changeset 17:2474cd44d10a draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit b6e11aa8e5fd1da27909207ec4f09cbbac467495
author iuc
date Fri, 29 Mar 2019 08:31:40 -0400
parents d837223d4ad2
children f8748e3fd865
files picard_CollectRnaSeqMetrics.xml read_group_macros.xml test-data/picard_CollectRnaSeqMetrics.gtf test-data/picard_CollectRnaSeqMetrics_test2.tab
diffstat 4 files changed, 252 insertions(+), 28 deletions(-) [+]
line wrap: on
line diff
--- a/picard_CollectRnaSeqMetrics.xml	Tue Oct 16 11:48:40 2018 -0400
+++ b/picard_CollectRnaSeqMetrics.xml	Fri Mar 29 08:31:40 2019 -0400
@@ -23,7 +23,7 @@
 
       #if str($gene_reference_source.gene_reference_source_selector) == "gtf"
         #if $gene_reference_source.refFlat.ext != 'gff3'
-            gtfToGenePred '${gene_reference_source.refFlat}' refFlat.tab.raw &&
+            gtfToGenePred -genePredExt '${gene_reference_source.refFlat}' refFlat.tab.raw &&
         #else
             gff3ToGenePred '${gene_reference_source.refFlat}' refFlat.tab.raw &&
         #end if
--- a/read_group_macros.xml	Tue Oct 16 11:48:40 2018 -0400
+++ b/read_group_macros.xml	Fri Mar 29 08:31:40 2019 -0400
@@ -242,7 +242,7 @@
         <param name="PU" type="text" label="Platform unit (PU)" help="Unique identifier (e.g. flowcell-barcode.lane for Illumina or slide for SOLiD)" optional="True" />
     </xml>
     <xml name="read_group_pu_required_param">
-        <param name="PU" type="text" label="Platform unit (PU)" help="Unique identifier (e.g. flowcell-barcode.lane for Illumina or slide for SOLiD)" optional="False" />
+        <param name="PU" type="text" value="run" label="Platform unit (PU)" help="Unique identifier (e.g. flowcell-barcode.lane for Illumina or slide for SOLiD)" optional="False" />
     </xml>
     <!-- Only ID is required - all groups available -->
     <xml name="read_group_inputs_spec">
--- a/test-data/picard_CollectRnaSeqMetrics.gtf	Tue Oct 16 11:48:40 2018 -0400
+++ b/test-data/picard_CollectRnaSeqMetrics.gtf	Fri Mar 29 08:31:40 2019 -0400
@@ -1,23 +1,144 @@
-chrM	hg19_knownGene	exon	236	368	0.000000	-	.	gene_id "uc004coq.4"; transcript_id "uc004coq.4"; 
-chrM	hg19_knownGene	exon	651	674	0.000000	+	.	gene_id "uc022bqo.2"; transcript_id "uc022bqo.2"; 
-chrM	hg19_knownGene	exon	1604	1634	0.000000	+	.	gene_id "uc004cor.1"; transcript_id "uc004cor.1"; 
-chrM	hg19_knownGene	exon	1844	4264	0.000000	+	.	gene_id "uc004cos.5"; transcript_id "uc004cos.5"; 
-chrM	hg19_knownGene	exon	5544	5566	0.000000	-	.	gene_id "uc022bqp.1"; transcript_id "uc022bqp.1"; 
-chrM	hg19_knownGene	exon	5586	5606	0.000000	-	.	gene_id "uc022bqq.1"; transcript_id "uc022bqq.1"; 
-chrM	hg19_knownGene	exon	5691	5714	0.000000	-	.	gene_id "uc022bqr.1"; transcript_id "uc022bqr.1"; 
-chrM	hg19_knownGene	exon	5905	7439	0.000000	+	.	gene_id "uc031tga.1"; transcript_id "uc031tga.1"; 
-chrM	hg19_knownGene	exon	7587	7982	0.000000	-	.	gene_id "uc022bqs.1"; transcript_id "uc022bqs.1"; 
-chrM	hg19_knownGene	exon	15504	15888	0.000000	-	.	gene_id "uc022bqs.1"; transcript_id "uc022bqs.1"; 
-chrM	hg19_knownGene	exon	7587	9208	0.000000	+	.	gene_id "uc011mfi.2"; transcript_id "uc011mfi.2"; 
-chrM	hg19_knownGene	exon	8367	8472	0.000000	-	.	gene_id "uc022bqt.1"; transcript_id "uc022bqt.1"; 
-chrM	hg19_knownGene	exon	13450	14149	0.000000	-	.	gene_id "uc022bqt.1"; transcript_id "uc022bqt.1"; 
-chrM	hg19_knownGene	exon	10060	10404	0.000000	+	.	gene_id "uc022bqu.2"; transcript_id "uc022bqu.2"; 
-chrM	hg19_knownGene	exon	10471	12138	0.000000	+	.	gene_id "uc004cov.5"; transcript_id "uc004cov.5"; 
-chrM	hg19_knownGene	exon	10761	11231	0.000000	-	.	gene_id "uc031tgb.1"; transcript_id "uc031tgb.1"; 
-chrM	hg19_knownGene	exon	13979	14149	0.000000	-	.	gene_id "uc031tgb.1"; transcript_id "uc031tgb.1"; 
-chrM	hg19_knownGene	exon	12208	12264	0.000000	+	.	gene_id "uc004cow.2"; transcript_id "uc004cow.2"; 
-chrM	hg19_knownGene	exon	12908	14149	0.000000	+	.	gene_id "uc004cox.4"; transcript_id "uc004cox.4"; 
-chrM	hg19_knownGene	exon	14675	14698	0.000000	-	.	gene_id "uc022bqv.1"; transcript_id "uc022bqv.1"; 
-chrM	hg19_knownGene	exon	14857	15888	0.000000	+	.	gene_id "uc022bqw.1"; transcript_id "uc022bqw.1"; 
-chrM	hg19_knownGene	exon	15960	16024	0.000000	-	.	gene_id "uc022bqx.1"; transcript_id "uc022bqx.1"; 
-chrM	hg19_knownGene	exon	15999	16571	0.000000	+	.	gene_id "uc004coz.1"; transcript_id "uc004coz.1"; 
\ No newline at end of file
+chrM	insdc	gene	577	647	.	+	.	gene_id "ENSG00000210049"; gene_version "1"; gene_name "MT-TF"; gene_source "insdc"; gene_biotype "Mt_tRNA";
+chrM	insdc	transcript	577	647	.	+	.	gene_id "ENSG00000210049"; gene_version "1"; transcript_id "ENST00000387314"; transcript_version "1"; gene_name "MT-TF"; gene_source "insdc"; gene_biotype "Mt_tRNA"; transcript_name "MT-TF-201"; transcript_source "insdc"; transcript_biotype "Mt_tRNA"; tag "basic";
+chrM	insdc	exon	577	647	.	+	.	gene_id "ENSG00000210049"; gene_version "1"; transcript_id "ENST00000387314"; transcript_version "1"; exon_number "1"; gene_name "MT-TF"; gene_source "insdc"; gene_biotype "Mt_tRNA"; transcript_name "MT-TF-201"; transcript_source "insdc"; transcript_biotype "Mt_tRNA"; exon_id "ENSE00001544501"; exon_version "1"; tag "basic";
+chrM	insdc	gene	648	1601	.	+	.	gene_id "ENSG00000211459"; gene_version "2"; gene_name "MT-RNR1"; gene_source "insdc"; gene_biotype "Mt_rRNA";
+chrM	insdc	transcript	648	1601	.	+	.	gene_id "ENSG00000211459"; gene_version "2"; transcript_id "ENST00000389680"; transcript_version "2"; gene_name "MT-RNR1"; gene_source "insdc"; gene_biotype "Mt_rRNA"; transcript_name "MT-RNR1-201"; transcript_source "insdc"; transcript_biotype "Mt_rRNA"; tag "basic";
+chrM	insdc	exon	648	1601	.	+	.	gene_id "ENSG00000211459"; gene_version "2"; transcript_id "ENST00000389680"; transcript_version "2"; exon_number "1"; gene_name "MT-RNR1"; gene_source "insdc"; gene_biotype "Mt_rRNA"; transcript_name "MT-RNR1-201"; transcript_source "insdc"; transcript_biotype "Mt_rRNA"; exon_id "ENSE00001544499"; exon_version "2"; tag "basic";
