Mercurial > repos > yhoogstrate > flaimapper
changeset 41:3cf217373ae2 draft default tip
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit bc077ab7d773c0764642ae8a439d6077ff64fd3c
| author | erasmus-medical-center |
|---|---|
| date | Fri, 20 Apr 2018 17:13:37 -0400 |
| parents | af0ee8dc5471 |
| children | |
| files | flaimapper.xml test-data/multilength_fragments_per_position_001.bam test-data/multilength_fragments_per_position_001.txt test-data/snord81.flaimapper.duck-15.gtf test-data/snord81.flaimapper.gtf test-data/snord81.flaimapper.offsets_5_5.gtf test-data/test_genomic_flaimapper_output.gtf |
| diffstat | 7 files changed, 41 insertions(+), 30 deletions(-) [+] |
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--- a/flaimapper.xml Wed Aug 16 11:07:37 2017 -0400 +++ b/flaimapper.xml Fri Apr 20 17:13:37 2018 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" encoding="UTF-8"?> -<tool id="flaimapper" name="FlaiMapper" version="2.5.0-0"> +<tool id="flaimapper" name="FlaiMapper" version="3.0.0-0"> <description>detects small ncRNA derived fragments in small RNA-Seq data</description> <requirements> - <requirement type="package" version="2.5.0">flaimapper</requirement> + <requirement type="package" version="3.0.0">flaimapper</requirement> </requirements> <version_command><![CDATA[ flaimapper --version 2>&1 | head -n 1 ]]></version_command> @@ -134,6 +134,14 @@ <output name="output" file="snord81.flaimapper.duck-15.gtf" /> </test> + + <!-- Tests a new feature that allows multiple fragments of different size, starting at one identical positions --> + <test> + <param name="alignment" value="multilength_fragments_per_position_001.bam" ftype="bam" /> + <param name="output_format" value="1" /> + + <output name="output" file="multilength_fragments_per_position_001.txt" /> + </test> </tests> <help><![CDATA[
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/multilength_fragments_per_position_001.txt Fri Apr 20 17:13:37 2018 -0400 @@ -0,0 +1,3 @@ +Fragment Size Reference sequence Start End Precursor Start in precursor End in precursor Sequence Corresponding-reads (start) Corresponding-reads (end) Corresponding-reads (total) +FM_SNORD78_000000000001 62 SNORD78 11 72 SNORD78 11 72 72 101 173 +FM_SNORD78_000000000002 29 SNORD78 44 72 SNORD78 44 72 27 101 128
--- a/test-data/snord81.flaimapper.duck-15.gtf Wed Aug 16 11:07:37 2017 -0400 +++ b/test-data/snord81.flaimapper.duck-15.gtf Fri Apr 20 17:13:37 2018 -0400 @@ -1,4 +1,4 @@ -HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19 flaimapper-v2.5.0 sncdRNA 47 68 171 . . gene_id "FM_HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19_000000000001" -HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19 flaimapper-v2.5.0 exon 43 72 171 . . gene_id "FM_HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19_000000000001" -HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19 flaimapper-v2.5.0 sncdRNA 15 37 99 . . gene_id "FM_HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19_000000000002" -HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19 flaimapper-v2.5.0 exon 11 41 99 . . gene_id "FM_HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19_000000000002" +HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19 flaimapper-v3.0.0 sncdRNA 47 68 171 . . gene_id "FM_HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19_000000000001" +HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19 flaimapper-v3.0.0 exon 43 72 171 . . gene_id "FM_HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19_000000000001" +HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19 flaimapper-v3.0.0 sncdRNA 15 37 99 . . gene_id "FM_HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19_000000000002" +HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19 flaimapper-v3.0.0 exon 11 41 99 . . gene_id "FM_HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19_000000000002"
--- a/test-data/snord81.flaimapper.gtf Wed Aug 16 11:07:37 2017 -0400 +++ b/test-data/snord81.flaimapper.gtf Fri Apr 20 17:13:37 2018 -0400 @@ -1,6 +1,6 @@ -HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19 flaimapper-v2.5.0 sncdRNA 47 68 171 . . gene_id "FM_HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19_000000000001" -HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19 flaimapper-v2.5.0 exon 43 72 171 . . gene_id "FM_HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19_000000000001" -HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19 flaimapper-v2.5.0 sncdRNA 15 37 99 . . gene_id "FM_HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19_000000000002" -HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19 flaimapper-v2.5.0 exon 11 41 99 . . gene_id "FM_HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19_000000000002" -HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19 flaimapper-v2.5.0 sncdRNA 55 80 82 . . gene_id "FM_HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19_000000000003" -HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19 flaimapper-v2.5.0 exon 51 84 82 . . gene_id "FM_HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19_000000000003" +HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19 flaimapper-v3.0.0 sncdRNA 47 68 171 . . gene_id "FM_HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19_000000000001" +HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19 flaimapper-v3.0.0 exon 43 72 171 . . gene_id "FM_HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19_000000000001" +HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19 flaimapper-v3.0.0 sncdRNA 15 37 99 . . gene_id "FM_HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19_000000000002" +HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19 flaimapper-v3.0.0 exon 11 41 99 . . gene_id "FM_HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19_000000000002" +HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19 flaimapper-v3.0.0 sncdRNA 55 80 82 . . gene_id "FM_HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19_000000000003" +HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19 flaimapper-v3.0.0 exon 51 84 82 . . gene_id "FM_HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19_000000000003"
--- a/test-data/snord81.flaimapper.offsets_5_5.gtf Wed Aug 16 11:07:37 2017 -0400 +++ b/test-data/snord81.flaimapper.offsets_5_5.gtf Fri Apr 20 17:13:37 2018 -0400 @@ -1,6 +1,6 @@ -HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19 flaimapper-v2.5.0 sncdRNA 47 68 171 . . gene_id "FM_HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19_000000000001" -HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19 flaimapper-v2.5.0 exon 42 73 171 . . gene_id "FM_HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19_000000000001" -HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19 flaimapper-v2.5.0 sncdRNA 15 37 99 . . gene_id "FM_HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19_000000000002" -HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19 flaimapper-v2.5.0 exon 10 42 99 . . gene_id "FM_HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19_000000000002" -HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19 flaimapper-v2.5.0 sncdRNA 55 80 82 . . gene_id "FM_HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19_000000000003" -HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19 flaimapper-v2.5.0 exon 50 85 82 . . gene_id "FM_HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19_000000000003" +HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19 flaimapper-v3.0.0 sncdRNA 47 68 171 . . gene_id "FM_HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19_000000000001" +HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19 flaimapper-v3.0.0 exon 42 73 171 . . gene_id "FM_HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19_000000000001" +HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19 flaimapper-v3.0.0 sncdRNA 15 37 99 . . gene_id "FM_HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19_000000000002" +HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19 flaimapper-v3.0.0 exon 10 42 99 . . gene_id "FM_HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19_000000000002" +HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19 flaimapper-v3.0.0 sncdRNA 55 80 82 . . gene_id "FM_HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19_000000000003" +HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19 flaimapper-v3.0.0 exon 50 85 82 . . gene_id "FM_HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19_000000000003"
--- a/test-data/test_genomic_flaimapper_output.gtf Wed Aug 16 11:07:37 2017 -0400 +++ b/test-data/test_genomic_flaimapper_output.gtf Fri Apr 20 17:13:37 2018 -0400 @@ -1,12 +1,12 @@ -chr1 flaimapper-v2.5.0 sncdRNA 261 290 20 . . gene_id "FM_chr1_000000000001" -chr1 flaimapper-v2.5.0 exon 257 294 20 . . gene_id "FM_chr1_000000000001" -chr1 flaimapper-v2.5.0 sncdRNA 221 250 19 . . gene_id "FM_chr1_000000000002" -chr1 flaimapper-v2.5.0 exon 217 254 19 . . gene_id "FM_chr1_000000000002" -chr1 flaimapper-v2.5.0 sncdRNA 401 430 20 . . gene_id "FM_chr1_000000000003" -chr1 flaimapper-v2.5.0 exon 397 434 20 . . gene_id "FM_chr1_000000000003" -chr22 flaimapper-v2.5.0 sncdRNA 101 150 20 . . gene_id "FM_chr22_000000000001" -chr22 flaimapper-v2.5.0 exon 97 154 20 . . gene_id "FM_chr22_000000000001" -chr22 flaimapper-v2.5.0 sncdRNA 371 400 20 . . gene_id "FM_chr22_000000000002" -chr22 flaimapper-v2.5.0 exon 367 404 20 . . gene_id "FM_chr22_000000000002" -chrY flaimapper-v2.5.0 sncdRNA 1 30 19 . . gene_id "FM_chrY_000000000001" -chrY flaimapper-v2.5.0 exon 1 34 19 . . gene_id "FM_chrY_000000000001" +chr1 flaimapper-v3.0.0 sncdRNA 261 290 20 . . gene_id "FM_chr1_000000000001" +chr1 flaimapper-v3.0.0 exon 257 294 20 . . gene_id "FM_chr1_000000000001" +chr1 flaimapper-v3.0.0 sncdRNA 221 250 19 . . gene_id "FM_chr1_000000000002" +chr1 flaimapper-v3.0.0 exon 217 254 19 . . gene_id "FM_chr1_000000000002" +chr1 flaimapper-v3.0.0 sncdRNA 401 430 20 . . gene_id "FM_chr1_000000000003" +chr1 flaimapper-v3.0.0 exon 397 434 20 . . gene_id "FM_chr1_000000000003" +chr22 flaimapper-v3.0.0 sncdRNA 101 150 20 . . gene_id "FM_chr22_000000000001" +chr22 flaimapper-v3.0.0 exon 97 154 20 . . gene_id "FM_chr22_000000000001" +chr22 flaimapper-v3.0.0 sncdRNA 371 400 20 . . gene_id "FM_chr22_000000000002" +chr22 flaimapper-v3.0.0 exon 367 404 20 . . gene_id "FM_chr22_000000000002" +chrY flaimapper-v3.0.0 sncdRNA 1 30 19 . . gene_id "FM_chrY_000000000001" +chrY flaimapper-v3.0.0 exon 1 34 19 . . gene_id "FM_chrY_000000000001"