0 0 OK 9.45986e+06 0 3.33035e+07 OK
-XLOC_000035 - - XLOC_000035 Xkr4 TSS38 chr1:3212367-3212439 - - 0 0 0 OK 2.80837e+07 0 8.76584e+07 OK
-XLOC_000036 - - XLOC_000036 Xkr4 TSS39 chr1:3212717-3212801 - - 3.784e+06 0 1.44868e+07 OK 0 0 0 OK
-XLOC_000037 - - XLOC_000037 Xkr4 TSS40 chr1:3213095-3213242 - - 5.10781e+06 0 1.69588e+07 OK 2.08209e+06 0 8.1421e+06 OK
-XLOC_000038 - - XLOC_000038 Xkr4 TSS41 chr1:3240606-3240633 - - 0 0 0 OK 0 0 0 OK
-XLOC_000039 - - XLOC_000039 Xkr4 TSS42 chr1:3242479-3242512 - - 0 0 0 OK 0 0 0 OK
-XLOC_000040 - - XLOC_000040 Xkr4 TSS43 chr1:3242633-3242923 - - 48522.7 0 185766 OK 424400 0 1.30289e+06 OK
-XLOC_000041 - - XLOC_000041 Xkr4 TSS44 chr1:3242924-3243005 - - 0 0 0 OK 0 0 0 OK
-XLOC_000042 - - XLOC_000042 Xkr4 TSS45 chr1:3243018-3243079 - - 0 0 0 OK 3.03053e+07 0 1.0669e+08 OK
-XLOC_000043 - - XLOC_000043 Xkr4 TSS46 chr1:3243108-3243154 - - 8.616e+07 0 3.29857e+08 OK 0 0 0 OK
-XLOC_000044 - - XLOC_000044 Xkr4 TSS47 chr1:3243347-3243401 - - 0 0 0 OK 5.79991e+07 0 2.04186e+08 OK
-XLOC_000045 - - XLOC_000045 Xkr4 TSS48 chr1:3254079-3254106 - - 0 0 0 OK 0 0 0 OK
-XLOC_000046 - - XLOC_000046 Xkr4 TSS49 chr1:3256974-3257011 - - 0 0 0 OK 2.35423e+09 0 8.28806e+09 OK
-XLOC_000047 - - XLOC_000047 Xkr4 TSS50 chr1:3277155-3277182 - - 0 0 0 OK 0 0 0 OK
-XLOC_000048 - - XLOC_000048 Xkr4 TSS51 chr1:3277190-3277218 - - 0 0 0 OK 0 0 0 OK
-XLOC_000049 - - XLOC_000049 Xkr4 TSS52 chr1:3277913-3278390 - - 228872 0 561229 OK 47662.2 0 156103 OK
-XLOC_000050 - - XLOC_000050 Xkr4 TSS54 chr1:3280117-3280144 - - 0 0 0 OK 0 0 0 OK
-XLOC_000051 - - XLOC_000051 Xkr4 TSS55 chr1:3280498-3280525 - - 0 0 0 OK 0 0 0 OK
-XLOC_000052 - - XLOC_000052 Xkr4 TSS56 chr1:3280686-3280741 - - 0 0 0 OK 2.61334e+07 0 1.02193e+08 OK
-XLOC_000053 - - XLOC_000053 Xkr4 TSS57 chr1:3282504-3282531 - - 0 0 0 OK 0 0 0 OK
-XLOC_000054 - - XLOC_000054 Xkr4 TSS58 chr1:3282650-3282677 - - 0 0 0 OK 0 0 0 OK
-XLOC_000055 - - XLOC_000055 Xkr4 TSS59 chr1:3282760-3282832 - - 0 0 0 OK 0 0 0 OK
-XLOC_000056 - - XLOC_000056 Xkr4 TSS60 chr1:3284966-3284993 - - 0 0 0 OK 0 0 0 OK
-XLOC_000057 - - XLOC_000057 Xkr4 TSS61 chr1:3290488-3290553 - - 0 0 0 OK 1.11503e+07 0 4.36026e+07 OK
-XLOC_000058 - - XLOC_000058 Xkr4 TSS62 chr1:3290798-3290859 - - 1.55919e+07 0 5.96926e+07 OK 0 0 0 OK
-XLOC_000059 - - XLOC_000059 Xkr4 TSS63 chr1:3290919-3291273 - - 294879 0 740137 OK 85971.3 0 281572 OK
-XLOC_000060 - - XLOC_000060 Xkr4 TSS65,TSS66 chr1:3299443-3299664 - - 807732 0 2.39786e+06 OK 156995 0 641748 OK
-XLOC_000061 - - XLOC_000061 Xkr4 TSS67 chr1:3299691-3299733 - - 0 0 0 OK 0 0 0 OK
-XLOC_000062 - - XLOC_000062 Xkr4 TSS68 chr1:3300051-3300078 - - 0 0 0 OK 0 0 0 OK
-XLOC_000063 - - XLOC_000063 Xkr4 TSS69 chr1:3307748-3307775 - - 0 0 0 OK 0 0 0 OK
-XLOC_000064 - - XLOC_000064 Xkr4 TSS70 chr1:3318620-3318647 - - 0 0 0 OK 0 0 0 OK
-XLOC_000065 - - XLOC_000065 Xkr4 TSS71 chr1:3318999-3319051 - - 0 0 0 OK 0 0 0 OK
-XLOC_000066 - - XLOC_000066 Xkr4 TSS72 chr1:3330527-3330554 - - 0 0 0 OK 0 0 0 OK
-XLOC_000067 - - XLOC_000067 Xkr4 TSS73 chr1:3351240-3351311 - - 7.68169e+06 0 2.94088e+07 OK 0 0 0 OK
-XLOC_000068 - - XLOC_000068 Xkr4 TSS74 chr1:3355887-3356119 - - 504790 0 1.59712e+06 OK 0 0 0 OK
-XLOC_000069 - - XLOC_000069 Xkr4 TSS75 chr1:3356180-3356225 - - 1.02717e+08 0 3.93246e+08 OK 0 0 0 OK
-XLOC_000070 - - XLOC_000070 Xkr4 TSS76 chr1:3363076-3363176 - - 3.81001e+06 0 1.38903e+07 OK 0 0 0 OK
-XLOC_000071 - - XLOC_000071 Xkr4 TSS77 chr1:3363214-3363278 - - 0 0 0 OK 0 0 0 OK
-XLOC_000072 - - XLOC_000072 Xkr4 TSS78 chr1:3363387-3363446 - - 5.53654e+07 0 1.77783e+08 OK 0 0 0 OK
-XLOC_000073 - - XLOC_000073 Xkr4 TSS79 chr1:3363753-3363849 - - 0 0 0 OK 0 0 0 OK
-XLOC_000074 - - XLOC_000074 Xkr4 TSS80 chr1:3364871-3364919 - - 6.28966e+07 0 2.40795e+08 OK 0 0 0 OK
-XLOC_000075 - - XLOC_000075 Xkr4 TSS81 chr1:3367135-3367162 - - 0 0 0 OK 0 0 0 OK
-XLOC_000076 - - XLOC_000076 Xkr4 TSS82 chr1:3367210-3367237 - - 0 0 0 OK 0 0 0 OK
-XLOC_000077 - - XLOC_000077 Xkr4 TSS83 chr1:3367333-3367382 - - 0 0 0 OK 0 0 0 OK
-XLOC_000078 - - XLOC_000078 Xkr4 TSS84 chr1:3369580-3369607 - - 0 0 0 OK 0 0 0 OK
-XLOC_000079 - - XLOC_000079 Xkr4 TSS85 chr1:3375001-3375028 - - 0 0 0 OK 0 0 0 OK
-XLOC_000080 - - XLOC_000080 Xkr4 TSS86 chr1:3377211-3377262 - - 0 0 0 OK 0 0 0 OK
-XLOC_000081 - - XLOC_000081 Xkr4 TSS87 chr1:3379888-3379915 - - 0 0 0 OK 0 0 0 OK
-XLOC_000082 - - XLOC_000082 Xkr4 TSS88 chr1:3386739-3386836 - - 0 0 0 OK 0 0 0 OK
-XLOC_000083 - - XLOC_000083 Xkr4 TSS89 chr1:3391325-3391352 - - 0 0 0 OK 0 0 0 OK
-XLOC_000084 - - XLOC_000084 Xkr4 TSS90 chr1:3435841-3435880 - - 0 0 0 OK 0 0 0 OK
-XLOC_000085 - - XLOC_000085 Xkr4 TSS91 chr1:3447761-3447788 - - 0 0 0 OK 0 0 0 OK
-XLOC_000086 - - XLOC_000086 Xkr4 TSS92 chr1:3450906-3450965 - - 0 0 0 OK 0 0 0 OK
-XLOC_000087 - - XLOC_000087 Xkr4 TSS93 chr1:3451051-3451109 - - 0 0 0 OK 0 0 0 OK
diff -r 9a9e3e83889b -r 9ba750f285e3 test-data/cuffdiff_out7.txt
--- a/test-data/cuffdiff_out7.txt Wed Nov 26 13:57:28 2014 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,89 +0,0 @@
-tracking_id class_code nearest_ref_id gene_id gene_short_name tss_id locus length coverage q1_FPKM q1_conf_lo q1_conf_hi q1_status q2_FPKM q2_conf_lo q2_conf_hi q2_status
-TSS1 - - XLOC_000001 Xkr4 TSS1 chr1:3204754-3204833 - - 0 0 0 OK 9.45986e+06 0 3.33035e+07 OK
-TSS10 - - XLOC_000008 - TSS10 chr1:3190858-3191434 - - 408511 54526.1 762496 OK 420354 61509.1 779200 OK
-TSS11 - - XLOC_000009 - TSS11 chr1:3191512-3192077 - - 433286 63552.3 803020 OK 842157 342520 1.34179e+06 OK
-TSS13 - - XLOC_000010 - TSS13 chr1:3192250-3192336 - - 3.44151e+06 0 1.31756e+07 OK 3.34455e+06 0 1.30786e+07 OK
-TSS14 - - XLOC_000011 - TSS14 chr1:3192441-3192494 - - 0 0 0 OK 9.7002e+07 0 3.17699e+08 OK
-TSS15 - - XLOC_000012 - TSS15 chr1:3192550-3192629 - - 0 0 0 OK 4.72993e+06 0 1.84961e+07 OK
-TSS16 - - XLOC_000013 - TSS16 chr1:3192649-3192676 - - 0 0 0 OK 0 0 0 OK
-TSS17 - - XLOC_000014 - TSS17 chr1:3192731-3192811 - - 0 0 0 OK 0 0 0 OK
-TSS18 - - XLOC_000015 - TSS18 chr1:3192940-3193042 - - 0 0 0 OK 6.86386e+06 0 2.14243e+07 OK
-TSS19 - - XLOC_000016 - TSS19 chr1:3194185-3194226 - - 0 0 0 OK 2.43637e+08 0 9.52723e+08 OK
-TSS2 - - XLOC_000002 - TSS2 chr1:3111449-3111490 - - 0 0 0 OK 2.43637e+08 0 9.52723e+08 OK
-TSS20 - - XLOC_000017 - TSS20 chr1:3194302-3194329 - - 0 0 0 OK 0 0 0 OK
-TSS21 - - XLOC_000018 - TSS21 chr1:3194706-3194733 - - 0 0 0 OK 0 0 0 OK
-TSS22 - - XLOC_000019 - TSS22 chr1:3195083-3195110 - - 0 0 0 OK 0 0 0 OK
-TSS23 - - XLOC_000020 - TSS23 chr1:3195450-3195477 - - 0 0 0 OK 0 0 0 OK
-TSS24 - - XLOC_000021 - TSS24 chr1:3197089-3197116 - - 0 0 0 OK 0 0 0 OK
-TSS25 - - XLOC_000022 - TSS25 chr1:3197246-3197273 - - 0 0 0 OK 0 0 0 OK
-TSS26 - - XLOC_000023 - TSS26 chr1:3197346-3197373 - - 0 0 0 OK 0 0 0 OK
-TSS27 - - XLOC_000024 - TSS27 chr1:3197425-3197452 - - 0 0 0 OK 0 0 0 OK
-TSS28 - - XLOC_000025 - TSS28 chr1:3200022-3200191 - - 826392 0 2.65361e+06 OK 803108 0 2.63033e+06 OK
-TSS29 - - XLOC_000026 - TSS29 chr1:3200325-3200352 - - 0 0 0 OK 0 0 0 OK
-TSS3 - - XLOC_000003 - TSS3 chr1:3111545-3111576 - - 0 0 0 OK 0 0 0 OK
-TSS30 - - XLOC_000027 - TSS30 chr1:3200430-3200457 - - 0 0 0 OK 0 0 0 OK
-TSS31 - - XLOC_000028 - TSS31 chr1:3201007-3201039 - - 0 0 0 OK 0 0 0 OK
-TSS32 - - XLOC_000029 - TSS32 chr1:3201077-3201481 - - 66791.3 0 214473 OK 324548 0 802006 OK
-TSS33 - - XLOC_000030 - TSS33 chr1:3201596-3201666 - - 1.6359e+07 0 5.96409e+07 OK 0 0 0 OK
-TSS34 - - XLOC_000031 - TSS34 chr1:3201672-3201699 - - 0 0 0 OK 0 0 0 OK
-TSS35 - - XLOC_000032 - TSS35 chr1:3201725-3201809 - - 1.5136e+07 0 4.63396e+07 OK 0 0 0 OK
-TSS36 - - XLOC_000033 Xkr4 TSS36 chr1:3211521-3211561 - - 0 0 0 OK 0 0 0 OK
-TSS37 - - XLOC_000034 Xkr4 TSS37 chr1:3212213-3212292 - - 0 0 0 OK 9.45986e+06 0 3.33035e+07 OK
-TSS38 - - XLOC_000035 Xkr4 TSS38 chr1:3212367-3212439 - - 0 0 0 OK 2.80837e+07 0 8.76584e+07 OK
-TSS39 - - XLOC_000036 Xkr4 TSS39 chr1:3212717-3212801 - - 3.784e+06 0 1.44868e+07 OK 0 0 0 OK
-TSS4 - - XLOC_000004 - TSS4 chr1:3174765-3174792 - - 0 0 0 OK 0 0 0 OK
-TSS40 - - XLOC_000037 Xkr4 TSS40 chr1:3213095-3213242 - - 5.10781e+06 0 1.69588e+07 OK 2.08209e+06 0 8.1421e+06 OK
-TSS41 - - XLOC_000038 Xkr4 TSS41 chr1:3240606-3240633 - - 0 0 0 OK 0 0 0 OK
-TSS42 - - XLOC_000039 Xkr4 TSS42 chr1:3242479-3242512 - - 0 0 0 OK 0 0 0 OK
-TSS43 - - XLOC_000040 Xkr4 TSS43 chr1:3242633-3242923 - - 48522.7 0 185766 OK 424400 0 1.30289e+06 OK
-TSS44 - - XLOC_000041 Xkr4 TSS44 chr1:3242924-3243005 - - 0 0 0 OK 0 0 0 OK
-TSS45 - - XLOC_000042 Xkr4 TSS45 chr1:3243018-3243079 - - 0 0 0 OK 3.03053e+07 0 1.0669e+08 OK
-TSS46 - - XLOC_000043 Xkr4 TSS46 chr1:3243108-3243154 - - 8.616e+07 0 3.29857e+08 OK 0 0 0 OK
-TSS47 - - XLOC_000044 Xkr4 TSS47 chr1:3243347-3243401 - - 0 0 0 OK 5.79991e+07 0 2.04186e+08 OK
-TSS48 - - XLOC_000045 Xkr4 TSS48 chr1:3254079-3254106 - - 0 0 0 OK 0 0 0 OK
-TSS49 - - XLOC_000046 Xkr4 TSS49 chr1:3256974-3257011 - - 0 0 0 OK 2.35423e+09 0 8.28806e+09 OK
-TSS5 - - XLOC_000005 - TSS5 chr1:3187401-3187428 - - 0 0 0 OK 0 0 0 OK
-TSS50 - - XLOC_000047 Xkr4 TSS50 chr1:3277155-3277182 - - 0 0 0 OK 0 0 0 OK
-TSS51 - - XLOC_000048 Xkr4 TSS51 chr1:3277190-3277218 - - 0 0 0 OK 0 0 0 OK
-TSS52 - - XLOC_000049 Xkr4 TSS52 chr1:3277913-3278390 - - 228872 0 561229 OK 47662.2 0 156103 OK
-TSS54 - - XLOC_000050 Xkr4 TSS54 chr1:3280117-3280144 - - 0 0 0 OK 0 0 0 OK
-TSS55 - - XLOC_000051 Xkr4 TSS55 chr1:3280498-3280525 - - 0 0 0 OK 0 0 0 OK
-TSS56 - - XLOC_000052 Xkr4 TSS56 chr1:3280686-3280741 - - 0 0 0 OK 2.61334e+07 0 1.02193e+08 OK
-TSS57 - - XLOC_000053 Xkr4 TSS57 chr1:3282504-3282531 - - 0 0 0 OK 0 0 0 OK
-TSS58 - - XLOC_000054 Xkr4 TSS58 chr1:3282650-3282677 - - 0 0 0 OK 0 0 0 OK
-TSS59 - - XLOC_000055 Xkr4 TSS59 chr1:3282760-3282832 - - 0 0 0 OK 0 0 0 OK
-TSS6 - - XLOC_000006 - TSS6 chr1:3188521-3188548 - - 0 0 0 OK 0 0 0 OK
-TSS60 - - XLOC_000056 Xkr4 TSS60 chr1:3284966-3284993 - - 0 0 0 OK 0 0 0 OK
-TSS61 - - XLOC_000057 Xkr4 TSS61 chr1:3290488-3290553 - - 0 0 0 OK 1.11503e+07 0 4.36026e+07 OK
-TSS62 - - XLOC_000058 Xkr4 TSS62 chr1:3290798-3290859 - - 1.55919e+07 0 5.96926e+07 OK 0 0 0 OK
-TSS63 - - XLOC_000059 Xkr4 TSS63 chr1:3290919-3291273 - - 294879 0 740137 OK 85971.3 0 281572 OK
-TSS65 - - XLOC_000060 Xkr4 TSS65 chr1:3299443-3299664 - - 807732 0 2.39056e+06 OK 156995 0 613917 OK
-TSS66 - - XLOC_000060 Xkr4 TSS66 chr1:3299443-3299664 - - 0 0 0 OK 0 0 0 OK
-TSS67 - - XLOC_000061 Xkr4 TSS67 chr1:3299691-3299733 - - 0 0 0 OK 0 0 0 OK
-TSS68 - - XLOC_000062 Xkr4 TSS68 chr1:3300051-3300078 - - 0 0 0 OK 0 0 0 OK
-TSS69 - - XLOC_000063 Xkr4 TSS69 chr1:3307748-3307775 - - 0 0 0 OK 0 0 0 OK
-TSS7 - - XLOC_000007 - TSS7 chr1:3189810-3190789 - - 358326 135086 581565 OK 522345 410780 633911 OK
-TSS70 - - XLOC_000064 Xkr4 TSS70 chr1:3318620-3318647 - - 0 0 0 OK 0 0 0 OK
-TSS71 - - XLOC_000065 Xkr4 TSS71 chr1:3318999-3319051 - - 0 0 0 OK 0 0 0 OK
-TSS72 - - XLOC_000066 Xkr4 TSS72 chr1:3330527-3330554 - - 0 0 0 OK 0 0 0 OK
-TSS73 - - XLOC_000067 Xkr4 TSS73 chr1:3351240-3351311 - - 7.68169e+06 0 2.94088e+07 OK 0 0 0 OK
-TSS74 - - XLOC_000068 Xkr4 TSS74 chr1:3355887-3356119 - - 504790 0 1.59712e+06 OK 0 0 0 OK
-TSS75 - - XLOC_000069 Xkr4 TSS75 chr1:3356180-3356225 - - 1.02717e+08 0 3.93246e+08 OK 0 0 0 OK
-TSS76 - - XLOC_000070 Xkr4 TSS76 chr1:3363076-3363176 - - 3.81001e+06 0 1.38903e+07 OK 0 0 0 OK