+chrM	insdc	gene	1602	1670	.	+	.	gene_id "ENSG00000210077"; gene_version "1"; gene_name "MT-TV"; gene_source "insdc"; gene_biotype "Mt_tRNA";
+chrM	insdc	transcript	1602	1670	.	+	.	gene_id "ENSG00000210077"; gene_version "1"; transcript_id "ENST00000387342"; transcript_version "1"; gene_name "MT-TV"; gene_source "insdc"; gene_biotype "Mt_tRNA"; transcript_name "MT-TV-201"; transcript_source "insdc"; transcript_biotype "Mt_tRNA"; tag "basic";
+chrM	insdc	exon	1602	1670	.	+	.	gene_id "ENSG00000210077"; gene_version "1"; transcript_id "ENST00000387342"; transcript_version "1"; exon_number "1"; gene_name "MT-TV"; gene_source "insdc"; gene_biotype "Mt_tRNA"; transcript_name "MT-TV-201"; transcript_source "insdc"; transcript_biotype "Mt_tRNA"; exon_id "ENSE00001544498"; exon_version "1"; tag "basic";
+chrM	insdc	gene	1671	3229	.	+	.	gene_id "ENSG00000210082"; gene_version "2"; gene_name "MT-RNR2"; gene_source "insdc"; gene_biotype "Mt_rRNA";
+chrM	insdc	transcript	1671	3229	.	+	.	gene_id "ENSG00000210082"; gene_version "2"; transcript_id "ENST00000387347"; transcript_version "2"; gene_name "MT-RNR2"; gene_source "insdc"; gene_biotype "Mt_rRNA"; transcript_name "MT-RNR2-201"; transcript_source "insdc"; transcript_biotype "Mt_rRNA"; tag "basic";
+chrM	insdc	exon	1671	3229	.	+	.	gene_id "ENSG00000210082"; gene_version "2"; transcript_id "ENST00000387347"; transcript_version "2"; exon_number "1"; gene_name "MT-RNR2"; gene_source "insdc"; gene_biotype "Mt_rRNA"; transcript_name "MT-RNR2-201"; transcript_source "insdc"; transcript_biotype "Mt_rRNA"; exon_id "ENSE00001544497"; exon_version "2"; tag "basic";
+chrM	insdc	gene	3230	3304	.	+	.	gene_id "ENSG00000209082"; gene_version "1"; gene_name "MT-TL1"; gene_source "insdc"; gene_biotype "Mt_tRNA";
+chrM	insdc	transcript	3230	3304	.	+	.	gene_id "ENSG00000209082"; gene_version "1"; transcript_id "ENST00000386347"; transcript_version "1"; gene_name "MT-TL1"; gene_source "insdc"; gene_biotype "Mt_tRNA"; transcript_name "MT-TL1-201"; transcript_source "insdc"; transcript_biotype "Mt_tRNA"; tag "basic";
+chrM	insdc	exon	3230	3304	.	+	.	gene_id "ENSG00000209082"; gene_version "1"; transcript_id "ENST00000386347"; transcript_version "1"; exon_number "1"; gene_name "MT-TL1"; gene_source "insdc"; gene_biotype "Mt_tRNA"; transcript_name "MT-TL1-201"; transcript_source "insdc"; transcript_biotype "Mt_tRNA"; exon_id "ENSE00002006242"; exon_version "1"; tag "basic";
+chrM	insdc	gene	3307	4262	.	+	.	gene_id "ENSG00000198888"; gene_version "2"; gene_name "MT-ND1"; gene_source "insdc"; gene_biotype "protein_coding";
+chrM	insdc	transcript	3307	4262	.	+	.	gene_id "ENSG00000198888"; gene_version "2"; transcript_id "ENST00000361390"; transcript_version "2"; gene_name "MT-ND1"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-ND1-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; tag "basic";
+chrM	insdc	exon	3307	4262	.	+	.	gene_id "ENSG00000198888"; gene_version "2"; transcript_id "ENST00000361390"; transcript_version "2"; exon_number "1"; gene_name "MT-ND1"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-ND1-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; exon_id "ENSE00001435714"; exon_version "2"; tag "basic";
+chrM	insdc	CDS	3307	4262	.	+	0	gene_id "ENSG00000198888"; gene_version "2"; transcript_id "ENST00000361390"; transcript_version "2"; exon_number "1"; gene_name "MT-ND1"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-ND1-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; protein_id "ENSP00000354687"; protein_version "2"; tag "basic";
+chrM	insdc	start_codon	3307	3309	.	+	0	gene_id "ENSG00000198888"; gene_version "2"; transcript_id "ENST00000361390"; transcript_version "2"; exon_number "1"; gene_name "MT-ND1"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-ND1-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; tag "basic";
+chrM	insdc	gene	4263	4331	.	+	.	gene_id "ENSG00000210100"; gene_version "1"; gene_name "MT-TI"; gene_source "insdc"; gene_biotype "Mt_tRNA";
+chrM	insdc	transcript	4263	4331	.	+	.	gene_id "ENSG00000210100"; gene_version "1"; transcript_id "ENST00000387365"; transcript_version "1"; gene_name "MT-TI"; gene_source "insdc"; gene_biotype "Mt_tRNA"; transcript_name "MT-TI-201"; transcript_source "insdc"; transcript_biotype "Mt_tRNA"; tag "basic";
+chrM	insdc	exon	4263	4331	.	+	.	gene_id "ENSG00000210100"; gene_version "1"; transcript_id "ENST00000387365"; transcript_version "1"; exon_number "1"; gene_name "MT-TI"; gene_source "insdc"; gene_biotype "Mt_tRNA"; transcript_name "MT-TI-201"; transcript_source "insdc"; transcript_biotype "Mt_tRNA"; exon_id "ENSE00001993597"; exon_version "1"; tag "basic";
+chrM	insdc	gene	4329	4400	.	-	.	gene_id "ENSG00000210107"; gene_version "1"; gene_name "MT-TQ"; gene_source "insdc"; gene_biotype "Mt_tRNA";
+chrM	insdc	transcript	4329	4400	.	-	.	gene_id "ENSG00000210107"; gene_version "1"; transcript_id "ENST00000387372"; transcript_version "1"; gene_name "MT-TQ"; gene_source "insdc"; gene_biotype "Mt_tRNA"; transcript_name "MT-TQ-201"; transcript_source "insdc"; transcript_biotype "Mt_tRNA"; tag "basic";
+chrM	insdc	exon	4329	4400	.	-	.	gene_id "ENSG00000210107"; gene_version "1"; transcript_id "ENST00000387372"; transcript_version "1"; exon_number "1"; gene_name "MT-TQ"; gene_source "insdc"; gene_biotype "Mt_tRNA"; transcript_name "MT-TQ-201"; transcript_source "insdc"; transcript_biotype "Mt_tRNA"; exon_id "ENSE00001544494"; exon_version "1"; tag "basic";
+chrM	insdc	gene	4402	4469	.	+	.	gene_id "ENSG00000210112"; gene_version "1"; gene_name "MT-TM"; gene_source "insdc"; gene_biotype "Mt_tRNA";
+chrM	insdc	transcript	4402	4469	.	+	.	gene_id "ENSG00000210112"; gene_version "1"; transcript_id "ENST00000387377"; transcript_version "1"; gene_name "MT-TM"; gene_source "insdc"; gene_biotype "Mt_tRNA"; transcript_name "MT-TM-201"; transcript_source "insdc"; transcript_biotype "Mt_tRNA"; tag "basic";
