# HG changeset patch
# User iuc
# Date 1658914095 0
# Node ID cef79931dda5de51b28103e22cc6e220ea6d69cd
# Parent  333a6e13b62234b8be3755501ea0e3f2b49cc346
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 7f649c10c5d874f466122af0d24803a4c6affabb

diff -r 333a6e13b622 -r cef79931dda5 stringtie.xml
--- a/stringtie.xml	Tue Nov 30 11:01:34 2021 +0000
+++ b/stringtie.xml	Wed Jul 27 09:28:15 2022 +0000
@@ -277,7 +277,7 @@
                 <param name="input_mode" value="short_reads"/>
                 <param name="input_bam" ftype="bam" value="stringtie_in1.bam" />
             </conditional>
-            <output name="output_gtf" file="stringtie_out1.gtf" ftype="gtf" lines_diff="4" />
+            <output name="output_gtf" file="stringtie_out1_re.gtf" ftype="gtf" compare="re_match" sort="true"/>
         </test>
         <!--Ensure fraction option works -->
         <test expect_num_outputs="1">
@@ -286,7 +286,7 @@
                 <param name="input_bam" ftype="bam" value="stringtie_in1.bam" />
             </conditional>            
             <param name="fraction" value="0.17" />
-            <output name="output_gtf" file="stringtie_out2.gtf" ftype="gtf" lines_diff="4" />
+            <output name="output_gtf" file="stringtie_out2_re.gtf" ftype="gtf" compare="re_match" sort="true"/>
         </test>
         <!--Ensure guide option works -->
         <test expect_num_outputs="1">
@@ -297,7 +297,7 @@
             <param name="use_guide" value="yes" />
             <param name="guide_gff_select" value="history" />
             <param name="ref_hist" ftype="gtf" value="stringtie_in.gtf" />
-            <output name="output_gtf" file="stringtie_out3.gtf" ftype="gtf" lines_diff="4"  />
+            <output name="output_gtf" file="stringtie_out3_re.gtf" ftype="gtf" compare="re_match" sort="true"/>
         </test>
         <!--Ensure guide with fraction works -->
         <test expect_num_outputs="1">
@@ -309,7 +309,7 @@
             <param name="guide_gff_select" value="history" />
             <param name="ref_hist" ftype="gtf" value="stringtie_in.gtf" />
             <param name="fraction" value="0.17" />
-            <output name="output_gtf" file="stringtie_out4.gtf" ftype="gtf" lines_diff="4" />
+            <output name="output_gtf" file="stringtie_out4_re.gtf" ftype="gtf" compare="re_match" sort="true"/>
         </test>
         <!--Ensure coverage and output for Ballgown works -->
         <test expect_num_outputs="7">
@@ -327,8 +327,8 @@
             <output name="transcript_expression" file="./ballgown/t_data.ctab" ftype="tabular" />
             <output name="exon_transcript_mapping" file="./ballgown/e2t.ctab" ftype="tabular" />
             <output name="intron_transcript_mapping" file="./ballgown/i2t.ctab" ftype="tabular" />
-            <output name="output_gtf" file="stringtie_out5.gtf" ftype="gtf" lines_diff="4" />
-            <output name="coverage" file="stringtie_out_coverage.gtf" ftype="gtf" />
+            <output name="output_gtf" file="stringtie_out5.gtf" ftype="gtf" compare="re_match" sort="true"/>
+            <output name="coverage" file="stringtie_out_coverage.gtf" ftype="gtf" compare="re_match" sort="true"/>
         </test>
         <!--Ensure output for edgeR works -->
         <test expect_num_outputs="5">
@@ -346,8 +346,8 @@
             <output name="gene_counts" file="gene_counts_edger.tsv" ftype="tabular" />