-TSS77 - - XLOC_000071 Xkr4 TSS77 chr1:3363214-3363278 - - 0 0 0 OK 0 0 0 OK
-TSS78 - - XLOC_000072 Xkr4 TSS78 chr1:3363387-3363446 - - 5.53654e+07 0 1.77783e+08 OK 0 0 0 OK
-TSS79 - - XLOC_000073 Xkr4 TSS79 chr1:3363753-3363849 - - 0 0 0 OK 0 0 0 OK
-TSS80 - - XLOC_000074 Xkr4 TSS80 chr1:3364871-3364919 - - 6.28966e+07 0 2.40795e+08 OK 0 0 0 OK
-TSS81 - - XLOC_000075 Xkr4 TSS81 chr1:3367135-3367162 - - 0 0 0 OK 0 0 0 OK
-TSS82 - - XLOC_000076 Xkr4 TSS82 chr1:3367210-3367237 - - 0 0 0 OK 0 0 0 OK
-TSS83 - - XLOC_000077 Xkr4 TSS83 chr1:3367333-3367382 - - 0 0 0 OK 0 0 0 OK
-TSS84 - - XLOC_000078 Xkr4 TSS84 chr1:3369580-3369607 - - 0 0 0 OK 0 0 0 OK
-TSS85 - - XLOC_000079 Xkr4 TSS85 chr1:3375001-3375028 - - 0 0 0 OK 0 0 0 OK
-TSS86 - - XLOC_000080 Xkr4 TSS86 chr1:3377211-3377262 - - 0 0 0 OK 0 0 0 OK
-TSS87 - - XLOC_000081 Xkr4 TSS87 chr1:3379888-3379915 - - 0 0 0 OK 0 0 0 OK
-TSS88 - - XLOC_000082 Xkr4 TSS88 chr1:3386739-3386836 - - 0 0 0 OK 0 0 0 OK
-TSS89 - - XLOC_000083 Xkr4 TSS89 chr1:3391325-3391352 - - 0 0 0 OK 0 0 0 OK
-TSS90 - - XLOC_000084 Xkr4 TSS90 chr1:3435841-3435880 - - 0 0 0 OK 0 0 0 OK
-TSS91 - - XLOC_000085 Xkr4 TSS91 chr1:3447761-3447788 - - 0 0 0 OK 0 0 0 OK
-TSS92 - - XLOC_000086 Xkr4 TSS92 chr1:3450906-3450965 - - 0 0 0 OK 0 0 0 OK
-TSS93 - - XLOC_000087 Xkr4 TSS93 chr1:3451051-3451109 - - 0 0 0 OK 0 0 0 OK
diff -r 9a9e3e83889b -r 9ba750f285e3 test-data/cuffdiff_out8.txt
--- a/test-data/cuffdiff_out8.txt Wed Nov 26 13:57:28 2014 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-tracking_id class_code nearest_ref_id gene_id gene_short_name tss_id locus length coverage
diff -r 9a9e3e83889b -r 9ba750f285e3 test-data/cuffdiff_out9.txt
--- a/test-data/cuffdiff_out9.txt Wed Nov 26 13:57:28 2014 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,89 +0,0 @@
-test_id gene_id gene locus sample_1 sample_2 status value_1 value_2 sqrt(JS) test_stat p_value q_value significant
-TSS1 XLOC_000001 Xkr4 chr1:3204754-3204833 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS10 XLOC_000008 - chr1:3190858-3191434 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS11 XLOC_000009 - chr1:3191512-3192077 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS13 XLOC_000010 - chr1:3192250-3192336 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS14 XLOC_000011 - chr1:3192441-3192494 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS15 XLOC_000012 - chr1:3192550-3192629 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS16 XLOC_000013 - chr1:3192649-3192676 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS17 XLOC_000014 - chr1:3192731-3192811 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS18 XLOC_000015 - chr1:3192940-3193042 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS19 XLOC_000016 - chr1:3194185-3194226 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS2 XLOC_000002 - chr1:3111449-3111490 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS20 XLOC_000017 - chr1:3194302-3194329 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS21 XLOC_000018 - chr1:3194706-3194733 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS22 XLOC_000019 - chr1:3195083-3195110 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS23 XLOC_000020 - chr1:3195450-3195477 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS24 XLOC_000021 - chr1:3197089-3197116 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS25 XLOC_000022 - chr1:3197246-3197273 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS26 XLOC_000023 - chr1:3197346-3197373 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS27 XLOC_000024 - chr1:3197425-3197452 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS28 XLOC_000025 - chr1:3200022-3200191 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS29 XLOC_000026 - chr1:3200325-3200352 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS3 XLOC_000003 - chr1:3111545-3111576 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS30 XLOC_000027 - chr1:3200430-3200457 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS31 XLOC_000028 - chr1:3201007-3201039 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS32 XLOC_000029 - chr1:3201077-3201481 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS33 XLOC_000030 - chr1:3201596-3201666 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS34 XLOC_000031 - chr1:3201672-3201699 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS35 XLOC_000032 - chr1:3201725-3201809 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS36 XLOC_000033 Xkr4 chr1:3211521-3211561 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS37 XLOC_000034 Xkr4 chr1:3212213-3212292 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS38 XLOC_000035 Xkr4 chr1:3212367-3212439 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS39 XLOC_000036 Xkr4 chr1:3212717-3212801 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS4 XLOC_000004 - chr1:3174765-3174792 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS40 XLOC_000037 Xkr4 chr1:3213095-3213242 q1 q2 NOTEST 0 0 0.249947 0 0.5526 1 no
-TSS41 XLOC_000038 Xkr4 chr1:3240606-3240633 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS42 XLOC_000039 Xkr4 chr1:3242479-3242512 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS43 XLOC_000040 Xkr4 chr1:3242633-3242923 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS44 XLOC_000041 Xkr4 chr1:3242924-3243005 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS45 XLOC_000042 Xkr4 chr1:3243018-3243079 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS46 XLOC_000043 Xkr4 chr1:3243108-3243154 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS47 XLOC_000044 Xkr4 chr1:3243347-3243401 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS48 XLOC_000045 Xkr4 chr1:3254079-3254106 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS49 XLOC_000046 Xkr4 chr1:3256974-3257011 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS5 XLOC_000005 - chr1:3187401-3187428 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS50 XLOC_000047 Xkr4 chr1:3277155-3277182 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS51 XLOC_000048 Xkr4 chr1:3277190-3277218 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS52 XLOC_000049 Xkr4 chr1:3277913-3278390 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS54 XLOC_000050 Xkr4 chr1:3280117-3280144 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS55 XLOC_000051 Xkr4 chr1:3280498-3280525 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS56 XLOC_000052 Xkr4 chr1:3280686-3280741 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS57 XLOC_000053 Xkr4 chr1:3282504-3282531 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS58 XLOC_000054 Xkr4 chr1:3282650-3282677 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS59 XLOC_000055 Xkr4 chr1:3282760-3282832 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS6 XLOC_000006 - chr1:3188521-3188548 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS60 XLOC_000056 Xkr4 chr1:3284966-3284993 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS61 XLOC_000057 Xkr4 chr1:3290488-3290553 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS62 XLOC_000058 Xkr4 chr1:3290798-3290859 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS63 XLOC_000059 Xkr4 chr1:3290919-3291273 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS65 XLOC_000060 Xkr4 chr1:3299443-3299664 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS66 XLOC_000060 Xkr4 chr1:3299443-3299664 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS67 XLOC_000061 Xkr4 chr1:3299691-3299733 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS68 XLOC_000062 Xkr4 chr1:3300051-3300078 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS69 XLOC_000063 Xkr4 chr1:3307748-3307775 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS7 XLOC_000007 - chr1:3189810-3190789 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS70 XLOC_000064 Xkr4 chr1:3318620-3318647 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS71 XLOC_000065 Xkr4 chr1:3318999-3319051 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS72 XLOC_000066 Xkr4 chr1:3330527-3330554 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS73 XLOC_000067 Xkr4 chr1:3351240-3351311 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS74 XLOC_000068 Xkr4 chr1:3355887-3356119 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS75 XLOC_000069 Xkr4 chr1:3356180-3356225 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS76 XLOC_000070 Xkr4 chr1:3363076-3363176 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS77 XLOC_000071 Xkr4 chr1:3363214-3363278 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS78 XLOC_000072 Xkr4 chr1:3363387-3363446 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS79 XLOC_000073 Xkr4 chr1:3363753-3363849 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS80 XLOC_000074 Xkr4 chr1:3364871-3364919 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS81 XLOC_000075 Xkr4 chr1:3367135-3367162 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS82 XLOC_000076 Xkr4 chr1:3367210-3367237 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS83 XLOC_000077 Xkr4 chr1:3367333-3367382 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS84 XLOC_000078 Xkr4 chr1:3369580-3369607 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS85 XLOC_000079 Xkr4 chr1:3375001-3375028 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS86 XLOC_000080 Xkr4 chr1:3377211-3377262 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS87 XLOC_000081 Xkr4 chr1:3379888-3379915 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS88 XLOC_000082 Xkr4 chr1:3386739-3386836 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS89 XLOC_000083 Xkr4 chr1:3391325-3391352 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS90 XLOC_000084 Xkr4 chr1:3435841-3435880 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS91 XLOC_000085 Xkr4 chr1:3447761-3447788 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS92 XLOC_000086 Xkr4 chr1:3450906-3450965 q1 q2 NOTEST 0 0 0 0 1 1 no
-TSS93 XLOC_000087 Xkr4 chr1:3451051-3451109 q1 q2 NOTEST 0 0 0 0 1 1 no
diff -r 9a9e3e83889b -r 9ba750f285e3 test-data/genes.exp
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/genes.exp Tue Oct 13 12:37:38 2015 -0400
@@ -0,0 +1,88 @@
+test_id gene_id gene locus sample_1 sample_2 status value_1 value_2 log2(fold_change) test_stat p_value q_value significant
+XLOC_000001 XLOC_000001 Xkr4 chr1:3204754-3204833 q1 q2 OK 0 9.45986e+06 inf -nan 0.01975 0.09875 no
+XLOC_000002 XLOC_000002 - chr1:3111449-3111490 q1 q2 OK 0 2.43637e+08 inf -nan 0.12465 0.181781 no
+XLOC_000003 XLOC_000003 - chr1:3111545-3111576 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000004 XLOC_000004 - chr1:3174765-3174792 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000005 XLOC_000005 - chr1:3187401-3187428 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000006 XLOC_000006 - chr1:3188521-3188548 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000007 XLOC_000007 - chr1:3189810-3190789 q1 q2 OK 358326 522345 0.543731 1.1445 0.1952 0.27328 no
+XLOC_000008 XLOC_000008 - chr1:3190858-3191434 q1 q2 OK 408511 420354 0.0412311 0.0469899 0.96715 0.96715 no