+chrM	insdc	exon	4402	4469	.	+	.	gene_id "ENSG00000210112"; gene_version "1"; transcript_id "ENST00000387377"; transcript_version "1"; exon_number "1"; gene_name "MT-TM"; gene_source "insdc"; gene_biotype "Mt_tRNA"; transcript_name "MT-TM-201"; transcript_source "insdc"; transcript_biotype "Mt_tRNA"; exon_id "ENSE00001544493"; exon_version "1"; tag "basic";
+chrM	insdc	gene	4470	5511	.	+	.	gene_id "ENSG00000198763"; gene_version "3"; gene_name "MT-ND2"; gene_source "insdc"; gene_biotype "protein_coding";
+chrM	insdc	transcript	4470	5511	.	+	.	gene_id "ENSG00000198763"; gene_version "3"; transcript_id "ENST00000361453"; transcript_version "3"; gene_name "MT-ND2"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-ND2-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; tag "basic";
+chrM	insdc	exon	4470	5511	.	+	.	gene_id "ENSG00000198763"; gene_version "3"; transcript_id "ENST00000361453"; transcript_version "3"; exon_number "1"; gene_name "MT-ND2"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-ND2-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; exon_id "ENSE00001435686"; exon_version "3"; tag "basic";
+chrM	insdc	CDS	4470	5511	.	+	0	gene_id "ENSG00000198763"; gene_version "3"; transcript_id "ENST00000361453"; transcript_version "3"; exon_number "1"; gene_name "MT-ND2"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-ND2-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; protein_id "ENSP00000355046"; protein_version "4"; tag "basic";
+chrM	insdc	start_codon	4470	4472	.	+	0	gene_id "ENSG00000198763"; gene_version "3"; transcript_id "ENST00000361453"; transcript_version "3"; exon_number "1"; gene_name "MT-ND2"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-ND2-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; tag "basic";
+chrM	insdc	gene	5512	5579	.	+	.	gene_id "ENSG00000210117"; gene_version "1"; gene_name "MT-TW"; gene_source "insdc"; gene_biotype "Mt_tRNA";
+chrM	insdc	transcript	5512	5579	.	+	.	gene_id "ENSG00000210117"; gene_version "1"; transcript_id "ENST00000387382"; transcript_version "1"; gene_name "MT-TW"; gene_source "insdc"; gene_biotype "Mt_tRNA"; transcript_name "MT-TW-201"; transcript_source "insdc"; transcript_biotype "Mt_tRNA"; tag "basic";
+chrM	insdc	exon	5512	5579	.	+	.	gene_id "ENSG00000210117"; gene_version "1"; transcript_id "ENST00000387382"; transcript_version "1"; exon_number "1"; gene_name "MT-TW"; gene_source "insdc"; gene_biotype "Mt_tRNA"; transcript_name "MT-TW-201"; transcript_source "insdc"; transcript_biotype "Mt_tRNA"; exon_id "ENSE00001544492"; exon_version "1"; tag "basic";
+chrM	insdc	gene	5587	5655	.	-	.	gene_id "ENSG00000210127"; gene_version "1"; gene_name "MT-TA"; gene_source "insdc"; gene_biotype "Mt_tRNA";
+chrM	insdc	transcript	5587	5655	.	-	.	gene_id "ENSG00000210127"; gene_version "1"; transcript_id "ENST00000387392"; transcript_version "1"; gene_name "MT-TA"; gene_source "insdc"; gene_biotype "Mt_tRNA"; transcript_name "MT-TA-201"; transcript_source "insdc"; transcript_biotype "Mt_tRNA"; tag "basic";
+chrM	insdc	exon	5587	5655	.	-	.	gene_id "ENSG00000210127"; gene_version "1"; transcript_id "ENST00000387392"; transcript_version "1"; exon_number "1"; gene_name "MT-TA"; gene_source "insdc"; gene_biotype "Mt_tRNA"; transcript_name "MT-TA-201"; transcript_source "insdc"; transcript_biotype "Mt_tRNA"; exon_id "ENSE00001544491"; exon_version "1"; tag "basic";
+chrM	insdc	gene	5657	5729	.	-	.	gene_id "ENSG00000210135"; gene_version "1"; gene_name "MT-TN"; gene_source "insdc"; gene_biotype "Mt_tRNA";
+chrM	insdc	transcript	5657	5729	.	-	.	gene_id "ENSG00000210135"; gene_version "1"; transcript_id "ENST00000387400"; transcript_version "1"; gene_name "MT-TN"; gene_source "insdc"; gene_biotype "Mt_tRNA"; transcript_name "MT-TN-201"; transcript_source "insdc"; transcript_biotype "Mt_tRNA"; tag "basic";
+chrM	insdc	exon	5657	5729	.	-	.	gene_id "ENSG00000210135"; gene_version "1"; transcript_id "ENST00000387400"; transcript_version "1"; exon_number "1"; gene_name "MT-TN"; gene_source "insdc"; gene_biotype "Mt_tRNA"; transcript_name "MT-TN-201"; transcript_source "insdc"; transcript_biotype "Mt_tRNA"; exon_id "ENSE00001544490"; exon_version "1"; tag "basic";
+chrM	insdc	gene	5761	5826	.	-	.	gene_id "ENSG00000210140"; gene_version "1"; gene_name "MT-TC"; gene_source "insdc"; gene_biotype "Mt_tRNA";
+chrM	insdc	transcript	5761	5826	.	-	.	gene_id "ENSG00000210140"; gene_version "1"; transcript_id "ENST00000387405"; transcript_version "1"; gene_name "MT-TC"; gene_source "insdc"; gene_biotype "Mt_tRNA"; transcript_name "MT-TC-201"; transcript_source "insdc"; transcript_biotype "Mt_tRNA"; tag "basic";
+chrM	insdc	exon	5761	5826	.	-	.	gene_id "ENSG00000210140"; gene_version "1"; transcript_id "ENST00000387405"; transcript_version "1"; exon_number "1"; gene_name "MT-TC"; gene_source "insdc"; gene_biotype "Mt_tRNA"; transcript_name "MT-TC-201"; transcript_source "insdc"; transcript_biotype "Mt_tRNA"; exon_id "ENSE00001544489"; exon_version "1"; tag "basic";
+chrM	insdc	gene	5826	5891	.	-	.	gene_id "ENSG00000210144"; gene_version "1"; gene_name "MT-TY"; gene_source "insdc"; gene_biotype "Mt_tRNA";
+chrM	insdc	transcript	5826	5891	.	-	.	gene_id "ENSG00000210144"; gene_version "1"; transcript_id "ENST00000387409"; transcript_version "1"; gene_name "MT-TY"; gene_source "insdc"; gene_biotype "Mt_tRNA"; transcript_name "MT-TY-201"; transcript_source "insdc"; transcript_biotype "Mt_tRNA"; tag "basic";
+chrM	insdc	exon	5826	5891	.	-	.	gene_id "ENSG00000210144"; gene_version "1"; transcript_id "ENST00000387409"; transcript_version "1"; exon_number "1"; gene_name "MT-TY"; gene_source "insdc"; gene_biotype "Mt_tRNA"; transcript_name "MT-TY-201"; transcript_source "insdc"; transcript_biotype "Mt_tRNA"; exon_id "ENSE00001544488"; exon_version "1"; tag "basic";
+chrM	insdc	gene	5904	7445	.	+	.	gene_id "ENSG00000198804"; gene_version "2"; gene_name "MT-CO1"; gene_source "insdc"; gene_biotype "protein_coding";