             <output name="transcript_counts" file="transcript_counts_edger.tsv" ftype="tabular" />
             <output name="legend" file="legend.tsv" ftype="tabular" />
-            <output name="output_gtf" file="stringtie_out6.gtf" ftype="gtf" lines_diff="4" />
-            <output name="coverage" file="stringtie_out_coverage.gtf" ftype="gtf" />
+            <output name="output_gtf" file="stringtie_out6.gtf" ftype="gtf" compare="re_match" sort="true"/>
+            <output name="coverage" file="stringtie_out_coverage.gtf" ftype="gtf" compare="re_match" sort="true"/>
         </test>
         <!--Ensure gene abundances output works -->
         <test expect_num_outputs="2">
@@ -360,7 +360,7 @@
             <param name="ref_hist" ftype="gtf" value="stringtie_in.gtf" />
             <param name="fraction" value="0.17" />
             <param name="abundance_estimation" value="true" />
-            <output name="output_gtf" file="stringtie_out4.gtf" ftype="gtf" lines_diff="4" />
+            <output name="output_gtf" file="stringtie_out4_re.gtf" ftype="gtf" compare="re_match" sort="true"/>
             <output name="gene_abundance_estimation" file="stringtie_out7.tsv" ftype="tabular" lines_diff="2" />
         </test>
         <!--Ensure another fraction value works -->
@@ -373,7 +373,7 @@
             <param name="guide_gff_select" value="history" />
             <param name="ref_hist" ftype="gtf" value="stringtie_in.gtf" />
             <param name="fraction" value="0.15" />
-            <output name="output_gtf" file="stringtie_out8.gtf" ftype="gtf" lines_diff="4" />
+            <output name="output_gtf" file="stringtie_out8.gtf" ftype="gtf" compare="re_match" sort="true"/>
         </test>
         <!--Ensure built-in GTFs work -->
         <test expect_num_outputs="1">
@@ -384,7 +384,7 @@
             <param name="use_guide" value="yes" />
             <param name="guide_gff_select" value="cached" />
             <param name="fraction" value="0.15" />
-            <output name="output_gtf" file="stringtie_out9.gtf" ftype="gtf" lines_diff="4" />
+            <output name="output_gtf" file="stringtie_out9.gtf" ftype="gtf" compare="re_match" sort="true"/>
         </test>
         <!-- Test long reads input -->
         <test expect_num_outputs="1">
@@ -395,7 +395,7 @@
             <param name="use_guide" value="yes" />
             <param name="guide_gff_select" value="cached" />
             <param name="fraction" value="0.15" />
-            <output name="output_gtf" file="stringtie_out10.gtf" ftype="gtf" lines_diff="4" />
+            <output name="output_gtf" file="stringtie_out10.gtf" ftype="gtf" compare="re_match" sort="true"/>
         </test>
         <!-- Test error splice option -->
         <test expect_num_outputs="1">
@@ -407,7 +407,7 @@
             <param name="use_guide" value="yes" />
             <param name="guide_gff_select" value="cached" />
             <param name="fraction" value="0.15" />
-            <output name="output_gtf" file="stringtie_out11.gtf" ftype="gtf" lines_diff="4" />
+            <output name="output_gtf" file="stringtie_out11.gtf" ftype="gtf"  compare="re_match" sort="true"/>
         </test>
         <!-- Test mixed reads input -->
         <test expect_num_outputs="1">
@@ -416,7 +416,7 @@
                 <param name="input_bam_short" ftype="bam" value="short_reads.bam" />