+XLOC_000009 XLOC_000009 - chr1:3191512-3192077 q1 q2 OK 433286 842157 0.958769 1.27887 0.20385 0.274413 no
+XLOC_000010 XLOC_000010 - chr1:3192250-3192336 q1 q2 OK 3.44151e+06 3.34455e+06 -0.0412311 -0.014084 0.67715 0.718189 no
+XLOC_000011 XLOC_000011 - chr1:3192441-3192494 q1 q2 OK 0 9.7002e+07 inf -nan 0.07975 0.181781 no
+XLOC_000012 XLOC_000012 - chr1:3192550-3192629 q1 q2 OK 0 4.72993e+06 inf -nan 0.12465 0.181781 no
+XLOC_000013 XLOC_000013 - chr1:3192649-3192676 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000014 XLOC_000014 - chr1:3192731-3192811 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000015 XLOC_000015 - chr1:3192940-3193042 q1 q2 OK 0 6.86386e+06 inf -nan 0.0612 0.181781 no
+XLOC_000016 XLOC_000016 - chr1:3194185-3194226 q1 q2 OK 0 2.43637e+08 inf -nan 0.12465 0.181781 no
+XLOC_000017 XLOC_000017 - chr1:3194302-3194329 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000018 XLOC_000018 - chr1:3194706-3194733 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000019 XLOC_000019 - chr1:3195083-3195110 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000020 XLOC_000020 - chr1:3195450-3195477 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000021 XLOC_000021 - chr1:3197089-3197116 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000022 XLOC_000022 - chr1:3197246-3197273 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000023 XLOC_000023 - chr1:3197346-3197373 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000024 XLOC_000024 - chr1:3197425-3197452 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000025 XLOC_000025 - chr1:3200022-3200191 q1 q2 OK 826392 803108 -0.0412311 -0.0180163 0.8625 0.887868 no
+XLOC_000026 XLOC_000026 - chr1:3200325-3200352 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000027 XLOC_000027 - chr1:3200430-3200457 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000028 XLOC_000028 - chr1:3201007-3201039 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000029 XLOC_000029 - chr1:3201077-3201481 q1 q2 OK 66791.3 324548 2.2807 1.1905 0.3026 0.383188 no
+XLOC_000030 XLOC_000030 - chr1:3201596-3201666 q1 q2 OK 1.6359e+07 0 -inf -nan 0.0148 0.09875 no
+XLOC_000031 XLOC_000031 - chr1:3201672-3201699 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000032 XLOC_000032 - chr1:3201725-3201809 q1 q2 OK 1.5136e+07 0 -inf -nan 0.06005 0.181781 no
+XLOC_000033 XLOC_000033 Xkr4 chr1:3211521-3211561 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000034 XLOC_000034 Xkr4 chr1:3212213-3212292 q1 q2 OK 0 9.45986e+06 inf -nan 0.01975 0.09875 no
+XLOC_000035 XLOC_000035 Xkr4 chr1:3212367-3212439 q1 q2 OK 0 2.80837e+07 inf -nan 0.0612 0.181781 no
+XLOC_000036 XLOC_000036 Xkr4 chr1:3212717-3212801 q1 q2 OK 3.784e+06 0 -inf -nan 0.12165 0.181781 no
+XLOC_000037 XLOC_000037 Xkr4 chr1:3213095-3213242 q1 q2 OK 5.10781e+06 2.08209e+06 -1.29467 -0.482193 0.5916 0.647062 no
+XLOC_000038 XLOC_000038 Xkr4 chr1:3240606-3240633 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000039 XLOC_000039 Xkr4 chr1:3242479-3242512 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000040 XLOC_000040 Xkr4 chr1:3242633-3242923 q1 q2 OK 48522.7 424400 3.12869 1.23747 0.38685 0.450823 no
+XLOC_000041 XLOC_000041 Xkr4 chr1:3242924-3243005 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000042 XLOC_000042 Xkr4 chr1:3243018-3243079 q1 q2 OK 0 3.03053e+07 inf -nan 0.01975 0.09875 no
+XLOC_000043 XLOC_000043 Xkr4 chr1:3243108-3243154 q1 q2 OK 8.616e+07 0 -inf -nan 0.12165 0.181781 no
+XLOC_000044 XLOC_000044 Xkr4 chr1:3243347-3243401 q1 q2 OK 0 5.79991e+07 inf -nan 0.01975 0.09875 no
+XLOC_000045 XLOC_000045 Xkr4 chr1:3254079-3254106 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000046 XLOC_000046 Xkr4 chr1:3256974-3257011 q1 q2 OK 0 2.35423e+09 inf -nan 0.01975 0.09875 no
+XLOC_000047 XLOC_000047 Xkr4 chr1:3277155-3277182 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000048 XLOC_000048 Xkr4 chr1:3277190-3277218 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000049 XLOC_000049 Xkr4 chr1:3277913-3278390 q1 q2 OK 228872 47662.2 -2.26362 -1.16262 0.30655 0.383188 no
+XLOC_000050 XLOC_000050 Xkr4 chr1:3280117-3280144 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000051 XLOC_000051 Xkr4 chr1:3280498-3280525 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000052 XLOC_000052 Xkr4 chr1:3280686-3280741 q1 q2 OK 0 2.61334e+07 inf -nan 0.12465 0.181781 no
+XLOC_000053 XLOC_000053 Xkr4 chr1:3282504-3282531 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000054 XLOC_000054 Xkr4 chr1:3282650-3282677 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000055 XLOC_000055 Xkr4 chr1:3282760-3282832 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000056 XLOC_000056 Xkr4 chr1:3284966-3284993 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000057 XLOC_000057 Xkr4 chr1:3290488-3290553 q1 q2 OK 0 1.11503e+07 inf -nan 0.12465 0.181781 no
+XLOC_000058 XLOC_000058 Xkr4 chr1:3290798-3290859 q1 q2 OK 1.55919e+07 0 -inf -nan 0.12165 0.181781 no
+XLOC_000059 XLOC_000059 Xkr4 chr1:3290919-3291273 q1 q2 OK 294879 85971.3 -1.7782 -0.902752 0.36915 0.445526 no
+XLOC_000060 XLOC_000060 Xkr4 chr1:3299443-3299664 q1 q2 OK 807732 156995 -2.36316 -0.89463 0.3993 0.450823 no
+XLOC_000061 XLOC_000061 Xkr4 chr1:3299691-3299733 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000062 XLOC_000062 Xkr4 chr1:3300051-3300078 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000063 XLOC_000063 Xkr4 chr1:3307748-3307775 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000064 XLOC_000064 Xkr4 chr1:3318620-3318647 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000065 XLOC_000065 Xkr4 chr1:3318999-3319051 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000066 XLOC_000066 Xkr4 chr1:3330527-3330554 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000067 XLOC_000067 Xkr4 chr1:3351240-3351311 q1 q2 OK 7.68169e+06 0 -inf -nan 0.12165 0.181781 no
+XLOC_000068 XLOC_000068 Xkr4 chr1:3355887-3356119 q1 q2 OK 504790 0 -inf -nan 0.04565 0.181781 no
+XLOC_000069 XLOC_000069 Xkr4 chr1:3356180-3356225 q1 q2 OK 1.02717e+08 0 -inf -nan 0.12165 0.181781 no
+XLOC_000070 XLOC_000070 Xkr4 chr1:3363076-3363176 q1 q2 OK 3.81001e+06 0 -inf -nan 0.0148 0.09875 no
+XLOC_000071 XLOC_000071 Xkr4 chr1:3363214-3363278 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000072 XLOC_000072 Xkr4 chr1:3363387-3363446 q1 q2 OK 5.53654e+07 0 -inf -nan 0.0773 0.181781 no
+XLOC_000073 XLOC_000073 Xkr4 chr1:3363753-3363849 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000074 XLOC_000074 Xkr4 chr1:3364871-3364919 q1 q2 OK 6.28966e+07 0 -inf -nan 0.12165 0.181781 no
+XLOC_000075 XLOC_000075 Xkr4 chr1:3367135-3367162 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000076 XLOC_000076 Xkr4 chr1:3367210-3367237 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000077 XLOC_000077 Xkr4 chr1:3367333-3367382 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000078 XLOC_000078 Xkr4 chr1:3369580-3369607 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000079 XLOC_000079 Xkr4 chr1:3375001-3375028 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000080 XLOC_000080 Xkr4 chr1:3377211-3377262 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000081 XLOC_000081 Xkr4 chr1:3379888-3379915 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000082 XLOC_000082 Xkr4 chr1:3386739-3386836 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000083 XLOC_000083 Xkr4 chr1:3391325-3391352 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000084 XLOC_000084 Xkr4 chr1:3435841-3435880 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000085 XLOC_000085 Xkr4 chr1:3447761-3447788 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000086 XLOC_000086 Xkr4 chr1:3450906-3450965 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000087 XLOC_000087 Xkr4 chr1:3451051-3451109 q1 q2 NOTEST 0 0 0 0 1 1 no
diff -r 9a9e3e83889b -r 9ba750f285e3 test-data/genes.fpkm_tracking
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/genes.fpkm_tracking Tue Oct 13 12:37:38 2015 -0400
@@ -0,0 +1,88 @@
+tracking_id class_code nearest_ref_id gene_id gene_short_name tss_id locus length coverage q1_FPKM q1_conf_lo q1_conf_hi q1_status q2_FPKM q2_conf_lo q2_conf_hi q2_status
+XLOC_000001 - - XLOC_000001 Xkr4 TSS1 chr1:3204754-3204833 - - 0 0 0 OK 9.45986e+06 0 3.33035e+07 OK
+XLOC_000002 - - XLOC_000002 - TSS2 chr1:3111449-3111490 - - 0 0 0 OK 2.43637e+08 0 9.52723e+08 OK
+XLOC_000003 - - XLOC_000003 - TSS3 chr1:3111545-3111576 - - 0 0 0 OK 0 0 0 OK
+XLOC_000004 - - XLOC_000004 - TSS4 chr1:3174765-3174792 - - 0 0 0 OK 0 0 0 OK
+XLOC_000005 - - XLOC_000005 - TSS5 chr1:3187401-3187428 - - 0 0 0 OK 0 0 0 OK
+XLOC_000006 - - XLOC_000006 - TSS6 chr1:3188521-3188548 - - 0 0 0 OK 0 0 0 OK
+XLOC_000007 - - XLOC_000007 - TSS7 chr1:3189810-3190789 - - 358326 135086 581565 OK 522345 410780 633911 OK
+XLOC_000008 - - XLOC_000008 - TSS10 chr1:3190858-3191434 - - 408511 54526.1 762496 OK 420354 61509.1 779200 OK
+XLOC_000009 - - XLOC_000009 - TSS11 chr1:3191512-3192077 - - 433286 63552.3 803020 OK 842157 342520 1.34179e+06 OK
+XLOC_000010 - - XLOC_000010 - TSS13 chr1:3192250-3192336 - - 3.44151e+06 0 1.31756e+07 OK 3.34455e+06 0 1.30786e+07 OK
+XLOC_000011 - - XLOC_000011 - TSS14 chr1:3192441-3192494 - - 0 0 0 OK 9.7002e+07 0 3.17699e+08 OK
+XLOC_000012 - - XLOC_000012 - TSS15 chr1:3192550-3192629 - - 0 0 0 OK 4.72993e+06 0 1.84961e+07 OK
+XLOC_000013 - - XLOC_000013 - TSS16 chr1:3192649-3192676 - - 0 0 0 OK 0 0 0 OK
+XLOC_000014 - - XLOC_000014 - TSS17 chr1:3192731-3192811 - - 0 0 0 OK 0 0 0 OK
+XLOC_000015 - - XLOC_000015 - TSS18 chr1:3192940-3193042 - - 0 0 0 OK 6.86386e+06 0 2.14243e+07 OK
+XLOC_000016 - - XLOC_000016 - TSS19 chr1:3194185-3194226 - - 0 0 0 OK 2.43637e+08 0 9.52723e+08 OK
+XLOC_000017 - - XLOC_000017 - TSS20 chr1:3194302-3194329 - - 0 0 0 OK 0 0 0 OK
+XLOC_000018 - - XLOC_000018 - TSS21 chr1:3194706-3194733 - - 0 0 0 OK 0 0 0 OK
+XLOC_000019 - - XLOC_000019 - TSS22 chr1:3195083-3195110 - - 0 0 0 OK 0 0 0 OK
+XLOC_000020 - - XLOC_000020 - TSS23 chr1:3195450-3195477 - - 0 0 0 OK 0 0 0 OK
+XLOC_000021 - - XLOC_000021 - TSS24 chr1:3197089-3197116 - - 0 0 0 OK 0 0 0 OK
+XLOC_000022 - - XLOC_000022 - TSS25 chr1:3197246-3197273 - - 0 0 0 OK 0 0 0 OK
+XLOC_000023 - - XLOC_000023 - TSS26 chr1:3197346-3197373 - - 0 0 0 OK 0 0 0 OK
+XLOC_000024 - - XLOC_000024 - TSS27 chr1:3197425-3197452 - - 0 0 0 OK 0 0 0 OK
+XLOC_000025 - - XLOC_000025 - TSS28 chr1:3200022-3200191 - - 826392 0 2.65361e+06 OK 803108 0 2.63033e+06 OK
+XLOC_000026 - - XLOC_000026 - TSS29 chr1:3200325-3200352 - - 0 0 0 OK 0 0 0 OK
+XLOC_000027 - - XLOC_000027 - TSS30 chr1:3200430-3200457 - - 0 0 0 OK 0 0 0 OK
+XLOC_000028 - - XLOC_000028 - TSS31 chr1:3201007-3201039 - - 0 0 0 OK 0 0 0 OK
+XLOC_000029 - - XLOC_000029 - TSS32 chr1:3201077-3201481 - - 66791.3 0 214473 OK 324548 0 802006 OK
+XLOC_000030 - - XLOC_000030 - TSS33 chr1:3201596-3201666 - - 1.6359e+07 0 5.96409e+07 OK 0 0 0 OK
+XLOC_000031 - - XLOC_000031 - TSS34 chr1:3201672-3201699 - - 0 0 0 OK 0 0 0 OK
+XLOC_000032 - - XLOC_000032 - TSS35 chr1:3201725-3201809 - - 1.5136e+07 0 4.63396e+07 OK 0 0 0 OK
+XLOC_000033 - - XLOC_000033 Xkr4 TSS36 chr1:3211521-3211561 - - 0 0 0 OK 0 0 0 OK
+XLOC_000034 - - XLOC_000034 Xkr4 TSS37 chr1:3212213-3212292 - - 0 0 0 OK 9.45986e+06 0 3.33035e+07 OK
