# HG changeset patch
# User erasmus-medical-center
# Date 1524258835 14400
# Node ID 0addbdbc1344b793d38fc2d94afe460a49024aa4
# Parent  4f22bd6127542948f4b1a66a525a133e617145c9
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit bc077ab7d773c0764642ae8a439d6077ff64fd3c

diff -r 4f22bd612754 -r 0addbdbc1344 flaimapper.xml
--- a/flaimapper.xml	Wed Aug 16 11:07:51 2017 -0400
+++ b/flaimapper.xml	Fri Apr 20 17:13:55 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[
diff -r 4f22bd612754 -r 0addbdbc1344 test-data/multilength_fragments_per_position_001.bam
Binary file test-data/multilength_fragments_per_position_001.bam has changed
diff -r 4f22bd612754 -r 0addbdbc1344 test-data/multilength_fragments_per_position_001.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/multilength_fragments_per_position_001.txt	Fri Apr 20 17:13:55 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
diff -r 4f22bd612754 -r 0addbdbc1344 test-data/snord81.flaimapper.duck-15.gtf
--- a/test-data/snord81.flaimapper.duck-15.gtf	Wed Aug 16 11:07:51 2017 -0400
+++ b/test-data/snord81.flaimapper.duck-15.gtf	Fri Apr 20 17:13:55 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"
diff -r 4f22bd612754 -r 0addbdbc1344 test-data/snord81.flaimapper.gtf
--- a/test-data/snord81.flaimapper.gtf	Wed Aug 16 11:07:51 2017 -0400
+++ b/test-data/snord81.flaimapper.gtf	Fri Apr 20 17:13:55 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"
diff -r 4f22bd612754 -r 0addbdbc1344 test-data/snord81.flaimapper.offsets_5_5.gtf
--- a/test-data/snord81.flaimapper.offsets_5_5.gtf	Wed Aug 16 11:07:51 2017 -0400
+++ b/test-data/snord81.flaimapper.offsets_5_5.gtf	Fri Apr 20 17:13:55 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"
diff -r 4f22bd612754 -r 0addbdbc1344 test-data/test_genomic_flaimapper_output.gtf
--- a/test-data/test_genomic_flaimapper_output.gtf	Wed Aug 16 11:07:51 2017 -0400
+++ b/test-data/test_genomic_flaimapper_output.gtf	Fri Apr 20 17:13:55 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"