+chrM	insdc	transcript	5904	7445	.	+	.	gene_id "ENSG00000198804"; gene_version "2"; transcript_id "ENST00000361624"; transcript_version "2"; gene_name "MT-CO1"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-CO1-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; tag "basic";
+chrM	insdc	exon	5904	7445	.	+	.	gene_id "ENSG00000198804"; gene_version "2"; transcript_id "ENST00000361624"; transcript_version "2"; exon_number "1"; gene_name "MT-CO1"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-CO1-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; exon_id "ENSE00001435647"; exon_version "2"; tag "basic";
+chrM	insdc	CDS	5904	7442	.	+	0	gene_id "ENSG00000198804"; gene_version "2"; transcript_id "ENST00000361624"; transcript_version "2"; exon_number "1"; gene_name "MT-CO1"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-CO1-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; protein_id "ENSP00000354499"; protein_version "2"; tag "basic";
+chrM	insdc	start_codon	5904	5906	.	+	0	gene_id "ENSG00000198804"; gene_version "2"; transcript_id "ENST00000361624"; transcript_version "2"; exon_number "1"; gene_name "MT-CO1"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-CO1-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; tag "basic";
+chrM	insdc	stop_codon	7443	7445	.	+	0	gene_id "ENSG00000198804"; gene_version "2"; transcript_id "ENST00000361624"; transcript_version "2"; exon_number "1"; gene_name "MT-CO1"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-CO1-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; tag "basic";
+chrM	insdc	gene	7446	7514	.	-	.	gene_id "ENSG00000210151"; gene_version "2"; gene_name "MT-TS1"; gene_source "insdc"; gene_biotype "Mt_tRNA";
+chrM	insdc	transcript	7446	7514	.	-	.	gene_id "ENSG00000210151"; gene_version "2"; transcript_id "ENST00000387416"; transcript_version "2"; gene_name "MT-TS1"; gene_source "insdc"; gene_biotype "Mt_tRNA"; transcript_name "MT-TS1-201"; transcript_source "insdc"; transcript_biotype "Mt_tRNA"; tag "basic";
+chrM	insdc	exon	7446	7514	.	-	.	gene_id "ENSG00000210151"; gene_version "2"; transcript_id "ENST00000387416"; transcript_version "2"; exon_number "1"; gene_name "MT-TS1"; gene_source "insdc"; gene_biotype "Mt_tRNA"; transcript_name "MT-TS1-201"; transcript_source "insdc"; transcript_biotype "Mt_tRNA"; exon_id "ENSE00001544487"; exon_version "2"; tag "basic";
+chrM	insdc	gene	7518	7585	.	+	.	gene_id "ENSG00000210154"; gene_version "1"; gene_name "MT-TD"; gene_source "insdc"; gene_biotype "Mt_tRNA";
+chrM	insdc	transcript	7518	7585	.	+	.	gene_id "ENSG00000210154"; gene_version "1"; transcript_id "ENST00000387419"; transcript_version "1"; gene_name "MT-TD"; gene_source "insdc"; gene_biotype "Mt_tRNA"; transcript_name "MT-TD-201"; transcript_source "insdc"; transcript_biotype "Mt_tRNA"; tag "basic";
+chrM	insdc	exon	7518	7585	.	+	.	gene_id "ENSG00000210154"; gene_version "1"; transcript_id "ENST00000387419"; transcript_version "1"; exon_number "1"; gene_name "MT-TD"; gene_source "insdc"; gene_biotype "Mt_tRNA"; transcript_name "MT-TD-201"; transcript_source "insdc"; transcript_biotype "Mt_tRNA"; exon_id "ENSE00001544486"; exon_version "1"; tag "basic";
+chrM	insdc	gene	7586	8269	.	+	.	gene_id "ENSG00000198712"; gene_version "1"; gene_name "MT-CO2"; gene_source "insdc"; gene_biotype "protein_coding";
+chrM	insdc	transcript	7586	8269	.	+	.	gene_id "ENSG00000198712"; gene_version "1"; transcript_id "ENST00000361739"; transcript_version "1"; gene_name "MT-CO2"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-CO2-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; tag "basic";
+chrM	insdc	exon	7586	8269	.	+	.	gene_id "ENSG00000198712"; gene_version "1"; transcript_id "ENST00000361739"; transcript_version "1"; exon_number "1"; gene_name "MT-CO2"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-CO2-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; exon_id "ENSE00001435613"; exon_version "1"; tag "basic";
+chrM	insdc	CDS	7586	8266	.	+	0	gene_id "ENSG00000198712"; gene_version "1"; transcript_id "ENST00000361739"; transcript_version "1"; exon_number "1"; gene_name "MT-CO2"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-CO2-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; protein_id "ENSP00000354876"; protein_version "1"; tag "basic";
+chrM	insdc	start_codon	7586	7588	.	+	0	gene_id "ENSG00000198712"; gene_version "1"; transcript_id "ENST00000361739"; transcript_version "1"; exon_number "1"; gene_name "MT-CO2"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-CO2-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; tag "basic";
+chrM	insdc	stop_codon	8267	8269	.	+	0	gene_id "ENSG00000198712"; gene_version "1"; transcript_id "ENST00000361739"; transcript_version "1"; exon_number "1"; gene_name "MT-CO2"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-CO2-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; tag "basic";
+chrM	insdc	gene	8295	8364	.	+	.	gene_id "ENSG00000210156"; gene_version "1"; gene_name "MT-TK"; gene_source "insdc"; gene_biotype "Mt_tRNA";
+chrM	insdc	transcript	8295	8364	.	+	.	gene_id "ENSG00000210156"; gene_version "1"; transcript_id "ENST00000387421"; transcript_version "1"; gene_name "MT-TK"; gene_source "insdc"; gene_biotype "Mt_tRNA"; transcript_name "MT-TK-201"; transcript_source "insdc"; transcript_biotype "Mt_tRNA"; tag "basic";
+chrM	insdc	exon	8295	8364	.	+	.	gene_id "ENSG00000210156"; gene_version "1"; transcript_id "ENST00000387421"; transcript_version "1"; exon_number "1"; gene_name "MT-TK"; gene_source "insdc"; gene_biotype "Mt_tRNA"; transcript_name "MT-TK-201"; transcript_source "insdc"; transcript_biotype "Mt_tRNA"; exon_id "ENSE00001544484"; exon_version "1"; tag "basic";
+chrM	insdc	gene	8366	8572	.	+	.	gene_id "ENSG00000228253"; gene_version "1"; gene_name "MT-ATP8"; gene_source "insdc"; gene_biotype "protein_coding";
+chrM	insdc	transcript	8366	8572	.	+	.	gene_id "ENSG00000228253"; gene_version "1"; transcript_id "ENST00000361851"; transcript_version "1"; gene_name "MT-ATP8"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-ATP8-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; tag "basic";