+XLOC_000035 - - XLOC_000035 Xkr4 TSS38 chr1:3212367-3212439 - - 0 0 0 OK 2.80837e+07 0 8.76584e+07 OK
+XLOC_000036 - - XLOC_000036 Xkr4 TSS39 chr1:3212717-3212801 - - 3.784e+06 0 1.44868e+07 OK 0 0 0 OK
+XLOC_000037 - - XLOC_000037 Xkr4 TSS40 chr1:3213095-3213242 - - 5.10781e+06 0 1.69588e+07 OK 2.08209e+06 0 8.1421e+06 OK
+XLOC_000038 - - XLOC_000038 Xkr4 TSS41 chr1:3240606-3240633 - - 0 0 0 OK 0 0 0 OK
+XLOC_000039 - - XLOC_000039 Xkr4 TSS42 chr1:3242479-3242512 - - 0 0 0 OK 0 0 0 OK
+XLOC_000040 - - XLOC_000040 Xkr4 TSS43 chr1:3242633-3242923 - - 48522.7 0 185766 OK 424400 0 1.30289e+06 OK
+XLOC_000041 - - XLOC_000041 Xkr4 TSS44 chr1:3242924-3243005 - - 0 0 0 OK 0 0 0 OK
+XLOC_000042 - - XLOC_000042 Xkr4 TSS45 chr1:3243018-3243079 - - 0 0 0 OK 3.03053e+07 0 1.0669e+08 OK
+XLOC_000043 - - XLOC_000043 Xkr4 TSS46 chr1:3243108-3243154 - - 8.616e+07 0 3.29857e+08 OK 0 0 0 OK
+XLOC_000044 - - XLOC_000044 Xkr4 TSS47 chr1:3243347-3243401 - - 0 0 0 OK 5.79991e+07 0 2.04186e+08 OK
+XLOC_000045 - - XLOC_000045 Xkr4 TSS48 chr1:3254079-3254106 - - 0 0 0 OK 0 0 0 OK
+XLOC_000046 - - XLOC_000046 Xkr4 TSS49 chr1:3256974-3257011 - - 0 0 0 OK 2.35423e+09 0 8.28806e+09 OK
+XLOC_000047 - - XLOC_000047 Xkr4 TSS50 chr1:3277155-3277182 - - 0 0 0 OK 0 0 0 OK
+XLOC_000048 - - XLOC_000048 Xkr4 TSS51 chr1:3277190-3277218 - - 0 0 0 OK 0 0 0 OK
+XLOC_000049 - - XLOC_000049 Xkr4 TSS52 chr1:3277913-3278390 - - 228872 0 561229 OK 47662.2 0 156103 OK
+XLOC_000050 - - XLOC_000050 Xkr4 TSS54 chr1:3280117-3280144 - - 0 0 0 OK 0 0 0 OK
+XLOC_000051 - - XLOC_000051 Xkr4 TSS55 chr1:3280498-3280525 - - 0 0 0 OK 0 0 0 OK
+XLOC_000052 - - XLOC_000052 Xkr4 TSS56 chr1:3280686-3280741 - - 0 0 0 OK 2.61334e+07 0 1.02193e+08 OK
+XLOC_000053 - - XLOC_000053 Xkr4 TSS57 chr1:3282504-3282531 - - 0 0 0 OK 0 0 0 OK
+XLOC_000054 - - XLOC_000054 Xkr4 TSS58 chr1:3282650-3282677 - - 0 0 0 OK 0 0 0 OK
+XLOC_000055 - - XLOC_000055 Xkr4 TSS59 chr1:3282760-3282832 - - 0 0 0 OK 0 0 0 OK
+XLOC_000056 - - XLOC_000056 Xkr4 TSS60 chr1:3284966-3284993 - - 0 0 0 OK 0 0 0 OK
+XLOC_000057 - - XLOC_000057 Xkr4 TSS61 chr1:3290488-3290553 - - 0 0 0 OK 1.11503e+07 0 4.36026e+07 OK
+XLOC_000058 - - XLOC_000058 Xkr4 TSS62 chr1:3290798-3290859 - - 1.55919e+07 0 5.96926e+07 OK 0 0 0 OK
+XLOC_000059 - - XLOC_000059 Xkr4 TSS63 chr1:3290919-3291273 - - 294879 0 740137 OK 85971.3 0 281572 OK
+XLOC_000060 - - XLOC_000060 Xkr4 TSS65,TSS66 chr1:3299443-3299664 - - 807732 0 2.39786e+06 OK 156995 0 641748 OK
+XLOC_000061 - - XLOC_000061 Xkr4 TSS67 chr1:3299691-3299733 - - 0 0 0 OK 0 0 0 OK
+XLOC_000062 - - XLOC_000062 Xkr4 TSS68 chr1:3300051-3300078 - - 0 0 0 OK 0 0 0 OK
+XLOC_000063 - - XLOC_000063 Xkr4 TSS69 chr1:3307748-3307775 - - 0 0 0 OK 0 0 0 OK
+XLOC_000064 - - XLOC_000064 Xkr4 TSS70 chr1:3318620-3318647 - - 0 0 0 OK 0 0 0 OK
+XLOC_000065 - - XLOC_000065 Xkr4 TSS71 chr1:3318999-3319051 - - 0 0 0 OK 0 0 0 OK
+XLOC_000066 - - XLOC_000066 Xkr4 TSS72 chr1:3330527-3330554 - - 0 0 0 OK 0 0 0 OK
+XLOC_000067 - - XLOC_000067 Xkr4 TSS73 chr1:3351240-3351311 - - 7.68169e+06 0 2.94088e+07 OK 0 0 0 OK
+XLOC_000068 - - XLOC_000068 Xkr4 TSS74 chr1:3355887-3356119 - - 504790 0 1.59712e+06 OK 0 0 0 OK
+XLOC_000069 - - XLOC_000069 Xkr4 TSS75 chr1:3356180-3356225 - - 1.02717e+08 0 3.93246e+08 OK 0 0 0 OK
+XLOC_000070 - - XLOC_000070 Xkr4 TSS76 chr1:3363076-3363176 - - 3.81001e+06 0 1.38903e+07 OK 0 0 0 OK
+XLOC_000071 - - XLOC_000071 Xkr4 TSS77 chr1:3363214-3363278 - - 0 0 0 OK 0 0 0 OK
+XLOC_000072 - - XLOC_000072 Xkr4 TSS78 chr1:3363387-3363446 - - 5.53654e+07 0 1.77783e+08 OK 0 0 0 OK
+XLOC_000073 - - XLOC_000073 Xkr4 TSS79 chr1:3363753-3363849 - - 0 0 0 OK 0 0 0 OK
+XLOC_000074 - - XLOC_000074 Xkr4 TSS80 chr1:3364871-3364919 - - 6.28966e+07 0 2.40795e+08 OK 0 0 0 OK
+XLOC_000075 - - XLOC_000075 Xkr4 TSS81 chr1:3367135-3367162 - - 0 0 0 OK 0 0 0 OK
+XLOC_000076 - - XLOC_000076 Xkr4 TSS82 chr1:3367210-3367237 - - 0 0 0 OK 0 0 0 OK
+XLOC_000077 - - XLOC_000077 Xkr4 TSS83 chr1:3367333-3367382 - - 0 0 0 OK 0 0 0 OK
+XLOC_000078 - - XLOC_000078 Xkr4 TSS84 chr1:3369580-3369607 - - 0 0 0 OK 0 0 0 OK
+XLOC_000079 - - XLOC_000079 Xkr4 TSS85 chr1:3375001-3375028 - - 0 0 0 OK 0 0 0 OK
+XLOC_000080 - - XLOC_000080 Xkr4 TSS86 chr1:3377211-3377262 - - 0 0 0 OK 0 0 0 OK
+XLOC_000081 - - XLOC_000081 Xkr4 TSS87 chr1:3379888-3379915 - - 0 0 0 OK 0 0 0 OK
+XLOC_000082 - - XLOC_000082 Xkr4 TSS88 chr1:3386739-3386836 - - 0 0 0 OK 0 0 0 OK
+XLOC_000083 - - XLOC_000083 Xkr4 TSS89 chr1:3391325-3391352 - - 0 0 0 OK 0 0 0 OK
+XLOC_000084 - - XLOC_000084 Xkr4 TSS90 chr1:3435841-3435880 - - 0 0 0 OK 0 0 0 OK
+XLOC_000085 - - XLOC_000085 Xkr4 TSS91 chr1:3447761-3447788 - - 0 0 0 OK 0 0 0 OK
+XLOC_000086 - - XLOC_000086 Xkr4 TSS92 chr1:3450906-3450965 - - 0 0 0 OK 0 0 0 OK
+XLOC_000087 - - XLOC_000087 Xkr4 TSS93 chr1:3451051-3451109 - - 0 0 0 OK 0 0 0 OK
diff -r 9a9e3e83889b -r 9ba750f285e3 test-data/isoforms.exp
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/isoforms.exp Tue Oct 13 12:37:38 2015 -0400
@@ -0,0 +1,91 @@
+test_id gene_id gene locus sample_1 sample_2 status value_1 value_2 log2(fold_change) test_stat p_value q_value significant
+TCONS_00000001 XLOC_000001 Xkr4 chr1:3204754-3204833 q1 q2 OK 0 9.45986e+06 inf -nan 0.01975 0.101571 no
+TCONS_00000002 XLOC_000002 - chr1:3111449-3111490 q1 q2 OK 0 2.43637e+08 inf -nan 0.12465 0.186975 no
+TCONS_00000003 XLOC_000003 - chr1:3111545-3111576 q1 q2 NOTEST 0 0 0 0 1 1 no
+TCONS_00000009 XLOC_000011 - chr1:3192441-3192494 q1 q2 OK 0 9.7002e+07 inf -nan 0.07975 0.186975 no
+TCONS_00000010 XLOC_000012 - chr1:3192550-3192629 q1 q2 OK 0 4.72993e+06 inf -nan 0.12465 0.186975 no
+TCONS_00000011 XLOC_000014 - chr1:3192731-3192811 q1 q2 NOTEST 0 0 0 0 1 1 no
+TCONS_00000012 XLOC_000015 - chr1:3192940-3193042 q1 q2 OK 0 6.86386e+06 inf -nan 0.0612 0.186975 no
+TCONS_00000013 XLOC_000016 - chr1:3194185-3194226 q1 q2 OK 0 2.43637e+08 inf -nan 0.12465 0.186975 no
+TCONS_00000014 XLOC_000017 - chr1:3194302-3194329 q1 q2 NOTEST 0 0 0 0 1 1 no
+TCONS_00000015 XLOC_000019 - chr1:3195083-3195110 q1 q2 NOTEST 0 0 0 0 1 1 no
+TCONS_00000016 XLOC_000020 - chr1:3195450-3195477 q1 q2 NOTEST 0 0 0 0 1 1 no
+TCONS_00000017 XLOC_000021 - chr1:3197089-3197116 q1 q2 NOTEST 0 0 0 0 1 1 no
+TCONS_00000018 XLOC_000022 - chr1:3197246-3197273 q1 q2 NOTEST 0 0 0 0 1 1 no
+TCONS_00000019 XLOC_000023 - chr1:3197346-3197373 q1 q2 NOTEST 0 0 0 0 1 1 no
+TCONS_00000020 XLOC_000025 - chr1:3200022-3200191 q1 q2 OK 826392 803108 -0.0412311 -0.0180163 0.8625 0.887143 no
+TCONS_00000021 XLOC_000026 - chr1:3200325-3200352 q1 q2 NOTEST 0 0 0 0 1 1 no
+TCONS_00000022 XLOC_000029 - chr1:3201077-3201481 q1 q2 OK 66791.3 324548 2.2807 1.1905 0.3026 0.380545 no
+TCONS_00000023 XLOC_000031 - chr1:3201672-3201699 q1 q2 NOTEST 0 0 0 0 1 1 no
+TCONS_00000024 XLOC_000034 Xkr4 chr1:3212213-3212292 q1 q2 OK 0 9.45986e+06 inf -nan 0.01975 0.101571 no
+TCONS_00000025 XLOC_000035 Xkr4 chr1:3212367-3212439 q1 q2 OK 0 2.80837e+07 inf -nan 0.0612 0.186975 no
+TCONS_00000026 XLOC_000037 Xkr4 chr1:3213095-3213242 q1 q2 OK 4.24463e+06 2.08209e+06 -1.0276 -0.36063 0.3844 0.435206 no
+TCONS_00000027 XLOC_000040 Xkr4 chr1:3242633-3242923 q1 q2 OK 48522.7 424400 3.12869 1.23747 0.38685 0.435206 no
+TCONS_00000028 XLOC_000042 Xkr4 chr1:3243018-3243079 q1 q2 OK 0 3.03053e+07 inf -nan 0.01975 0.101571 no
+TCONS_00000029 XLOC_000044 Xkr4 chr1:3243347-3243401 q1 q2 OK 0 5.79991e+07 inf -nan 0.01975 0.101571 no
+TCONS_00000030 XLOC_000046 Xkr4 chr1:3256974-3257011 q1 q2 OK 0 2.35423e+09 inf -nan 0.01975 0.101571 no
+TCONS_00000031 XLOC_000048 Xkr4 chr1:3277190-3277218 q1 q2 NOTEST 0 0 0 0 1 1 no
+TCONS_00000033 XLOC_000052 Xkr4 chr1:3280686-3280741 q1 q2 OK 0 2.61334e+07 inf -nan 0.12465 0.186975 no
+TCONS_00000034 XLOC_000057 Xkr4 chr1:3290488-3290553 q1 q2 OK 0 1.11503e+07 inf -nan 0.12465 0.186975 no
+TCONS_00000037 XLOC_000060 Xkr4 chr1:3299443-3299664 q1 q2 NOTEST 0 0 0 0 1 1 no
+TCONS_00000038 XLOC_000062 Xkr4 chr1:3300051-3300078 q1 q2 NOTEST 0 0 0 0 1 1 no
+TCONS_00000039 XLOC_000065 Xkr4 chr1:3318999-3319051 q1 q2 NOTEST 0 0 0 0 1 1 no
+TCONS_00000040 XLOC_000068 Xkr4 chr1:3355887-3356119 q1 q2 NOTEST 0 0 0 0 1 1 no
+TCONS_00000041 XLOC_000071 Xkr4 chr1:3363214-3363278 q1 q2 NOTEST 0 0 0 0 1 1 no
+TCONS_00000042 XLOC_000073 Xkr4 chr1:3363753-3363849 q1 q2 NOTEST 0 0 0 0 1 1 no
+TCONS_00000043 XLOC_000075 Xkr4 chr1:3367135-3367162 q1 q2 NOTEST 0 0 0 0 1 1 no
+TCONS_00000044 XLOC_000077 Xkr4 chr1:3367333-3367382 q1 q2 NOTEST 0 0 0 0 1 1 no
+TCONS_00000045 XLOC_000080 Xkr4 chr1:3377211-3377262 q1 q2 NOTEST 0 0 0 0 1 1 no
+TCONS_00000046 XLOC_000083 Xkr4 chr1:3391325-3391352 q1 q2 NOTEST 0 0 0 0 1 1 no
+TCONS_00000047 XLOC_000084 Xkr4 chr1:3435841-3435880 q1 q2 NOTEST 0 0 0 0 1 1 no
+TCONS_00000048 XLOC_000085 Xkr4 chr1:3447761-3447788 q1 q2 NOTEST 0 0 0 0 1 1 no
+TCONS_00000049 XLOC_000086 Xkr4 chr1:3450906-3450965 q1 q2 NOTEST 0 0 0 0 1 1 no
+TCONS_00000050 XLOC_000087 Xkr4 chr1:3451051-3451109 q1 q2 NOTEST 0 0 0 0 1 1 no
+TCONS_00000051 XLOC_000004 - chr1:3174765-3174792 q1 q2 NOTEST 0 0 0 0 1 1 no
+TCONS_00000052 XLOC_000005 - chr1:3187401-3187428 q1 q2 NOTEST 0 0 0 0 1 1 no
+TCONS_00000053 XLOC_000006 - chr1:3188521-3188548 q1 q2 NOTEST 0 0 0 0 1 1 no
+TCONS_00000054 XLOC_000007 - chr1:3189810-3190789 q1 q2 OK 358326 522345 0.543731 1.1445 0.1952 0.270969 no
+TCONS_00000055 XLOC_000008 - chr1:3190858-3191434 q1 q2 OK 408511 420354 0.0412311 0.0469899 0.96715 0.96715 no
+TCONS_00000056 XLOC_000009 - chr1:3191512-3192077 q1 q2 OK 433286 842157 0.958769 1.27887 0.20385 0.2718 no
+TCONS_00000057 XLOC_000010 - chr1:3192250-3192336 q1 q2 OK 3.44151e+06 3.34455e+06 -0.0412311 -0.014084 0.67715 0.716982 no
+TCONS_00000058 XLOC_000013 - chr1:3192649-3192676 q1 q2 NOTEST 0 0 0 0 1 1 no
+TCONS_00000059 XLOC_000018 - chr1:3194706-3194733 q1 q2 NOTEST 0 0 0 0 1 1 no
+TCONS_00000060 XLOC_000024 - chr1:3197425-3197452 q1 q2 NOTEST 0 0 0 0 1 1 no
+TCONS_00000062 XLOC_000027 - chr1:3200430-3200457 q1 q2 NOTEST 0 0 0 0 1 1 no
+TCONS_00000063 XLOC_000028 - chr1:3201007-3201039 q1 q2 NOTEST 0 0 0 0 1 1 no
+TCONS_00000065 XLOC_000030 - chr1:3201596-3201666 q1 q2 OK 1.6359e+07 0 -inf -nan 0.0148 0.101571 no
+TCONS_00000066 XLOC_000032 - chr1:3201725-3201809 q1 q2 OK 1.5136e+07 0 -inf -nan 0.06005 0.186975 no
+TCONS_00000067 XLOC_000033 Xkr4 chr1:3211521-3211561 q1 q2 NOTEST 0 0 0 0 1 1 no
+TCONS_00000068 XLOC_000036 Xkr4 chr1:3212717-3212801 q1 q2 OK 3.784e+06 0 -inf -nan 0.12165 0.186975 no
+TCONS_00000069 XLOC_000037 Xkr4 chr1:3213095-3213242 q1 q2 OK 863189 0 -inf -nan 0.1957 0.270969 no
+TCONS_00000070 XLOC_000038 Xkr4 chr1:3240606-3240633 q1 q2 NOTEST 0 0 0 0 1 1 no
+TCONS_00000071 XLOC_000039 Xkr4 chr1:3242479-3242512 q1 q2 NOTEST 0 0 0 0 1 1 no
+TCONS_00000072 XLOC_000041 Xkr4 chr1:3242924-3243005 q1 q2 NOTEST 0 0 0 0 1 1 no
+TCONS_00000073 XLOC_000043 Xkr4 chr1:3243108-3243154 q1 q2 OK 8.616e+07 0 -inf -nan 0.12165 0.186975 no
+TCONS_00000074 XLOC_000045 Xkr4 chr1:3254079-3254106 q1 q2 NOTEST 0 0 0 0 1 1 no
+TCONS_00000075 XLOC_000047 Xkr4 chr1:3277155-3277182 q1 q2 NOTEST 0 0 0 0 1 1 no
+TCONS_00000076 XLOC_000049 Xkr4 chr1:3277913-3278390 q1 q2 OK 228872 47662.2 -2.26362 -1.16262 0.30655 0.380545 no
+TCONS_00000077 XLOC_000050 Xkr4 chr1:3280117-3280144 q1 q2 NOTEST 0 0 0 0 1 1 no