                 <param name="input_bam_long" ftype="bam" value="long_reads.bam" />
             </conditional>            
-            <output name="output_gtf" file="stringtie_out12.gtf" ftype="gtf" lines_diff="4" />
+            <output name="output_gtf" file="stringtie_out12.gtf" ftype="gtf" compare="re_match" sort="true"/>
         </test>
     </tests>
     <help><![CDATA[
diff -r 333a6e13b622 -r cef79931dda5 stringtie_merge.xml
--- a/stringtie_merge.xml	Tue Nov 30 11:01:34 2021 +0000
+++ b/stringtie_merge.xml	Wed Jul 27 09:28:15 2022 +0000
@@ -43,12 +43,12 @@
         <test>
             <param name="input_gtf" ftype="gtf" value="stringtie_out1.gtf,stringtie_out2.gtf,stringtie_out3.gtf,stringtie_out4.gtf" />
             <param name="guide_gff" ftype="gtf" value="stringtie_in.gtf" />
-            <output name="out_gtf" file="stringtie_merge_out1.gtf" ftype="gtf" lines_diff="4" />
+            <output name="out_gtf" file="stringtie_merge_out1.gtf" ftype="gtf" compare="re_match" sort="true" />
         </test>
         <test>
             <param name="input_gtf" ftype="gtf" value="stringtie_merge_in1.gtf,stringtie_merge_in2.gtf" />
             <param name="guide_gff" ftype="gtf" value="stringtie_merge_in3.gtf" />
-            <output name="out_gtf" file="stringtie_merge_out2.gtf" ftype="gtf" lines_diff="4" />
+            <output name="out_gtf" file="stringtie_merge_out2.gtf" ftype="gtf" compare="re_match" sort="true" />
         </test>
         <test>
             <param name="input_gtf" ftype="gtf" value="stringtie_merge_in1.gtf,stringtie_merge_in2.gtf" />
diff -r 333a6e13b622 -r cef79931dda5 test-data/stringtie_merge_out1.gtf
--- a/test-data/stringtie_merge_out1.gtf	Tue Nov 30 11:01:34 2021 +0000
+++ b/test-data/stringtie_merge_out1.gtf	Wed Jul 27 09:28:15 2022 +0000
@@ -1,6 +1,6 @@
-# stringtie --merge -p 1 -G /tmp/tmp9cgbzsli/files/f/8/0/dataset_f808ceaa-08fb-4e16-8d00-3af3bd707ede.dat -m 50 -c 0 -F 1.0 -T 1.0 -f 0.01 -g 250 -o /tmp/tmp9cgbzsli/files/1/2/f/dataset_12ff3ea2-5306-479a-915b-9af32e1defa1.dat /tmp/tmp9cgbzsli/files/5/e/0/dataset_5e0ac785-035b-41ca-acb3-1276d358574d.dat /tmp/tmp9cgbzsli/files/b/3/1/dataset_b3195d2c-e25d-4c21-a9f8-14c79961b98b.dat /tmp/tmp9cgbzsli/files/a/5/f/dataset_a5f7edd6-3748-4854-bd0d-68c03c3ba68e.dat /tmp/tmp9cgbzsli/files/4/5/d/dataset_45d17dfd-c663-43fd-a2ef-e41dd94caa53.dat
-# StringTie version 2.1.7
-test_chromosome	StringTie	transcript	53	550	1000	+	.	gene_id "MSTRG.1"; transcript_id "CUFF.1.1"; ref_gene_id "CUFF.1"; 
-test_chromosome	StringTie	exon	53	250	1000	+	.	gene_id "MSTRG.1"; transcript_id "CUFF.1.1"; exon_number "1"; ref_gene_id "CUFF.1"; 
-test_chromosome	StringTie	exon	351	400	1000	+	.	gene_id "MSTRG.1"; transcript_id "CUFF.1.1"; exon_number "2"; ref_gene_id "CUFF.1"; 
-test_chromosome	StringTie	exon	501	550	1000	+	.	gene_id "MSTRG.1"; transcript_id "CUFF.1.1"; exon_number "3"; ref_gene_id "CUFF.1"; 
+# StringTie version 2\.1\.7
+# stringtie --merge -p [0-9]+ -G /[-_/a-zA-Z0-9]+\.dat -m 50 -c 0 -F 1\.0 -T 1\.0 -f 0\.01 -g 250 -o /[-_/a-zA-Z0-9]+\.dat /[-_/a-zA-Z0-9]+\.dat /[-_/a-zA-Z0-9]+\.dat /[-_/a-zA-Z0-9]+\.dat /[-_/a-zA-Z0-9]+\.dat
+test_chromosome\tStringTie\texon\t351\t400\t1000\t\+\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "CUFF\.[0-9]+\.1"; exon_number "[0-9]+"; ref_gene_id "CUFF\.[0-9]+"; 