+chrM	insdc	exon	8366	8572	.	+	.	gene_id "ENSG00000228253"; gene_version "1"; transcript_id "ENST00000361851"; transcript_version "1"; exon_number "1"; gene_name "MT-ATP8"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-ATP8-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; exon_id "ENSE00001435286"; exon_version "1"; tag "basic";
+chrM	insdc	CDS	8366	8569	.	+	0	gene_id "ENSG00000228253"; gene_version "1"; transcript_id "ENST00000361851"; transcript_version "1"; exon_number "1"; gene_name "MT-ATP8"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-ATP8-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; protein_id "ENSP00000355265"; protein_version "1"; tag "basic";
+chrM	insdc	start_codon	8366	8368	.	+	0	gene_id "ENSG00000228253"; gene_version "1"; transcript_id "ENST00000361851"; transcript_version "1"; exon_number "1"; gene_name "MT-ATP8"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-ATP8-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; tag "basic";
+chrM	insdc	stop_codon	8570	8572	.	+	0	gene_id "ENSG00000228253"; gene_version "1"; transcript_id "ENST00000361851"; transcript_version "1"; exon_number "1"; gene_name "MT-ATP8"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-ATP8-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; tag "basic";
+chrM	insdc	gene	8527	9207	.	+	.	gene_id "ENSG00000198899"; gene_version "2"; gene_name "MT-ATP6"; gene_source "insdc"; gene_biotype "protein_coding";
+chrM	insdc	transcript	8527	9207	.	+	.	gene_id "ENSG00000198899"; gene_version "2"; transcript_id "ENST00000361899"; transcript_version "2"; gene_name "MT-ATP6"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-ATP6-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; tag "basic";
+chrM	insdc	exon	8527	9207	.	+	.	gene_id "ENSG00000198899"; gene_version "2"; transcript_id "ENST00000361899"; transcript_version "2"; exon_number "1"; gene_name "MT-ATP6"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-ATP6-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; exon_id "ENSE00001727012"; exon_version "2"; tag "basic";
+chrM	insdc	CDS	8527	9204	.	+	0	gene_id "ENSG00000198899"; gene_version "2"; transcript_id "ENST00000361899"; transcript_version "2"; exon_number "1"; gene_name "MT-ATP6"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-ATP6-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; protein_id "ENSP00000354632"; protein_version "2"; tag "basic";
+chrM	insdc	start_codon	8527	8529	.	+	0	gene_id "ENSG00000198899"; gene_version "2"; transcript_id "ENST00000361899"; transcript_version "2"; exon_number "1"; gene_name "MT-ATP6"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-ATP6-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; tag "basic";
+chrM	insdc	stop_codon	9205	9207	.	+	0	gene_id "ENSG00000198899"; gene_version "2"; transcript_id "ENST00000361899"; transcript_version "2"; exon_number "1"; gene_name "MT-ATP6"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-ATP6-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; tag "basic";
+chrM	insdc	gene	9207	9990	.	+	.	gene_id "ENSG00000198938"; gene_version "2"; gene_name "MT-CO3"; gene_source "insdc"; gene_biotype "protein_coding";
+chrM	insdc	transcript	9207	9990	.	+	.	gene_id "ENSG00000198938"; gene_version "2"; transcript_id "ENST00000362079"; transcript_version "2"; gene_name "MT-CO3"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-CO3-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; tag "basic";
+chrM	insdc	exon	9207	9990	.	+	.	gene_id "ENSG00000198938"; gene_version "2"; transcript_id "ENST00000362079"; transcript_version "2"; exon_number "1"; gene_name "MT-CO3"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-CO3-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; exon_id "ENSE00001608952"; exon_version "2"; tag "basic";
+chrM	insdc	CDS	9207	9990	.	+	0	gene_id "ENSG00000198938"; gene_version "2"; transcript_id "ENST00000362079"; transcript_version "2"; exon_number "1"; gene_name "MT-CO3"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-CO3-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; protein_id "ENSP00000354982"; protein_version "2"; tag "basic";
+chrM	insdc	start_codon	9207	9209	.	+	0	gene_id "ENSG00000198938"; gene_version "2"; transcript_id "ENST00000362079"; transcript_version "2"; exon_number "1"; gene_name "MT-CO3"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-CO3-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; tag "basic";
+chrM	insdc	gene	9991	10058	.	+	.	gene_id "ENSG00000210164"; gene_version "1"; gene_name "MT-TG"; gene_source "insdc"; gene_biotype "Mt_tRNA";
+chrM	insdc	transcript	9991	10058	.	+	.	gene_id "ENSG00000210164"; gene_version "1"; transcript_id "ENST00000387429"; transcript_version "1"; gene_name "MT-TG"; gene_source "insdc"; gene_biotype "Mt_tRNA"; transcript_name "MT-TG-201"; transcript_source "insdc"; transcript_biotype "Mt_tRNA"; tag "basic";
+chrM	insdc	exon	9991	10058	.	+	.	gene_id "ENSG00000210164"; gene_version "1"; transcript_id "ENST00000387429"; transcript_version "1"; exon_number "1"; gene_name "MT-TG"; gene_source "insdc"; gene_biotype "Mt_tRNA"; transcript_name "MT-TG-201"; transcript_source "insdc"; transcript_biotype "Mt_tRNA"; exon_id "ENSE00001544483"; exon_version "1"; tag "basic";
+chrM	insdc	gene	10059	10404	.	+	.	gene_id "ENSG00000198840"; gene_version "2"; gene_name "MT-ND3"; gene_source "insdc"; gene_biotype "protein_coding";
+chrM	insdc	transcript	10059	10404	.	+	.	gene_id "ENSG00000198840"; gene_version "2"; transcript_id "ENST00000361227"; transcript_version "2"; gene_name "MT-ND3"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-ND3-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; tag "basic";
+chrM	insdc	exon	10059	10404	.	+	.	gene_id "ENSG00000198840"; gene_version "2"; transcript_id "ENST00000361227"; transcript_version "2"; exon_number "1"; gene_name "MT-ND3"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-ND3-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; exon_id "ENSE00001435444"; exon_version "2"; tag "basic";