+TCONS_00000078 XLOC_000051 Xkr4 chr1:3280498-3280525 q1 q2 NOTEST 0 0 0 0 1 1 no
+TCONS_00000079 XLOC_000053 Xkr4 chr1:3282504-3282531 q1 q2 NOTEST 0 0 0 0 1 1 no
+TCONS_00000080 XLOC_000054 Xkr4 chr1:3282650-3282677 q1 q2 NOTEST 0 0 0 0 1 1 no
+TCONS_00000081 XLOC_000055 Xkr4 chr1:3282760-3282832 q1 q2 NOTEST 0 0 0 0 1 1 no
+TCONS_00000082 XLOC_000056 Xkr4 chr1:3284966-3284993 q1 q2 NOTEST 0 0 0 0 1 1 no
+TCONS_00000083 XLOC_000058 Xkr4 chr1:3290798-3290859 q1 q2 OK 1.55919e+07 0 -inf -nan 0.12165 0.186975 no
+TCONS_00000084 XLOC_000059 Xkr4 chr1:3290919-3291273 q1 q2 OK 294879 85971.3 -1.7782 -0.902752 0.36915 0.435206 no
+TCONS_00000085 XLOC_000060 Xkr4 chr1:3299443-3299664 q1 q2 OK 807732 156995 -2.36316 -0.933704 0.4205 0.458727 no
+TCONS_00000086 XLOC_000061 Xkr4 chr1:3299691-3299733 q1 q2 NOTEST 0 0 0 0 1 1 no
+TCONS_00000087 XLOC_000063 Xkr4 chr1:3307748-3307775 q1 q2 NOTEST 0 0 0 0 1 1 no
+TCONS_00000088 XLOC_000064 Xkr4 chr1:3318620-3318647 q1 q2 NOTEST 0 0 0 0 1 1 no
+TCONS_00000089 XLOC_000066 Xkr4 chr1:3330527-3330554 q1 q2 NOTEST 0 0 0 0 1 1 no
+TCONS_00000090 XLOC_000067 Xkr4 chr1:3351240-3351311 q1 q2 OK 7.68169e+06 0 -inf -nan 0.12165 0.186975 no
+TCONS_00000091 XLOC_000068 Xkr4 chr1:3355887-3356119 q1 q2 OK 504790 0 -inf -nan 0.05945 0.186975 no
+TCONS_00000092 XLOC_000069 Xkr4 chr1:3356180-3356225 q1 q2 OK 1.02717e+08 0 -inf -nan 0.12165 0.186975 no
+TCONS_00000093 XLOC_000070 Xkr4 chr1:3363076-3363176 q1 q2 OK 3.81001e+06 0 -inf -nan 0.0148 0.101571 no
+TCONS_00000094 XLOC_000072 Xkr4 chr1:3363387-3363446 q1 q2 OK 5.53654e+07 0 -inf -nan 0.0773 0.186975 no
+TCONS_00000095 XLOC_000074 Xkr4 chr1:3364871-3364919 q1 q2 OK 6.28966e+07 0 -inf -nan 0.12165 0.186975 no
+TCONS_00000096 XLOC_000076 Xkr4 chr1:3367210-3367237 q1 q2 NOTEST 0 0 0 0 1 1 no
+TCONS_00000097 XLOC_000078 Xkr4 chr1:3369580-3369607 q1 q2 NOTEST 0 0 0 0 1 1 no
+TCONS_00000098 XLOC_000079 Xkr4 chr1:3375001-3375028 q1 q2 NOTEST 0 0 0 0 1 1 no
+TCONS_00000099 XLOC_000081 Xkr4 chr1:3379888-3379915 q1 q2 NOTEST 0 0 0 0 1 1 no
+TCONS_00000100 XLOC_000082 Xkr4 chr1:3386739-3386836 q1 q2 NOTEST 0 0 0 0 1 1 no
diff -r 9a9e3e83889b -r 9ba750f285e3 test-data/isoforms.fpkm_tracking
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/isoforms.fpkm_tracking Tue Oct 13 12:37:38 2015 -0400
@@ -0,0 +1,91 @@
+tracking_id class_code nearest_ref_id gene_id gene_short_name tss_id locus length coverage q1_FPKM q1_conf_lo q1_conf_hi q1_status q2_FPKM q2_conf_lo q2_conf_hi q2_status
+TCONS_00000001 c Xkr4 XLOC_000001 Xkr4 TSS1 chr1:3204754-3204833 79 - 0 0 0 OK 9.45986e+06 0 3.33035e+07 OK
+TCONS_00000002 - - XLOC_000002 - TSS2 chr1:3111449-3111490 41 - 0 0 0 OK 2.43637e+08 0 9.52723e+08 OK
+TCONS_00000003 - - XLOC_000003 - TSS3 chr1:3111545-3111576 31 - 0 0 0 OK 0 0 0 OK
+TCONS_00000009 - - XLOC_000011 - TSS14 chr1:3192441-3192494 53 - 0 0 0 OK 9.7002e+07 0 3.17699e+08 OK
+TCONS_00000010 - - XLOC_000012 - TSS15 chr1:3192550-3192629 79 - 0 0 0 OK 4.72993e+06 0 1.84961e+07 OK
+TCONS_00000011 - - XLOC_000014 - TSS17 chr1:3192731-3192811 80 - 0 0 0 OK 0 0 0 OK
+TCONS_00000012 - - XLOC_000015 - TSS18 chr1:3192940-3193042 102 - 0 0 0 OK 6.86386e+06 0 2.14243e+07 OK
+TCONS_00000013 - - XLOC_000016 - TSS19 chr1:3194185-3194226 41 - 0 0 0 OK 2.43637e+08 0 9.52723e+08 OK
+TCONS_00000014 - - XLOC_000017 - TSS20 chr1:3194302-3194329 27 - 0 0 0 OK 0 0 0 OK
+TCONS_00000015 - - XLOC_000019 - TSS22 chr1:3195083-3195110 27 - 0 0 0 OK 0 0 0 OK
+TCONS_00000016 - - XLOC_000020 - TSS23 chr1:3195450-3195477 27 - 0 0 0 OK 0 0 0 OK
+TCONS_00000017 - - XLOC_000021 - TSS24 chr1:3197089-3197116 27 - 0 0 0 OK 0 0 0 OK
+TCONS_00000018 - - XLOC_000022 - TSS25 chr1:3197246-3197273 27 - 0 0 0 OK 0 0 0 OK
+TCONS_00000019 - - XLOC_000023 - TSS26 chr1:3197346-3197373 27 - 0 0 0 OK 0 0 0 OK
+TCONS_00000020 - - XLOC_000025 - TSS28 chr1:3200022-3200191 169 - 826392 0 2.65361e+06 OK 803108 0 2.63033e+06 OK
+TCONS_00000021 - - XLOC_000026 - TSS29 chr1:3200325-3200352 27 - 0 0 0 OK 0 0 0 OK
+TCONS_00000022 - - XLOC_000029 - TSS32 chr1:3201077-3201481 404 - 66791.3 0 214473 OK 324548 0 802006 OK
+TCONS_00000023 - - XLOC_000031 - TSS34 chr1:3201672-3201699 27 - 0 0 0 OK 0 0 0 OK
+TCONS_00000024 i Xkr4 XLOC_000034 Xkr4 TSS37 chr1:3212213-3212292 79 - 0 0 0 OK 9.45986e+06 0 3.33035e+07 OK
+TCONS_00000025 i Xkr4 XLOC_000035 Xkr4 TSS38 chr1:3212367-3212439 72 - 0 0 0 OK 2.80837e+07 0 8.76584e+07 OK
+TCONS_00000026 i Xkr4 XLOC_000037 Xkr4 TSS40 chr1:3213095-3213242 97 - 4.24463e+06 0 1.55814e+07 OK 2.08209e+06 0 8.14187e+06 OK
+TCONS_00000027 i Xkr4 XLOC_000040 Xkr4 TSS43 chr1:3242633-3242923 290 - 48522.7 0 185766 OK 424400 0 1.30289e+06 OK
+TCONS_00000028 i Xkr4 XLOC_000042 Xkr4 TSS45 chr1:3243018-3243079 61 - 0 0 0 OK 3.03053e+07 0 1.0669e+08 OK
+TCONS_00000029 i Xkr4 XLOC_000044 Xkr4 TSS47 chr1:3243347-3243401 54 - 0 0 0 OK 5.79991e+07 0 2.04186e+08 OK
+TCONS_00000030 i Xkr4 XLOC_000046 Xkr4 TSS49 chr1:3256974-3257011 37 - 0 0 0 OK 2.35423e+09 0 8.28806e+09 OK
+TCONS_00000031 i Xkr4 XLOC_000048 Xkr4 TSS51 chr1:3277190-3277218 28 - 0 0 0 OK 0 0 0 OK
+TCONS_00000033 i Xkr4 XLOC_000052 Xkr4 TSS56 chr1:3280686-3280741 55 - 0 0 0 OK 2.61334e+07 0 1.02193e+08 OK
+TCONS_00000034 i Xkr4 XLOC_000057 Xkr4 TSS61 chr1:3290488-3290553 65 - 0 0 0 OK 1.11503e+07 0 4.36026e+07 OK
+TCONS_00000037 i Xkr4 XLOC_000060 Xkr4 TSS66 chr1:3299443-3299664 55 - 0 0 163195 OK 0 0 163195 OK
+TCONS_00000038 i Xkr4 XLOC_000062 Xkr4 TSS68 chr1:3300051-3300078 27 - 0 0 0 OK 0 0 0 OK
+TCONS_00000039 i Xkr4 XLOC_000065 Xkr4 TSS71 chr1:3318999-3319051 52 - 0 0 0 OK 0 0 0 OK
+TCONS_00000040 i Xkr4 XLOC_000068 Xkr4 TSS74 chr1:3355887-3356119 27 - 0 0 332434 OK 0 0 0 OK
+TCONS_00000041 i Xkr4 XLOC_000071 Xkr4 TSS77 chr1:3363214-3363278 64 - 0 0 0 OK 0 0 0 OK
+TCONS_00000042 i Xkr4 XLOC_000073 Xkr4 TSS79 chr1:3363753-3363849 96 - 0 0 0 OK 0 0 0 OK
+TCONS_00000043 i Xkr4 XLOC_000075 Xkr4 TSS81 chr1:3367135-3367162 27 - 0 0 0 OK 0 0 0 OK
+TCONS_00000044 i Xkr4 XLOC_000077 Xkr4 TSS83 chr1:3367333-3367382 49 - 0 0 0 OK 0 0 0 OK
+TCONS_00000045 i Xkr4 XLOC_000080 Xkr4 TSS86 chr1:3377211-3377262 51 - 0 0 0 OK 0 0 0 OK
+TCONS_00000046 i Xkr4 XLOC_000083 Xkr4 TSS89 chr1:3391325-3391352 27 - 0 0 0 OK 0 0 0 OK
+TCONS_00000047 i Xkr4 XLOC_000084 Xkr4 TSS90 chr1:3435841-3435880 39 - 0 0 0 OK 0 0 0 OK
+TCONS_00000048 i Xkr4 XLOC_000085 Xkr4 TSS91 chr1:3447761-3447788 27 - 0 0 0 OK 0 0 0 OK
+TCONS_00000049 i Xkr4 XLOC_000086 Xkr4 TSS92 chr1:3450906-3450965 59 - 0 0 0 OK 0 0 0 OK
+TCONS_00000050 i Xkr4 XLOC_000087 Xkr4 TSS93 chr1:3451051-3451109 58 - 0 0 0 OK 0 0 0 OK
+TCONS_00000051 - - XLOC_000004 - TSS4 chr1:3174765-3174792 27 - 0 0 0 OK 0 0 0 OK
+TCONS_00000052 - - XLOC_000005 - TSS5 chr1:3187401-3187428 27 - 0 0 0 OK 0 0 0 OK
+TCONS_00000053 - - XLOC_000006 - TSS6 chr1:3188521-3188548 27 - 0 0 0 OK 0 0 0 OK
+TCONS_00000054 - - XLOC_000007 - TSS7 chr1:3189810-3190789 979 - 358326 135086 581565 OK 522345 410780 633911 OK
+TCONS_00000055 - - XLOC_000008 - TSS10 chr1:3190858-3191434 576 - 408511 54526.1 762496 OK 420354 61509.1 779200 OK
+TCONS_00000056 - - XLOC_000009 - TSS11 chr1:3191512-3192077 565 - 433286 63552.3 803020 OK 842157 342520 1.34179e+06 OK
+TCONS_00000057 - - XLOC_000010 - TSS13 chr1:3192250-3192336 86 - 3.44151e+06 0 1.31756e+07 OK 3.34455e+06 0 1.30786e+07 OK
+TCONS_00000058 - - XLOC_000013 - TSS16 chr1:3192649-3192676 27 - 0 0 0 OK 0 0 0 OK
+TCONS_00000059 - - XLOC_000018 - TSS21 chr1:3194706-3194733 27 - 0 0 0 OK 0 0 0 OK
+TCONS_00000060 - - XLOC_000024 - TSS27 chr1:3197425-3197452 27 - 0 0 0 OK 0 0 0 OK
+TCONS_00000062 - - XLOC_000027 - TSS30 chr1:3200430-3200457 27 - 0 0 0 OK 0 0 0 OK
+TCONS_00000063 - - XLOC_000028 - TSS31 chr1:3201007-3201039 32 - 0 0 0 OK 0 0 0 OK
+TCONS_00000065 - - XLOC_000030 - TSS33 chr1:3201596-3201666 70 - 1.6359e+07 0 5.96409e+07 OK 0 0 0 OK
+TCONS_00000066 - - XLOC_000032 - TSS35 chr1:3201725-3201809 84 - 1.5136e+07 0 4.63396e+07 OK 0 0 0 OK
+TCONS_00000067 i Xkr4 XLOC_000033 Xkr4 TSS36 chr1:3211521-3211561 40 - 0 0 0 OK 0 0 0 OK
+TCONS_00000068 i Xkr4 XLOC_000036 Xkr4 TSS39 chr1:3212717-3212801 84 - 3.784e+06 0 1.44868e+07 OK 0 0 0 OK
+TCONS_00000069 i Xkr4 XLOC_000037 Xkr4 TSS40 chr1:3213095-3213242 124 - 863189 0 4.25222e+06 OK 0 0 72384.9 OK
+TCONS_00000070 i Xkr4 XLOC_000038 Xkr4 TSS41 chr1:3240606-3240633 27 - 0 0 0 OK 0 0 0 OK
+TCONS_00000071 i Xkr4 XLOC_000039 Xkr4 TSS42 chr1:3242479-3242512 33 - 0 0 0 OK 0 0 0 OK
+TCONS_00000072 i Xkr4 XLOC_000041 Xkr4 TSS44 chr1:3242924-3243005 81 - 0 0 0 OK 0 0 0 OK
+TCONS_00000073 i Xkr4 XLOC_000043 Xkr4 TSS46 chr1:3243108-3243154 46 - 8.616e+07 0 3.29857e+08 OK 0 0 0 OK
+TCONS_00000074 i Xkr4 XLOC_000045 Xkr4 TSS48 chr1:3254079-3254106 27 - 0 0 0 OK 0 0 0 OK
+TCONS_00000075 i Xkr4 XLOC_000047 Xkr4 TSS50 chr1:3277155-3277182 27 - 0 0 0 OK 0 0 0 OK
+TCONS_00000076 i Xkr4 XLOC_000049 Xkr4 TSS52 chr1:3277913-3278390 477 - 228872 0 561229 OK 47662.2 0 156103 OK
+TCONS_00000077 i Xkr4 XLOC_000050 Xkr4 TSS54 chr1:3280117-3280144 27 - 0 0 0 OK 0 0 0 OK
+TCONS_00000078 i Xkr4 XLOC_000051 Xkr4 TSS55 chr1:3280498-3280525 27 - 0 0 0 OK 0 0 0 OK
+TCONS_00000079 i Xkr4 XLOC_000053 Xkr4 TSS57 chr1:3282504-3282531 27 - 0 0 0 OK 0 0 0 OK
+TCONS_00000080 i Xkr4 XLOC_000054 Xkr4 TSS58 chr1:3282650-3282677 27 - 0 0 0 OK 0 0 0 OK
+TCONS_00000081 i Xkr4 XLOC_000055 Xkr4 TSS59 chr1:3282760-3282832 72 - 0 0 0 OK 0 0 0 OK
+TCONS_00000082 i Xkr4 XLOC_000056 Xkr4 TSS60 chr1:3284966-3284993 27 - 0 0 0 OK 0 0 0 OK
+TCONS_00000083 i Xkr4 XLOC_000058 Xkr4 TSS62 chr1:3290798-3290859 61 - 1.55919e+07 0 5.96926e+07 OK 0 0 0 OK
+TCONS_00000084 i Xkr4 XLOC_000059 Xkr4 TSS63 chr1:3290919-3291273 354 - 294879 0 740137 OK 85971.3 0 281572 OK
+TCONS_00000085 i Xkr4 XLOC_000060 Xkr4 TSS65 chr1:3299443-3299664 197 - 807732 0 2.39056e+06 OK 156995 0 613917 OK
+TCONS_00000086 i Xkr4 XLOC_000061 Xkr4 TSS67 chr1:3299691-3299733 42 - 0 0 0 OK 0 0 0 OK
+TCONS_00000087 i Xkr4 XLOC_000063 Xkr4 TSS69 chr1:3307748-3307775 27 - 0 0 0 OK 0 0 0 OK
+TCONS_00000088 i Xkr4 XLOC_000064 Xkr4 TSS70 chr1:3318620-3318647 27 - 0 0 0 OK 0 0 0 OK
+TCONS_00000089 i Xkr4 XLOC_000066 Xkr4 TSS72 chr1:3330527-3330554 27 - 0 0 0 OK 0 0 0 OK
+TCONS_00000090 i Xkr4 XLOC_000067 Xkr4 TSS73 chr1:3351240-3351311 71 - 7.68169e+06 0 2.94088e+07 OK 0 0 0 OK
+TCONS_00000091 i Xkr4 XLOC_000068 Xkr4 TSS74 chr1:3355887-3356119 212 - 504790 0 1.54544e+06 OK 0 0 0 OK
+TCONS_00000092 i Xkr4 XLOC_000069 Xkr4 TSS75 chr1:3356180-3356225 45 - 1.02717e+08 0 3.93246e+08 OK 0 0 0 OK
+TCONS_00000093 i Xkr4 XLOC_000070 Xkr4 TSS76 chr1:3363076-3363176 100 - 3.81001e+06 0 1.38903e+07 OK 0 0 0 OK
+TCONS_00000094 i Xkr4 XLOC_000072 Xkr4 TSS78 chr1:3363387-3363446 59 - 5.53654e+07 0 1.77783e+08 OK 0 0 0 OK
+TCONS_00000095 i Xkr4 XLOC_000074 Xkr4 TSS80 chr1:3364871-3364919 48 - 6.28966e+07 0 2.40795e+08 OK 0 0 0 OK
+TCONS_00000096 i Xkr4 XLOC_000076 Xkr4 TSS82 chr1:3367210-3367237 27 - 0 0 0 OK 0 0 0 OK
+TCONS_00000097 i Xkr4 XLOC_000078 Xkr4 TSS84 chr1:3369580-3369607 27 - 0 0 0 OK 0 0 0 OK
+TCONS_00000098 i Xkr4 XLOC_000079 Xkr4 TSS85 chr1:3375001-3375028 27 - 0 0 0 OK 0 0 0 OK
+TCONS_00000099 i Xkr4 XLOC_000081 Xkr4 TSS87 chr1:3379888-3379915 27 - 0 0 0 OK 0 0 0 OK
+TCONS_00000100 i Xkr4 XLOC_000082 Xkr4 TSS88 chr1:3386739-3386836 97 - 0 0 0 OK 0 0 0 OK