+test_chromosome\tStringTie\texon\t501\t550\t1000\t\+\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "CUFF\.[0-9]+\.1"; exon_number "[0-9]+"; ref_gene_id "CUFF\.[0-9]+"; 
+test_chromosome\tStringTie\texon\t53\t250\t1000\t\+\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "CUFF\.[0-9]+\.1"; exon_number "[0-9]+"; ref_gene_id "CUFF\.[0-9]+"; 
+test_chromosome\tStringTie\ttranscript\t53\t550\t1000\t\+\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; 
diff -r 333a6e13b622 -r cef79931dda5 test-data/stringtie_merge_out2.gtf
--- a/test-data/stringtie_merge_out2.gtf	Tue Nov 30 11:01:34 2021 +0000
+++ b/test-data/stringtie_merge_out2.gtf	Wed Jul 27 09:28:15 2022 +0000
@@ -1,100 +1,100 @@
-# stringtie --merge -p 1 -G /tmp/tmp9cgbzsli/files/d/3/d/dataset_d3debef6-0cc0-44aa-898c-086d4fa8adb0.dat -m 50 -c 0 -F 1.0 -T 1.0 -f 0.01 -g 250 -o /tmp/tmp9cgbzsli/files/b/4/d/dataset_b4dd908f-5f52-428f-bc2c-ba62cd00a83e.dat /tmp/tmp9cgbzsli/files/8/1/a/dataset_81a6719e-2f36-40ca-9d63-325d6eadd1d3.dat /tmp/tmp9cgbzsli/files/2/2/f/dataset_22f857ec-0df8-40d8-ba00-28b709b98b03.dat
-# StringTie version 2.1.7
-chr1	StringTie	transcript	3189811	3193042	1000	.	.	gene_id "MSTRG.1"; transcript_id "MSTRG.1.1"; 
-chr1	StringTie	exon	3189811	3193042	1000	.	.	gene_id "MSTRG.1"; transcript_id "MSTRG.1.1"; exon_number "1"; 
-chr1	StringTie	transcript	3200023	3200191	1000	.	.	gene_id "MSTRG.2"; transcript_id "MSTRG.2.1"; 
-chr1	StringTie	exon	3200023	3200191	1000	.	.	gene_id "MSTRG.2"; transcript_id "MSTRG.2.1"; exon_number "1"; 
-chr1	StringTie	transcript	3201078	3201809	1000	.	.	gene_id "MSTRG.3"; transcript_id "MSTRG.3.1"; 
-chr1	StringTie	exon	3201078	3201809	1000	.	.	gene_id "MSTRG.3"; transcript_id "MSTRG.3.1"; exon_number "1"; 
-chr1	StringTie	transcript	3204563	3661579	1000	-	.	gene_id "MSTRG.4"; transcript_id "Xkr4"; ref_gene_id "Xkr4"; 
-chr1	StringTie	exon	3204563	3207049	1000	-	.	gene_id "MSTRG.4"; transcript_id "Xkr4"; exon_number "1"; ref_gene_id "Xkr4"; 
-chr1	StringTie	exon	3411783	3411982	1000	-	.	gene_id "MSTRG.4"; transcript_id "Xkr4"; exon_number "2"; ref_gene_id "Xkr4"; 
-chr1	StringTie	exon	3660633	3661579	1000	-	.	gene_id "MSTRG.4"; transcript_id "Xkr4"; exon_number "3"; ref_gene_id "Xkr4"; 
-chr1	StringTie	transcript	3212214	3212439	1000	.	.	gene_id "MSTRG.5"; transcript_id "MSTRG.5.1"; 
-chr1	StringTie	exon	3212214	3212439	1000	.	.	gene_id "MSTRG.5"; transcript_id "MSTRG.5.1"; exon_number "1"; 
-chr1	StringTie	transcript	3212718	3212801	1000	.	.	gene_id "MSTRG.6"; transcript_id "MSTRG.6.1"; 
-chr1	StringTie	exon	3212718	3212801	1000	.	.	gene_id "MSTRG.6"; transcript_id "MSTRG.6.1"; exon_number "1"; 
-chr1	StringTie	transcript	3213096	3213242	1000	.	.	gene_id "MSTRG.7"; transcript_id "MSTRG.7.1"; 
-chr1	StringTie	exon	3213096	3213242	1000	.	.	gene_id "MSTRG.7"; transcript_id "MSTRG.7.1"; exon_number "1"; 
-chr1	StringTie	transcript	3242634	3243079	1000	.	.	gene_id "MSTRG.8"; transcript_id "MSTRG.8.1"; 
-chr1	StringTie	exon	3242634	3243079	1000	.	.	gene_id "MSTRG.8"; transcript_id "MSTRG.8.1"; exon_number "1"; 
-chr1	StringTie	transcript	3243348	3243401	1000	.	.	gene_id "MSTRG.9"; transcript_id "MSTRG.9.1"; 
-chr1	StringTie	exon	3243348	3243401	1000	.	.	gene_id "MSTRG.9"; transcript_id "MSTRG.9.1"; exon_number "1"; 
-chr1	StringTie	transcript	3277914	3278390	1000	.	.	gene_id "MSTRG.10"; transcript_id "MSTRG.10.1"; 