+chrM	insdc	CDS	10059	10404	.	+	0	gene_id "ENSG00000198840"; gene_version "2"; transcript_id "ENST00000361227"; transcript_version "2"; exon_number "1"; gene_name "MT-ND3"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-ND3-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; protein_id "ENSP00000355206"; protein_version "2"; tag "basic";
+chrM	insdc	start_codon	10059	10061	.	+	0	gene_id "ENSG00000198840"; gene_version "2"; transcript_id "ENST00000361227"; transcript_version "2"; exon_number "1"; gene_name "MT-ND3"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-ND3-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; tag "basic";
+chrM	insdc	gene	10405	10469	.	+	.	gene_id "ENSG00000210174"; gene_version "1"; gene_name "MT-TR"; gene_source "insdc"; gene_biotype "Mt_tRNA";
+chrM	insdc	transcript	10405	10469	.	+	.	gene_id "ENSG00000210174"; gene_version "1"; transcript_id "ENST00000387439"; transcript_version "1"; gene_name "MT-TR"; gene_source "insdc"; gene_biotype "Mt_tRNA"; transcript_name "MT-TR-201"; transcript_source "insdc"; transcript_biotype "Mt_tRNA"; tag "basic";
+chrM	insdc	exon	10405	10469	.	+	.	gene_id "ENSG00000210174"; gene_version "1"; transcript_id "ENST00000387439"; transcript_version "1"; exon_number "1"; gene_name "MT-TR"; gene_source "insdc"; gene_biotype "Mt_tRNA"; transcript_name "MT-TR-201"; transcript_source "insdc"; transcript_biotype "Mt_tRNA"; exon_id "ENSE00001544482"; exon_version "1"; tag "basic";
+chrM	insdc	gene	10470	10766	.	+	.	gene_id "ENSG00000212907"; gene_version "2"; gene_name "MT-ND4L"; gene_source "insdc"; gene_biotype "protein_coding";
+chrM	insdc	transcript	10470	10766	.	+	.	gene_id "ENSG00000212907"; gene_version "2"; transcript_id "ENST00000361335"; transcript_version "1"; gene_name "MT-ND4L"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-ND4L-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; tag "basic";
+chrM	insdc	exon	10470	10766	.	+	.	gene_id "ENSG00000212907"; gene_version "2"; transcript_id "ENST00000361335"; transcript_version "1"; exon_number "1"; gene_name "MT-ND4L"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-ND4L-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; exon_id "ENSE00001596097"; exon_version "1"; tag "basic";
+chrM	insdc	CDS	10470	10763	.	+	0	gene_id "ENSG00000212907"; gene_version "2"; transcript_id "ENST00000361335"; transcript_version "1"; exon_number "1"; gene_name "MT-ND4L"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-ND4L-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; protein_id "ENSP00000354728"; protein_version "1"; tag "basic";
+chrM	insdc	start_codon	10470	10472	.	+	0	gene_id "ENSG00000212907"; gene_version "2"; transcript_id "ENST00000361335"; transcript_version "1"; exon_number "1"; gene_name "MT-ND4L"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-ND4L-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; tag "basic";
+chrM	insdc	stop_codon	10764	10766	.	+	0	gene_id "ENSG00000212907"; gene_version "2"; transcript_id "ENST00000361335"; transcript_version "1"; exon_number "1"; gene_name "MT-ND4L"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-ND4L-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; tag "basic";
+chrM	insdc	gene	10760	12137	.	+	.	gene_id "ENSG00000198886"; gene_version "2"; gene_name "MT-ND4"; gene_source "insdc"; gene_biotype "protein_coding";
+chrM	insdc	transcript	10760	12137	.	+	.	gene_id "ENSG00000198886"; gene_version "2"; transcript_id "ENST00000361381"; transcript_version "2"; gene_name "MT-ND4"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-ND4-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; tag "basic";
+chrM	insdc	exon	10760	12137	.	+	.	gene_id "ENSG00000198886"; gene_version "2"; transcript_id "ENST00000361381"; transcript_version "2"; exon_number "1"; gene_name "MT-ND4"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-ND4-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; exon_id "ENSE00001666004"; exon_version "2"; tag "basic";
+chrM	insdc	CDS	10760	12137	.	+	0	gene_id "ENSG00000198886"; gene_version "2"; transcript_id "ENST00000361381"; transcript_version "2"; exon_number "1"; gene_name "MT-ND4"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-ND4-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; protein_id "ENSP00000354961"; protein_version "2"; tag "basic";
+chrM	insdc	start_codon	10760	10762	.	+	0	gene_id "ENSG00000198886"; gene_version "2"; transcript_id "ENST00000361381"; transcript_version "2"; exon_number "1"; gene_name "MT-ND4"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-ND4-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; tag "basic";
+chrM	insdc	gene	12138	12206	.	+	.	gene_id "ENSG00000210176"; gene_version "1"; gene_name "MT-TH"; gene_source "insdc"; gene_biotype "Mt_tRNA";
+chrM	insdc	transcript	12138	12206	.	+	.	gene_id "ENSG00000210176"; gene_version "1"; transcript_id "ENST00000387441"; transcript_version "1"; gene_name "MT-TH"; gene_source "insdc"; gene_biotype "Mt_tRNA"; transcript_name "MT-TH-201"; transcript_source "insdc"; transcript_biotype "Mt_tRNA"; tag "basic";
+chrM	insdc	exon	12138	12206	.	+	.	gene_id "ENSG00000210176"; gene_version "1"; transcript_id "ENST00000387441"; transcript_version "1"; exon_number "1"; gene_name "MT-TH"; gene_source "insdc"; gene_biotype "Mt_tRNA"; transcript_name "MT-TH-201"; transcript_source "insdc"; transcript_biotype "Mt_tRNA"; exon_id "ENSE00001544480"; exon_version "1"; tag "basic";
+chrM	insdc	gene	12207	12265	.	+	.	gene_id "ENSG00000210184"; gene_version "1"; gene_name "MT-TS2"; gene_source "insdc"; gene_biotype "Mt_tRNA";
+chrM	insdc	transcript	12207	12265	.	+	.	gene_id "ENSG00000210184"; gene_version "1"; transcript_id "ENST00000387449"; transcript_version "1"; gene_name "MT-TS2"; gene_source "insdc"; gene_biotype "Mt_tRNA"; transcript_name "MT-TS2-201"; transcript_source "insdc"; transcript_biotype "Mt_tRNA"; tag "basic";