diff -r 9a9e3e83889b -r 9ba750f285e3 test-data/promoters.diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/promoters.diff Tue Oct 13 12:37:38 2015 -0400
@@ -0,0 +1,88 @@
+test_id gene_id gene locus sample_1 sample_2 status value_1 value_2 sqrt(JS) test_stat p_value q_value significant
+XLOC_000001 XLOC_000001 Xkr4 chr1:3204754-3204833 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000002 XLOC_000002 - chr1:3111449-3111490 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000003 XLOC_000003 - chr1:3111545-3111576 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000004 XLOC_000004 - chr1:3174765-3174792 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000005 XLOC_000005 - chr1:3187401-3187428 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000006 XLOC_000006 - chr1:3188521-3188548 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000007 XLOC_000007 - chr1:3189810-3190789 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000008 XLOC_000008 - chr1:3190858-3191434 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000009 XLOC_000009 - chr1:3191512-3192077 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000010 XLOC_000010 - chr1:3192250-3192336 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000011 XLOC_000011 - chr1:3192441-3192494 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000012 XLOC_000012 - chr1:3192550-3192629 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000013 XLOC_000013 - chr1:3192649-3192676 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000014 XLOC_000014 - chr1:3192731-3192811 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000015 XLOC_000015 - chr1:3192940-3193042 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000016 XLOC_000016 - chr1:3194185-3194226 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000017 XLOC_000017 - chr1:3194302-3194329 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000018 XLOC_000018 - chr1:3194706-3194733 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000019 XLOC_000019 - chr1:3195083-3195110 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000020 XLOC_000020 - chr1:3195450-3195477 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000021 XLOC_000021 - chr1:3197089-3197116 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000022 XLOC_000022 - chr1:3197246-3197273 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000023 XLOC_000023 - chr1:3197346-3197373 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000024 XLOC_000024 - chr1:3197425-3197452 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000025 XLOC_000025 - chr1:3200022-3200191 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000026 XLOC_000026 - chr1:3200325-3200352 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000027 XLOC_000027 - chr1:3200430-3200457 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000028 XLOC_000028 - chr1:3201007-3201039 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000029 XLOC_000029 - chr1:3201077-3201481 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000030 XLOC_000030 - chr1:3201596-3201666 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000031 XLOC_000031 - chr1:3201672-3201699 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000032 XLOC_000032 - chr1:3201725-3201809 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000033 XLOC_000033 Xkr4 chr1:3211521-3211561 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000034 XLOC_000034 Xkr4 chr1:3212213-3212292 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000035 XLOC_000035 Xkr4 chr1:3212367-3212439 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000036 XLOC_000036 Xkr4 chr1:3212717-3212801 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000037 XLOC_000037 Xkr4 chr1:3213095-3213242 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000038 XLOC_000038 Xkr4 chr1:3240606-3240633 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000039 XLOC_000039 Xkr4 chr1:3242479-3242512 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000040 XLOC_000040 Xkr4 chr1:3242633-3242923 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000041 XLOC_000041 Xkr4 chr1:3242924-3243005 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000042 XLOC_000042 Xkr4 chr1:3243018-3243079 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000043 XLOC_000043 Xkr4 chr1:3243108-3243154 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000044 XLOC_000044 Xkr4 chr1:3243347-3243401 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000045 XLOC_000045 Xkr4 chr1:3254079-3254106 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000046 XLOC_000046 Xkr4 chr1:3256974-3257011 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000047 XLOC_000047 Xkr4 chr1:3277155-3277182 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000048 XLOC_000048 Xkr4 chr1:3277190-3277218 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000049 XLOC_000049 Xkr4 chr1:3277913-3278390 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000050 XLOC_000050 Xkr4 chr1:3280117-3280144 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000051 XLOC_000051 Xkr4 chr1:3280498-3280525 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000052 XLOC_000052 Xkr4 chr1:3280686-3280741 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000053 XLOC_000053 Xkr4 chr1:3282504-3282531 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000054 XLOC_000054 Xkr4 chr1:3282650-3282677 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000055 XLOC_000055 Xkr4 chr1:3282760-3282832 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000056 XLOC_000056 Xkr4 chr1:3284966-3284993 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000057 XLOC_000057 Xkr4 chr1:3290488-3290553 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000058 XLOC_000058 Xkr4 chr1:3290798-3290859 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000059 XLOC_000059 Xkr4 chr1:3290919-3291273 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000060 XLOC_000060 Xkr4 chr1:3299443-3299664 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000061 XLOC_000061 Xkr4 chr1:3299691-3299733 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000062 XLOC_000062 Xkr4 chr1:3300051-3300078 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000063 XLOC_000063 Xkr4 chr1:3307748-3307775 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000064 XLOC_000064 Xkr4 chr1:3318620-3318647 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000065 XLOC_000065 Xkr4 chr1:3318999-3319051 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000066 XLOC_000066 Xkr4 chr1:3330527-3330554 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000067 XLOC_000067 Xkr4 chr1:3351240-3351311 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000068 XLOC_000068 Xkr4 chr1:3355887-3356119 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000069 XLOC_000069 Xkr4 chr1:3356180-3356225 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000070 XLOC_000070 Xkr4 chr1:3363076-3363176 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000071 XLOC_000071 Xkr4 chr1:3363214-3363278 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000072 XLOC_000072 Xkr4 chr1:3363387-3363446 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000073 XLOC_000073 Xkr4 chr1:3363753-3363849 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000074 XLOC_000074 Xkr4 chr1:3364871-3364919 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000075 XLOC_000075 Xkr4 chr1:3367135-3367162 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000076 XLOC_000076 Xkr4 chr1:3367210-3367237 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000077 XLOC_000077 Xkr4 chr1:3367333-3367382 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000078 XLOC_000078 Xkr4 chr1:3369580-3369607 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000079 XLOC_000079 Xkr4 chr1:3375001-3375028 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000080 XLOC_000080 Xkr4 chr1:3377211-3377262 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000081 XLOC_000081 Xkr4 chr1:3379888-3379915 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000082 XLOC_000082 Xkr4 chr1:3386739-3386836 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000083 XLOC_000083 Xkr4 chr1:3391325-3391352 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000084 XLOC_000084 Xkr4 chr1:3435841-3435880 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000085 XLOC_000085 Xkr4 chr1:3447761-3447788 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000086 XLOC_000086 Xkr4 chr1:3450906-3450965 q1 q2 NOTEST 0 0 0 0 1 1 no
+XLOC_000087 XLOC_000087 Xkr4 chr1:3451051-3451109 q1 q2 NOTEST 0 0 0 0 1 1 no
diff -r 9a9e3e83889b -r 9ba750f285e3 test-data/splicing.diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/splicing.diff Tue Oct 13 12:37:38 2015 -0400
@@ -0,0 +1,89 @@
+test_id gene_id gene locus sample_1 sample_2 status value_1 value_2 sqrt(JS) test_stat p_value q_value significant
+TSS1 XLOC_000001 Xkr4 chr1:3204754-3204833 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS10 XLOC_000008 - chr1:3190858-3191434 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS11 XLOC_000009 - chr1:3191512-3192077 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS13 XLOC_000010 - chr1:3192250-3192336 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS14 XLOC_000011 - chr1:3192441-3192494 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS15 XLOC_000012 - chr1:3192550-3192629 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS16 XLOC_000013 - chr1:3192649-3192676 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS17 XLOC_000014 - chr1:3192731-3192811 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS18 XLOC_000015 - chr1:3192940-3193042 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS19 XLOC_000016 - chr1:3194185-3194226 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS2 XLOC_000002 - chr1:3111449-3111490 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS20 XLOC_000017 - chr1:3194302-3194329 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS21 XLOC_000018 - chr1:3194706-3194733 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS22 XLOC_000019 - chr1:3195083-3195110 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS23 XLOC_000020 - chr1:3195450-3195477 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS24 XLOC_000021 - chr1:3197089-3197116 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS25 XLOC_000022 - chr1:3197246-3197273 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS26 XLOC_000023 - chr1:3197346-3197373 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS27 XLOC_000024 - chr1:3197425-3197452 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS28 XLOC_000025 - chr1:3200022-3200191 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS29 XLOC_000026 - chr1:3200325-3200352 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS3 XLOC_000003 - chr1:3111545-3111576 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS30 XLOC_000027 - chr1:3200430-3200457 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS31 XLOC_000028 - chr1:3201007-3201039 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS32 XLOC_000029 - chr1:3201077-3201481 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS33 XLOC_000030 - chr1:3201596-3201666 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS34 XLOC_000031 - chr1:3201672-3201699 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS35 XLOC_000032 - chr1:3201725-3201809 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS36 XLOC_000033 Xkr4 chr1:3211521-3211561 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS37 XLOC_000034 Xkr4 chr1:3212213-3212292 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS38 XLOC_000035 Xkr4 chr1:3212367-3212439 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS39 XLOC_000036 Xkr4 chr1:3212717-3212801 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS4 XLOC_000004 - chr1:3174765-3174792 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS40 XLOC_000037 Xkr4 chr1:3213095-3213242 q1 q2 NOTEST 0 0 0.249947 0 0.5526 1 no