+chrM	insdc	exon	12207	12265	.	+	.	gene_id "ENSG00000210184"; gene_version "1"; transcript_id "ENST00000387449"; transcript_version "1"; exon_number "1"; gene_name "MT-TS2"; gene_source "insdc"; gene_biotype "Mt_tRNA"; transcript_name "MT-TS2-201"; transcript_source "insdc"; transcript_biotype "Mt_tRNA"; exon_id "ENSE00001544479"; exon_version "1"; tag "basic";
+chrM	insdc	gene	12266	12336	.	+	.	gene_id "ENSG00000210191"; gene_version "1"; gene_name "MT-TL2"; gene_source "insdc"; gene_biotype "Mt_tRNA";
+chrM	insdc	transcript	12266	12336	.	+	.	gene_id "ENSG00000210191"; gene_version "1"; transcript_id "ENST00000387456"; transcript_version "1"; gene_name "MT-TL2"; gene_source "insdc"; gene_biotype "Mt_tRNA"; transcript_name "MT-TL2-201"; transcript_source "insdc"; transcript_biotype "Mt_tRNA"; tag "basic";
+chrM	insdc	exon	12266	12336	.	+	.	gene_id "ENSG00000210191"; gene_version "1"; transcript_id "ENST00000387456"; transcript_version "1"; exon_number "1"; gene_name "MT-TL2"; gene_source "insdc"; gene_biotype "Mt_tRNA"; transcript_name "MT-TL2-201"; transcript_source "insdc"; transcript_biotype "Mt_tRNA"; exon_id "ENSE00001544478"; exon_version "1"; tag "basic";
+chrM	insdc	gene	12337	14148	.	+	.	gene_id "ENSG00000198786"; gene_version "2"; gene_name "MT-ND5"; gene_source "insdc"; gene_biotype "protein_coding";
+chrM	insdc	transcript	12337	14148	.	+	.	gene_id "ENSG00000198786"; gene_version "2"; transcript_id "ENST00000361567"; transcript_version "2"; gene_name "MT-ND5"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-ND5-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; tag "basic";
+chrM	insdc	exon	12337	14148	.	+	.	gene_id "ENSG00000198786"; gene_version "2"; transcript_id "ENST00000361567"; transcript_version "2"; exon_number "1"; gene_name "MT-ND5"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-ND5-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; exon_id "ENSE00001435330"; exon_version "2"; tag "basic";
+chrM	insdc	CDS	12337	14145	.	+	0	gene_id "ENSG00000198786"; gene_version "2"; transcript_id "ENST00000361567"; transcript_version "2"; exon_number "1"; gene_name "MT-ND5"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-ND5-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; protein_id "ENSP00000354813"; protein_version "2"; tag "basic";
+chrM	insdc	start_codon	12337	12339	.	+	0	gene_id "ENSG00000198786"; gene_version "2"; transcript_id "ENST00000361567"; transcript_version "2"; exon_number "1"; gene_name "MT-ND5"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-ND5-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; tag "basic";
+chrM	insdc	stop_codon	14146	14148	.	+	0	gene_id "ENSG00000198786"; gene_version "2"; transcript_id "ENST00000361567"; transcript_version "2"; exon_number "1"; gene_name "MT-ND5"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-ND5-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; tag "basic";
+chrM	insdc	gene	14149	14673	.	-	.	gene_id "ENSG00000198695"; gene_version "2"; gene_name "MT-ND6"; gene_source "insdc"; gene_biotype "protein_coding";
+chrM	insdc	transcript	14149	14673	.	-	.	gene_id "ENSG00000198695"; gene_version "2"; transcript_id "ENST00000361681"; transcript_version "2"; gene_name "MT-ND6"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-ND6-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; tag "basic";
+chrM	insdc	exon	14149	14673	.	-	.	gene_id "ENSG00000198695"; gene_version "2"; transcript_id "ENST00000361681"; transcript_version "2"; exon_number "1"; gene_name "MT-ND6"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-ND6-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; exon_id "ENSE00001434974"; exon_version "2"; tag "basic";
+chrM	insdc	CDS	14152	14673	.	-	0	gene_id "ENSG00000198695"; gene_version "2"; transcript_id "ENST00000361681"; transcript_version "2"; exon_number "1"; gene_name "MT-ND6"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-ND6-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; protein_id "ENSP00000354665"; protein_version "2"; tag "basic";
+chrM	insdc	start_codon	14671	14673	.	-	0	gene_id "ENSG00000198695"; gene_version "2"; transcript_id "ENST00000361681"; transcript_version "2"; exon_number "1"; gene_name "MT-ND6"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-ND6-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; tag "basic";
+chrM	insdc	stop_codon	14149	14151	.	-	0	gene_id "ENSG00000198695"; gene_version "2"; transcript_id "ENST00000361681"; transcript_version "2"; exon_number "1"; gene_name "MT-ND6"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-ND6-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; tag "basic";
+chrM	insdc	gene	14674	14742	.	-	.	gene_id "ENSG00000210194"; gene_version "1"; gene_name "MT-TE"; gene_source "insdc"; gene_biotype "Mt_tRNA";
+chrM	insdc	transcript	14674	14742	.	-	.	gene_id "ENSG00000210194"; gene_version "1"; transcript_id "ENST00000387459"; transcript_version "1"; gene_name "MT-TE"; gene_source "insdc"; gene_biotype "Mt_tRNA"; transcript_name "MT-TE-201"; transcript_source "insdc"; transcript_biotype "Mt_tRNA"; tag "basic";
+chrM	insdc	exon	14674	14742	.	-	.	gene_id "ENSG00000210194"; gene_version "1"; transcript_id "ENST00000387459"; transcript_version "1"; exon_number "1"; gene_name "MT-TE"; gene_source "insdc"; gene_biotype "Mt_tRNA"; transcript_name "MT-TE-201"; transcript_source "insdc"; transcript_biotype "Mt_tRNA"; exon_id "ENSE00001544476"; exon_version "1"; tag "basic";
+chrM	insdc	gene	14747	15887	.	+	.	gene_id "ENSG00000198727"; gene_version "2"; gene_name "MT-CYB"; gene_source "insdc"; gene_biotype "protein_coding";
+chrM	insdc	transcript	14747	15887	.	+	.	gene_id "ENSG00000198727"; gene_version "2"; transcript_id "ENST00000361789"; transcript_version "2"; gene_name "MT-CYB"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-CYB-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; tag "basic";