+TSS41 XLOC_000038 Xkr4 chr1:3240606-3240633 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS42 XLOC_000039 Xkr4 chr1:3242479-3242512 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS43 XLOC_000040 Xkr4 chr1:3242633-3242923 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS44 XLOC_000041 Xkr4 chr1:3242924-3243005 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS45 XLOC_000042 Xkr4 chr1:3243018-3243079 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS46 XLOC_000043 Xkr4 chr1:3243108-3243154 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS47 XLOC_000044 Xkr4 chr1:3243347-3243401 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS48 XLOC_000045 Xkr4 chr1:3254079-3254106 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS49 XLOC_000046 Xkr4 chr1:3256974-3257011 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS5 XLOC_000005 - chr1:3187401-3187428 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS50 XLOC_000047 Xkr4 chr1:3277155-3277182 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS51 XLOC_000048 Xkr4 chr1:3277190-3277218 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS52 XLOC_000049 Xkr4 chr1:3277913-3278390 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS54 XLOC_000050 Xkr4 chr1:3280117-3280144 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS55 XLOC_000051 Xkr4 chr1:3280498-3280525 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS56 XLOC_000052 Xkr4 chr1:3280686-3280741 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS57 XLOC_000053 Xkr4 chr1:3282504-3282531 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS58 XLOC_000054 Xkr4 chr1:3282650-3282677 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS59 XLOC_000055 Xkr4 chr1:3282760-3282832 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS6 XLOC_000006 - chr1:3188521-3188548 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS60 XLOC_000056 Xkr4 chr1:3284966-3284993 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS61 XLOC_000057 Xkr4 chr1:3290488-3290553 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS62 XLOC_000058 Xkr4 chr1:3290798-3290859 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS63 XLOC_000059 Xkr4 chr1:3290919-3291273 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS65 XLOC_000060 Xkr4 chr1:3299443-3299664 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS66 XLOC_000060 Xkr4 chr1:3299443-3299664 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS67 XLOC_000061 Xkr4 chr1:3299691-3299733 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS68 XLOC_000062 Xkr4 chr1:3300051-3300078 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS69 XLOC_000063 Xkr4 chr1:3307748-3307775 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS7 XLOC_000007 - chr1:3189810-3190789 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS70 XLOC_000064 Xkr4 chr1:3318620-3318647 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS71 XLOC_000065 Xkr4 chr1:3318999-3319051 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS72 XLOC_000066 Xkr4 chr1:3330527-3330554 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS73 XLOC_000067 Xkr4 chr1:3351240-3351311 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS74 XLOC_000068 Xkr4 chr1:3355887-3356119 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS75 XLOC_000069 Xkr4 chr1:3356180-3356225 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS76 XLOC_000070 Xkr4 chr1:3363076-3363176 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS77 XLOC_000071 Xkr4 chr1:3363214-3363278 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS78 XLOC_000072 Xkr4 chr1:3363387-3363446 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS79 XLOC_000073 Xkr4 chr1:3363753-3363849 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS80 XLOC_000074 Xkr4 chr1:3364871-3364919 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS81 XLOC_000075 Xkr4 chr1:3367135-3367162 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS82 XLOC_000076 Xkr4 chr1:3367210-3367237 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS83 XLOC_000077 Xkr4 chr1:3367333-3367382 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS84 XLOC_000078 Xkr4 chr1:3369580-3369607 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS85 XLOC_000079 Xkr4 chr1:3375001-3375028 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS86 XLOC_000080 Xkr4 chr1:3377211-3377262 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS87 XLOC_000081 Xkr4 chr1:3379888-3379915 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS88 XLOC_000082 Xkr4 chr1:3386739-3386836 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS89 XLOC_000083 Xkr4 chr1:3391325-3391352 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS90 XLOC_000084 Xkr4 chr1:3435841-3435880 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS91 XLOC_000085 Xkr4 chr1:3447761-3447788 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS92 XLOC_000086 Xkr4 chr1:3450906-3450965 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS93 XLOC_000087 Xkr4 chr1:3451051-3451109 q1 q2 NOTEST 0 0 0 0 1 1 no
diff -r 9a9e3e83889b -r 9ba750f285e3 test-data/tss.groups_exp
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tss.groups_exp Tue Oct 13 12:37:38 2015 -0400
@@ -0,0 +1,89 @@
+test_id gene_id gene locus sample_1 sample_2 status value_1 value_2 log2(fold_change) test_stat p_value q_value significant
+TSS1 XLOC_000001 Xkr4 chr1:3204754-3204833 q1 q2 OK 0 9.45986e+06 inf -nan 0.01975 0.09875 no
+TSS10 XLOC_000008 - chr1:3190858-3191434 q1 q2 OK 408511 420354 0.0412311 0.0469899 0.96715 0.96715 no
+TSS11 XLOC_000009 - chr1:3191512-3192077 q1 q2 OK 433286 842157 0.958769 1.27887 0.20385 0.274413 no
+TSS13 XLOC_000010 - chr1:3192250-3192336 q1 q2 OK 3.44151e+06 3.34455e+06 -0.0412311 -0.014084 0.67715 0.718189 no
+TSS14 XLOC_000011 - chr1:3192441-3192494 q1 q2 OK 0 9.7002e+07 inf -nan 0.07975 0.181781 no
+TSS15 XLOC_000012 - chr1:3192550-3192629 q1 q2 OK 0 4.72993e+06 inf -nan 0.12465 0.181781 no
+TSS16 XLOC_000013 - chr1:3192649-3192676 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS17 XLOC_000014 - chr1:3192731-3192811 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS18 XLOC_000015 - chr1:3192940-3193042 q1 q2 OK 0 6.86386e+06 inf -nan 0.0612 0.181781 no
+TSS19 XLOC_000016 - chr1:3194185-3194226 q1 q2 OK 0 2.43637e+08 inf -nan 0.12465 0.181781 no
+TSS2 XLOC_000002 - chr1:3111449-3111490 q1 q2 OK 0 2.43637e+08 inf -nan 0.12465 0.181781 no
+TSS20 XLOC_000017 - chr1:3194302-3194329 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS21 XLOC_000018 - chr1:3194706-3194733 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS22 XLOC_000019 - chr1:3195083-3195110 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS23 XLOC_000020 - chr1:3195450-3195477 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS24 XLOC_000021 - chr1:3197089-3197116 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS25 XLOC_000022 - chr1:3197246-3197273 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS26 XLOC_000023 - chr1:3197346-3197373 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS27 XLOC_000024 - chr1:3197425-3197452 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS28 XLOC_000025 - chr1:3200022-3200191 q1 q2 OK 826392 803108 -0.0412311 -0.0180163 0.8625 0.887868 no
+TSS29 XLOC_000026 - chr1:3200325-3200352 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS3 XLOC_000003 - chr1:3111545-3111576 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS30 XLOC_000027 - chr1:3200430-3200457 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS31 XLOC_000028 - chr1:3201007-3201039 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS32 XLOC_000029 - chr1:3201077-3201481 q1 q2 OK 66791.3 324548 2.2807 1.1905 0.3026 0.383188 no
+TSS33 XLOC_000030 - chr1:3201596-3201666 q1 q2 OK 1.6359e+07 0 -inf -nan 0.0148 0.09875 no
+TSS34 XLOC_000031 - chr1:3201672-3201699 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS35 XLOC_000032 - chr1:3201725-3201809 q1 q2 OK 1.5136e+07 0 -inf -nan 0.06005 0.181781 no
+TSS36 XLOC_000033 Xkr4 chr1:3211521-3211561 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS37 XLOC_000034 Xkr4 chr1:3212213-3212292 q1 q2 OK 0 9.45986e+06 inf -nan 0.01975 0.09875 no
+TSS38 XLOC_000035 Xkr4 chr1:3212367-3212439 q1 q2 OK 0 2.80837e+07 inf -nan 0.0612 0.181781 no
+TSS39 XLOC_000036 Xkr4 chr1:3212717-3212801 q1 q2 OK 3.784e+06 0 -inf -nan 0.12165 0.181781 no
+TSS4 XLOC_000004 - chr1:3174765-3174792 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS40 XLOC_000037 Xkr4 chr1:3213095-3213242 q1 q2 OK 5.10781e+06 2.08209e+06 -1.29467 -0.482193 0.5916 0.647062 no
+TSS41 XLOC_000038 Xkr4 chr1:3240606-3240633 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS42 XLOC_000039 Xkr4 chr1:3242479-3242512 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS43 XLOC_000040 Xkr4 chr1:3242633-3242923 q1 q2 OK 48522.7 424400 3.12869 1.23747 0.38685 0.451325 no
+TSS44 XLOC_000041 Xkr4 chr1:3242924-3243005 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS45 XLOC_000042 Xkr4 chr1:3243018-3243079 q1 q2 OK 0 3.03053e+07 inf -nan 0.01975 0.09875 no
+TSS46 XLOC_000043 Xkr4 chr1:3243108-3243154 q1 q2 OK 8.616e+07 0 -inf -nan 0.12165 0.181781 no
+TSS47 XLOC_000044 Xkr4 chr1:3243347-3243401 q1 q2 OK 0 5.79991e+07 inf -nan 0.01975 0.09875 no
+TSS48 XLOC_000045 Xkr4 chr1:3254079-3254106 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS49 XLOC_000046 Xkr4 chr1:3256974-3257011 q1 q2 OK 0 2.35423e+09 inf -nan 0.01975 0.09875 no
+TSS5 XLOC_000005 - chr1:3187401-3187428 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS50 XLOC_000047 Xkr4 chr1:3277155-3277182 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS51 XLOC_000048 Xkr4 chr1:3277190-3277218 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS52 XLOC_000049 Xkr4 chr1:3277913-3278390 q1 q2 OK 228872 47662.2 -2.26362 -1.16262 0.30655 0.383188 no
+TSS54 XLOC_000050 Xkr4 chr1:3280117-3280144 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS55 XLOC_000051 Xkr4 chr1:3280498-3280525 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS56 XLOC_000052 Xkr4 chr1:3280686-3280741 q1 q2 OK 0 2.61334e+07 inf -nan 0.12465 0.181781 no
+TSS57 XLOC_000053 Xkr4 chr1:3282504-3282531 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS58 XLOC_000054 Xkr4 chr1:3282650-3282677 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS59 XLOC_000055 Xkr4 chr1:3282760-3282832 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS6 XLOC_000006 - chr1:3188521-3188548 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS60 XLOC_000056 Xkr4 chr1:3284966-3284993 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS61 XLOC_000057 Xkr4 chr1:3290488-3290553 q1 q2 OK 0 1.11503e+07 inf -nan 0.12465 0.181781 no
+TSS62 XLOC_000058 Xkr4 chr1:3290798-3290859 q1 q2 OK 1.55919e+07 0 -inf -nan 0.12165 0.181781 no
+TSS63 XLOC_000059 Xkr4 chr1:3290919-3291273 q1 q2 OK 294879 85971.3 -1.7782 -0.902752 0.36915 0.445526 no
+TSS65 XLOC_000060 Xkr4 chr1:3299443-3299664 q1 q2 OK 807732 156995 -2.36316 -0.933704 0.4205 0.474758 no
+TSS66 XLOC_000060 Xkr4 chr1:3299443-3299664 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS67 XLOC_000061 Xkr4 chr1:3299691-3299733 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS68 XLOC_000062 Xkr4 chr1:3300051-3300078 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS69 XLOC_000063 Xkr4 chr1:3307748-3307775 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS7 XLOC_000007 - chr1:3189810-3190789 q1 q2 OK 358326 522345 0.543731 1.1445 0.1952 0.27328 no
+TSS70 XLOC_000064 Xkr4 chr1:3318620-3318647 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS71 XLOC_000065 Xkr4 chr1:3318999-3319051 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS72 XLOC_000066 Xkr4 chr1:3330527-3330554 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS73 XLOC_000067 Xkr4 chr1:3351240-3351311 q1 q2 OK 7.68169e+06 0 -inf -nan 0.12165 0.181781 no
+TSS74 XLOC_000068 Xkr4 chr1:3355887-3356119 q1 q2 OK 504790 0 -inf -nan 0.04565 0.181781 no
+TSS75 XLOC_000069 Xkr4 chr1:3356180-3356225 q1 q2 OK 1.02717e+08 0 -inf -nan 0.12165 0.181781 no
+TSS76 XLOC_000070 Xkr4 chr1:3363076-3363176 q1 q2 OK 3.81001e+06 0 -inf -nan 0.0148 0.09875 no
+TSS77 XLOC_000071 Xkr4 chr1:3363214-3363278 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS78 XLOC_000072 Xkr4 chr1:3363387-3363446 q1 q2 OK 5.53654e+07 0 -inf -nan 0.0773 0.181781 no
+TSS79 XLOC_000073 Xkr4 chr1:3363753-3363849 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS80 XLOC_000074 Xkr4 chr1:3364871-3364919 q1 q2 OK 6.28966e+07 0 -inf -nan 0.12165 0.181781 no
+TSS81 XLOC_000075 Xkr4 chr1:3367135-3367162 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS82 XLOC_000076 Xkr4 chr1:3367210-3367237 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS83 XLOC_000077 Xkr4 chr1:3367333-3367382 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS84 XLOC_000078 Xkr4 chr1:3369580-3369607 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS85 XLOC_000079 Xkr4 chr1:3375001-3375028 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS86 XLOC_000080 Xkr4 chr1:3377211-3377262 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS87 XLOC_000081 Xkr4 chr1:3379888-3379915 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS88 XLOC_000082 Xkr4 chr1:3386739-3386836 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS89 XLOC_000083 Xkr4 chr1:3391325-3391352 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS90 XLOC_000084 Xkr4 chr1:3435841-3435880 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS91 XLOC_000085 Xkr4 chr1:3447761-3447788 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS92 XLOC_000086 Xkr4 chr1:3450906-3450965 q1 q2 NOTEST 0 0 0 0 1 1 no
+TSS93 XLOC_000087 Xkr4 chr1:3451051-3451109 q1 q2 NOTEST 0 0 0 0 1 1 no
diff -r 9a9e3e83889b -r 9ba750f285e3 test-data/tss.groups_fpkm_tracking
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tss.groups_fpkm_tracking Tue Oct 13 12:37:38 2015 -0400
@@ -0,0 +1,89 @@
+tracking_id class_code nearest_ref_id gene_id gene_short_name tss_id locus length coverage q1_FPKM q1_conf_lo q1_conf_hi q1_status q2_FPKM q2_conf_lo q2_conf_hi q2_status
+TSS1 - - XLOC_000001 Xkr4 TSS1 chr1:3204754-3204833 - - 0 0 0 OK 9.45986e+06 0 3.33035e+07 OK
+TSS10 - - XLOC_000008 - TSS10 chr1:3190858-3191434 - - 408511 54526.1 762496 OK 420354 61509.1 779200 OK
+TSS11 - - XLOC_000009 - TSS11 chr1:3191512-3192077 - - 433286 63552.3 803020 OK 842157 342520 1.34179e+06 OK
+TSS13 - - XLOC_000010 - TSS13 chr1:3192250-3192336 - - 3.44151e+06 0 1.31756e+07 OK 3.34455e+06 0 1.30786e+07 OK
+TSS14 - - XLOC_000011 - TSS14 chr1:3192441-3192494 - - 0 0 0 OK 9.7002e+07 0 3.17699e+08 OK
+TSS15 - - XLOC_000012 - TSS15 chr1:3192550-3192629 - - 0 0 0 OK 4.72993e+06 0 1.84961e+07 OK
+TSS16 - - XLOC_000013 - TSS16 chr1:3192649-3192676 - - 0 0 0 OK 0 0 0 OK
+TSS17 - - XLOC_000014 - TSS17 chr1:3192731-3192811 - - 0 0 0 OK 0 0 0 OK
+TSS18 - - XLOC_000015 - TSS18 chr1:3192940-3193042 - - 0 0 0 OK 6.86386e+06 0 2.14243e+07 OK
+TSS19 - - XLOC_000016 - TSS19 chr1:3194185-3194226 - - 0 0 0 OK 2.43637e+08 0 9.52723e+08 OK
+TSS2 - - XLOC_000002 - TSS2 chr1:3111449-3111490 - - 0 0 0 OK 2.43637e+08 0 9.52723e+08 OK
+TSS20 - - XLOC_000017 - TSS20 chr1:3194302-3194329 - - 0 0 0 OK 0 0 0 OK
+TSS21 - - XLOC_000018 - TSS21 chr1:3194706-3194733 - - 0 0 0 OK 0 0 0 OK
+TSS22 - - XLOC_000019 - TSS22 chr1:3195083-3195110 - - 0 0 0 OK 0 0 0 OK
+TSS23 - - XLOC_000020 - TSS23 chr1:3195450-3195477 - - 0 0 0 OK 0 0 0 OK
+TSS24 - - XLOC_000021 - TSS24 chr1:3197089-3197116 - - 0 0 0 OK 0 0 0 OK
+TSS25 - - XLOC_000022 - TSS25 chr1:3197246-3197273 - - 0 0 0 OK 0 0 0 OK
+TSS26 - - XLOC_000023 - TSS26 chr1:3197346-3197373 - - 0 0 0 OK 0 0 0 OK
+TSS27 - - XLOC_000024 - TSS27 chr1:3197425-3197452 - - 0 0 0 OK 0 0 0 OK
+TSS28 - - XLOC_000025 - TSS28 chr1:3200022-3200191 - - 826392 0 2.65361e+06 OK 803108 0 2.63033e+06 OK
+TSS29 - - XLOC_000026 - TSS29 chr1:3200325-3200352 - - 0 0 0 OK 0 0 0 OK
+TSS3 - - XLOC_000003 - TSS3 chr1:3111545-3111576 - - 0 0 0 OK 0 0 0 OK
+TSS30 - - XLOC_000027 - TSS30 chr1:3200430-3200457 - - 0 0 0 OK 0 0 0 OK
+TSS31 - - XLOC_000028 - TSS31 chr1:3201007-3201039 - - 0 0 0 OK 0 0 0 OK
+TSS32 - - XLOC_000029 - TSS32 chr1:3201077-3201481 - - 66791.3 0 214473 OK 324548 0 802006 OK
+TSS33 - - XLOC_000030 - TSS33 chr1:3201596-3201666 - - 1.6359e+07 0 5.96409e+07 OK 0 0 0 OK
+TSS34 - - XLOC_000031 - TSS34 chr1:3201672-3201699 - - 0 0 0 OK 0 0 0 OK
+TSS35 - - XLOC_000032 - TSS35 chr1:3201725-3201809 - - 1.5136e+07 0 4.63396e+07 OK 0 0 0 OK
+TSS36 - - XLOC_000033 Xkr4 TSS36 chr1:3211521-3211561 - - 0 0 0 OK 0 0 0 OK
+TSS37 - - XLOC_000034 Xkr4 TSS37 chr1:3212213-3212292 - - 0 0 0 OK 9.45986e+06 0 3.33035e+07 OK
+TSS38 - - XLOC_000035 Xkr4 TSS38 chr1:3212367-3212439 - - 0 0 0 OK 2.80837e+07 0 8.76584e+07 OK
+TSS39 - - XLOC_000036 Xkr4 TSS39 chr1:3212717-3212801 - - 3.784e+06 0 1.44868e+07 OK 0 0 0 OK
+TSS4 - - XLOC_000004 - TSS4 chr1:3174765-3174792 - - 0 0 0 OK 0 0 0 OK
+TSS40 - - XLOC_000037 Xkr4 TSS40 chr1:3213095-3213242 - - 5.10781e+06 0 1.69588e+07 OK 2.08209e+06 0 8.1421e+06 OK
+TSS41 - - XLOC_000038 Xkr4 TSS41 chr1:3240606-3240633 - - 0 0 0 OK 0 0 0 OK
+TSS42 - - XLOC_000039 Xkr4 TSS42 chr1:3242479-3242512 - - 0 0 0 OK 0 0 0 OK
+TSS43 - - XLOC_000040 Xkr4 TSS43 chr1:3242633-3242923 - - 48522.7 0 185766 OK 424400 0 1.30289e+06 OK
+TSS44 - - XLOC_000041 Xkr4 TSS44 chr1:3242924-3243005 - - 0 0 0 OK 0 0 0 OK
+TSS45 - - XLOC_000042 Xkr4 TSS45 chr1:3243018-3243079 - - 0 0 0 OK 3.03053e+07 0 1.0669e+08 OK
+TSS46 - - XLOC_000043 Xkr4 TSS46 chr1:3243108-3243154 - - 8.616e+07 0 3.29857e+08 OK 0 0 0 OK
+TSS47 - - XLOC_000044 Xkr4 TSS47 chr1:3243347-3243401 - - 0 0 0 OK 5.79991e+07 0 2.04186e+08 OK
+TSS48 - - XLOC_000045 Xkr4 TSS48 chr1:3254079-3254106 - - 0 0 0 OK 0 0 0 OK
+TSS49 - - XLOC_000046 Xkr4 TSS49 chr1:3256974-3257011 - - 0 0 0 OK 2.35423e+09 0 8.28806e+09 OK
+TSS5 - - XLOC_000005 - TSS5 chr1:3187401-3187428 - - 0 0 0 OK 0 0 0 OK
+TSS50 - - XLOC_000047 Xkr4 TSS50 chr1:3277155-3277182 - - 0 0 0 OK 0 0 0 OK
+TSS51 - - XLOC_000048 Xkr4 TSS51 chr1:3277190-3277218 - - 0 0 0 OK 0 0 0 OK
+TSS52 - - XLOC_000049 Xkr4 TSS52 chr1:3277913-3278390 - - 228872 0 561229 OK 47662.2 0 156103 OK
+TSS54 - - XLOC_000050 Xkr4 TSS54 chr1:3280117-3280144 - - 0 0 0 OK 0 0 0 OK
+TSS55 - - XLOC_000051 Xkr4 TSS55 chr1:3280498-3280525 - - 0 0 0 OK 0 0 0 OK
+TSS56 - - XLOC_000052 Xkr4 TSS56 chr1:3280686-3280741 - - 0 0 0 OK 2.61334e+07 0 1.02193e+08 OK
+TSS57 - - XLOC_000053 Xkr4 TSS57 chr1:3282504-3282531 - - 0 0 0 OK 0 0 0 OK
+TSS58 - - XLOC_000054 Xkr4 TSS58 chr1:3282650-3282677 - - 0 0 0 OK 0 0 0 OK
+TSS59 - - XLOC_000055 Xkr4 TSS59 chr1:3282760-3282832 - - 0 0 0 OK 0 0 0 OK
+TSS6 - - XLOC_000006 - TSS6 chr1:3188521-3188548 - - 0 0 0 OK 0 0 0 OK
+TSS60 - - XLOC_000056 Xkr4 TSS60 chr1:3284966-3284993 - - 0 0 0 OK 0 0 0 OK
+TSS61 - - XLOC_000057 Xkr4 TSS61 chr1:3290488-3290553 - - 0 0 0 OK 1.11503e+07 0 4.36026e+07 OK
+TSS62 - - XLOC_000058 Xkr4 TSS62 chr1:3290798-3290859 - - 1.55919e+07 0 5.96926e+07 OK 0 0 0 OK
+TSS63 - - XLOC_000059 Xkr4 TSS63 chr1:3290919-3291273 - - 294879 0 740137 OK 85971.3 0 281572 OK
+TSS65 - - XLOC_000060 Xkr4 TSS65 chr1:3299443-3299664 - - 807732 0 2.39056e+06 OK 156995 0 613917 OK
+TSS66 - - XLOC_000060 Xkr4 TSS66 chr1:3299443-3299664 - - 0 0 0 OK 0 0 0 OK
+TSS67 - - XLOC_000061 Xkr4 TSS67 chr1:3299691-3299733 - - 0 0 0 OK 0 0 0 OK
+TSS68 - - XLOC_000062 Xkr4 TSS68 chr1:3300051-3300078 - - 0 0 0 OK 0 0 0 OK
+TSS69 - - XLOC_000063 Xkr4 TSS69 chr1:3307748-3307775 - - 0 0 0 OK 0 0 0 OK
+TSS7 - - XLOC_000007 - TSS7 chr1:3189810-3190789 - - 358326 135086 581565 OK 522345 410780 633911 OK
+TSS70 - - XLOC_000064 Xkr4 TSS70 chr1:3318620-3318647 - - 0 0 0 OK 0 0 0 OK
+TSS71 - - XLOC_000065 Xkr4 TSS71 chr1:3318999-3319051 - - 0 0 0 OK 0 0 0 OK
+TSS72 - - XLOC_000066 Xkr4 TSS72 chr1:3330527-3330554 - - 0 0 0 OK 0 0 0 OK
+TSS73 - - XLOC_000067 Xkr4 TSS73 chr1:3351240-3351311 - - 7.68169e+06 0 2.94088e+07 OK 0 0 0 OK
+TSS74 - - XLOC_000068 Xkr4 TSS74 chr1:3355887-3356119 - - 504790 0 1.59712e+06 OK 0 0 0 OK
+TSS75 - - XLOC_000069 Xkr4 TSS75 chr1:3356180-3356225 - - 1.02717e+08 0 3.93246e+08 OK 0 0 0 OK
+TSS76 - - XLOC_000070 Xkr4 TSS76 chr1:3363076-3363176 - - 3.81001e+06 0 1.38903e+07 OK 0 0 0 OK
+TSS77 - - XLOC_000071 Xkr4 TSS77 chr1:3363214-3363278 - - 0 0 0 OK 0 0 0 OK
+TSS78 - - XLOC_000072 Xkr4 TSS78 chr1:3363387-3363446 - - 5.53654e+07 0 1.77783e+08 OK 0 0 0 OK
+TSS79 - - XLOC_000073 Xkr4 TSS79 chr1:3363753-3363849 - - 0 0 0 OK 0 0 0 OK
+TSS80 - - XLOC_000074 Xkr4 TSS80 chr1:3364871-3364919 - - 6.28966e+07 0 2.40795e+08 OK 0 0 0 OK
+TSS81 - - XLOC_000075 Xkr4 TSS81 chr1:3367135-3367162 - - 0 0 0 OK 0 0 0 OK
+TSS82 - - XLOC_000076 Xkr4 TSS82 chr1:3367210-3367237 - - 0 0 0 OK 0 0 0 OK
+TSS83 - - XLOC_000077 Xkr4 TSS83 chr1:3367333-3367382 - - 0 0 0 OK 0 0 0 OK
+TSS84 - - XLOC_000078 Xkr4 TSS84 chr1:3369580-3369607 - - 0 0 0 OK 0 0 0 OK
+TSS85 - - XLOC_000079 Xkr4 TSS85 chr1:3375001-3375028 - - 0 0 0 OK 0 0 0 OK
+TSS86 - - XLOC_000080 Xkr4 TSS86 chr1:3377211-3377262 - - 0 0 0 OK 0 0 0 OK
+TSS87 - - XLOC_000081 Xkr4 TSS87 chr1:3379888-3379915 - - 0 0 0 OK 0 0 0 OK
+TSS88 - - XLOC_000082 Xkr4 TSS88 chr1:3386739-3386836 - - 0 0 0 OK 0 0 0 OK
+TSS89 - - XLOC_000083 Xkr4 TSS89 chr1:3391325-3391352 - - 0 0 0 OK 0 0 0 OK
+TSS90 - - XLOC_000084 Xkr4 TSS90 chr1:3435841-3435880 - - 0 0 0 OK 0 0 0 OK
+TSS91 - - XLOC_000085 Xkr4 TSS91 chr1:3447761-3447788 - - 0 0 0 OK 0 0 0 OK
+TSS92 - - XLOC_000086 Xkr4 TSS92 chr1:3450906-3450965 - - 0 0 0 OK 0 0 0 OK
+TSS93 - - XLOC_000087 Xkr4 TSS93 chr1:3451051-3451109 - - 0 0 0 OK 0 0 0 OK
diff -r 9a9e3e83889b -r 9ba750f285e3 tool_dependencies.xml
--- a/tool_dependencies.xml Wed Nov 26 13:57:28 2014 -0500
+++ b/tool_dependencies.xml Tue Oct 13 12:37:38 2015 -0400
@@ -1,6 +1,12 @@
+
+ $REPOSITORY_INSTALL_DIR
+
+
+
+