+chrM	insdc	exon	14747	15887	.	+	.	gene_id "ENSG00000198727"; gene_version "2"; transcript_id "ENST00000361789"; transcript_version "2"; exon_number "1"; gene_name "MT-CYB"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-CYB-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; exon_id "ENSE00001436074"; exon_version "2"; tag "basic";
+chrM	insdc	CDS	14747	15887	.	+	0	gene_id "ENSG00000198727"; gene_version "2"; transcript_id "ENST00000361789"; transcript_version "2"; exon_number "1"; gene_name "MT-CYB"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-CYB-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; protein_id "ENSP00000354554"; protein_version "2"; tag "basic";
+chrM	insdc	start_codon	14747	14749	.	+	0	gene_id "ENSG00000198727"; gene_version "2"; transcript_id "ENST00000361789"; transcript_version "2"; exon_number "1"; gene_name "MT-CYB"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-CYB-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; tag "basic";
+chrM	insdc	gene	15888	15953	.	+	.	gene_id "ENSG00000210195"; gene_version "2"; gene_name "MT-TT"; gene_source "insdc"; gene_biotype "Mt_tRNA";
+chrM	insdc	transcript	15888	15953	.	+	.	gene_id "ENSG00000210195"; gene_version "2"; transcript_id "ENST00000387460"; transcript_version "2"; gene_name "MT-TT"; gene_source "insdc"; gene_biotype "Mt_tRNA"; transcript_name "MT-TT-201"; transcript_source "insdc"; transcript_biotype "Mt_tRNA"; tag "basic";
+chrM	insdc	exon	15888	15953	.	+	.	gene_id "ENSG00000210195"; gene_version "2"; transcript_id "ENST00000387460"; transcript_version "2"; exon_number "1"; gene_name "MT-TT"; gene_source "insdc"; gene_biotype "Mt_tRNA"; transcript_name "MT-TT-201"; transcript_source "insdc"; transcript_biotype "Mt_tRNA"; exon_id "ENSE00001544475"; exon_version "2"; tag "basic";
+chrM	insdc	gene	15956	16023	.	-	.	gene_id "ENSG00000210196"; gene_version "2"; gene_name "MT-TP"; gene_source "insdc"; gene_biotype "Mt_tRNA";
+chrM	insdc	transcript	15956	16023	.	-	.	gene_id "ENSG00000210196"; gene_version "2"; transcript_id "ENST00000387461"; transcript_version "2"; gene_name "MT-TP"; gene_source "insdc"; gene_biotype "Mt_tRNA"; transcript_name "MT-TP-201"; transcript_source "insdc"; transcript_biotype "Mt_tRNA"; tag "basic";
+chrM	insdc	exon	15956	16023	.	-	.	gene_id "ENSG00000210196"; gene_version "2"; transcript_id "ENST00000387461"; transcript_version "2"; exon_number "1"; gene_name "MT-TP"; gene_source "insdc"; gene_biotype "Mt_tRNA"; transcript_name "MT-TP-201"; transcript_source "insdc"; transcript_biotype "Mt_tRNA"; exon_id "ENSE00001544473"; exon_version "2"; tag "basic";
--- a/test-data/picard_CollectRnaSeqMetrics_test2.tab	Tue Oct 16 11:48:40 2018 -0400
+++ b/test-data/picard_CollectRnaSeqMetrics_test2.tab	Fri Mar 29 08:31:40 2019 -0400
@@ -1,10 +1,113 @@
 ## htsjdk.samtools.metrics.StringHeader
-# CollectRnaSeqMetrics REF_FLAT=refFlat.tab STRAND_SPECIFICITY=NONE MINIMUM_LENGTH=500 CHART_OUTPUT=/tmp/tmpYRm8q4/files/000/dataset_34.dat RRNA_FRAGMENT_PERCENTAGE=0.8 METRIC_ACCUMULATION_LEVEL=[ALL_READS] INPUT=picard_CollectRnaSeqMetrics_bam OUTPUT=/tmp/tmpYRm8q4/files/000/dataset_35.dat ASSUME_SORTED=true VALIDATION_STRINGENCY=LENIENT REFERENCE_SEQUENCE=localref.fa    STOP_AFTER=0 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false
+# picard.analysis.CollectRnaSeqMetrics REF_FLAT=refFlat.tab STRAND_SPECIFICITY=NONE MINIMUM_LENGTH=500 CHART_OUTPUT=/opt/galaxy/galaxy/database/files/033/dataset_33778.dat RRNA_FRAGMENT_PERCENTAGE=0.8 METRIC_ACCUMULATION_LEVEL=[ALL_READS] INPUT=picard_CollectRnaSeqMetrics_bam OUTPUT=/opt/galaxy/galaxy/database/files/033/dataset_33779.dat ASSUME_SORTED=true VALIDATION_STRINGENCY=LENIENT REFERENCE_SEQUENCE=localref.fa    STOP_AFTER=0 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
 ## htsjdk.samtools.metrics.StringHeader
-# Started on: Sat Apr 14 09:30:06 CEST 2018
+# Started on: Thu Jan 31 11:57:28 GMT 2019
 
 ## METRICS CLASS	picard.analysis.RnaSeqMetrics
 PF_BASES	PF_ALIGNED_BASES	RIBOSOMAL_BASES	CODING_BASES	UTR_BASES	INTRONIC_BASES	INTERGENIC_BASES	IGNORED_READS	CORRECT_STRAND_READS	INCORRECT_STRAND_READS	NUM_R1_TRANSCRIPT_STRAND_READS	NUM_R2_TRANSCRIPT_STRAND_READS	NUM_UNEXPLAINED_READS	PCT_R1_TRANSCRIPT_STRAND_READS	PCT_R2_TRANSCRIPT_STRAND_READS	PCT_RIBOSOMAL_BASES	PCT_CODING_BASES	PCT_UTR_BASES	PCT_INTRONIC_BASES	PCT_INTERGENIC_BASES	PCT_MRNA_BASES	PCT_USABLE_BASES	PCT_CORRECT_STRAND_READS	MEDIAN_CV_COVERAGE	MEDIAN_5PRIME_BIAS	MEDIAN_3PRIME_BIAS	MEDIAN_5PRIME_TO_3PRIME_BIAS	SAMPLE	LIBRARY	READ_GROUP
-48870	48712		0	0	0	48712	0	0	0	0	0	0	0	0		0	0	0	1	0	0	0	0	0	0	0			
+48870	48712		40205	8172	0	335	0	0	0	118	141	5	0.455598	0.544402		0.825361	0.167762	0	0.006877	0.993123	0.989912	0	0.801606	0.364744	0.224119	0.579618			
 
+## HISTOGRAM	java.lang.Integer
+normalized_position	All_Reads.normalized_coverage
+0	0.228841
+1	0.251223
+2	0.223738
+3	0.233838
+4	0.256581
+5	0.266966
+6	0.271332
+7	0.265645
+8	0.260346
+9	0.231289
+10	0.269298
+11	0.326408
+12	0.373618
+13	0.473463
+14	0.54793
+15	0.577498
+16	0.542569
+17	0.558467
+18	0.650338
+19	0.635229
+20	0.574853
+21	0.588563
+22	0.650078
+23	0.686162
+24	0.634014
+25	0.644335
+26	0.631052
+27	0.639668
+28	0.705101
+29	0.778048
+30	0.736876
+31	0.70567
+32	0.707551
+33	0.76318
+34	0.852513
+35	0.873038
+36	0.943469
+37	1.040668
+38	1.070803
+39	1.117516
+40	1.166565
+41	1.178104
+42	1.151426
+43	1.209844
+44	1.198299
+45	1.132792
+46	1.149512
+47	1.21306
+48	1.345953
+49	1.32854
+50	1.309067
+51	1.296104
+52	1.346535
+53	1.450902
+54	1.475516
+55	1.548883
+56	1.628424
+57	1.665228
+58	1.612393
+59	1.653451
+60	1.599084
+61	1.674705
+62	1.670767
+63	1.759351
+64	1.771555
+65	1.653379
+66	1.634736
+67	1.642939
+68	1.587437
+69	1.558905
+70	1.571999
+71	1.620224
+72	1.57181
+73	1.545141
+74	1.433348
+75	1.497304
+76	1.693651
+77	1.728257
+78	1.754671
+79	1.731652
+80	1.713865
+81	1.641332
+82	1.515711
+83	1.413569
+84	1.441502
+85	1.330984
+86	1.269559
+87	1.225153
+88	1.133803
+89	0.956795
+90	0.793511
+91	0.692324
+92	0.542889
+93	0.499087
+94	0.422605
+95	0.338219
+96	0.272388
+97	0.207126
+98	0.152439
+99	0.095696
+100	0.069183