-chr1	StringTie	exon	3277914	3278390	1000	.	.	gene_id "MSTRG.10"; transcript_id "MSTRG.10.1"; exon_number "1"; 
-chr1	StringTie	transcript	3280687	3280741	1000	.	.	gene_id "MSTRG.11"; transcript_id "MSTRG.11.1"; 
-chr1	StringTie	exon	3280687	3280741	1000	.	.	gene_id "MSTRG.11"; transcript_id "MSTRG.11.1"; exon_number "1"; 
-chr1	StringTie	transcript	3282761	3282832	1000	.	.	gene_id "MSTRG.12"; transcript_id "MSTRG.12.1"; 
-chr1	StringTie	exon	3282761	3282832	1000	.	.	gene_id "MSTRG.12"; transcript_id "MSTRG.12.1"; exon_number "1"; 
-chr1	StringTie	transcript	3290489	3291273	1000	.	.	gene_id "MSTRG.13"; transcript_id "MSTRG.13.1"; 
-chr1	StringTie	exon	3290489	3291273	1000	.	.	gene_id "MSTRG.13"; transcript_id "MSTRG.13.1"; exon_number "1"; 
-chr1	StringTie	transcript	3299444	3299664	1000	.	.	gene_id "MSTRG.14"; transcript_id "MSTRG.14.1"; 
-chr1	StringTie	exon	3299444	3299664	1000	.	.	gene_id "MSTRG.14"; transcript_id "MSTRG.14.1"; exon_number "1"; 
-chr1	StringTie	transcript	3319000	3319051	1000	.	.	gene_id "MSTRG.15"; transcript_id "MSTRG.15.1"; 
-chr1	StringTie	exon	3319000	3319051	1000	.	.	gene_id "MSTRG.15"; transcript_id "MSTRG.15.1"; exon_number "1"; 
-chr1	StringTie	transcript	3351241	3351311	1000	.	.	gene_id "MSTRG.16"; transcript_id "MSTRG.16.1"; 
-chr1	StringTie	exon	3351241	3351311	1000	.	.	gene_id "MSTRG.16"; transcript_id "MSTRG.16.1"; exon_number "1"; 
-chr1	StringTie	transcript	3355908	3356119	1000	.	.	gene_id "MSTRG.17"; transcript_id "MSTRG.17.1"; 
-chr1	StringTie	exon	3355908	3356119	1000	.	.	gene_id "MSTRG.17"; transcript_id "MSTRG.17.1"; exon_number "1"; 
-chr1	StringTie	transcript	3363077	3363446	1000	.	.	gene_id "MSTRG.18"; transcript_id "MSTRG.18.1"; 
-chr1	StringTie	exon	3363077	3363446	1000	.	.	gene_id "MSTRG.18"; transcript_id "MSTRG.18.1"; exon_number "1"; 
-chr1	StringTie	transcript	3363754	3363849	1000	.	.	gene_id "MSTRG.19"; transcript_id "MSTRG.19.1"; 
-chr1	StringTie	exon	3363754	3363849	1000	.	.	gene_id "MSTRG.19"; transcript_id "MSTRG.19.1"; exon_number "1"; 
-chr1	StringTie	transcript	3377212	3377262	1000	.	.	gene_id "MSTRG.20"; transcript_id "MSTRG.20.1"; 
-chr1	StringTie	exon	3377212	3377262	1000	.	.	gene_id "MSTRG.20"; transcript_id "MSTRG.20.1"; exon_number "1"; 
-chr1	StringTie	transcript	3386740	3386836	1000	.	.	gene_id "MSTRG.21"; transcript_id "MSTRG.21.1"; 
-chr1	StringTie	exon	3386740	3386836	1000	.	.	gene_id "MSTRG.21"; transcript_id "MSTRG.21.1"; exon_number "1"; 
-chr1	StringTie	transcript	3450907	3451109	1000	.	.	gene_id "MSTRG.22"; transcript_id "MSTRG.22.1"; 
-chr1	StringTie	exon	3450907	3451109	1000	.	.	gene_id "MSTRG.22"; transcript_id "MSTRG.22.1"; exon_number "1"; 
-chr1	mm9_refFlat	transcript	4334224	4350473	.	-	.	gene_id "Rp1"; transcript_id "Rp1"; ref_gene_id "Rp1";
-chr1	mm9_refFlat	exon	4334224	4340172	.	-	.	gene_id "Rp1"; transcript_id "Rp1"; exon_number "1";
-chr1	mm9_refFlat	exon	4341991	4342162	.	-	.	gene_id "Rp1"; transcript_id "Rp1"; exon_number "2";
-chr1	mm9_refFlat	exon	4342283	4342918	.	-	.	gene_id "Rp1"; transcript_id "Rp1"; exon_number "3";
-chr1	mm9_refFlat	exon	4350281	4350473	.	-	.	gene_id "Rp1"; transcript_id "Rp1"; exon_number "4";
-chr1	mm9_refFlat	transcript	4481009	4486494	.	-	.	gene_id "Sox17"; transcript_id "Sox17"; ref_gene_id "Sox17";
-chr1	mm9_refFlat	exon	4481009	4482749	.	-	.	gene_id "Sox17"; transcript_id "Sox17"; exon_number "1";
-chr1	mm9_refFlat	exon	4483181	4483547	.	-	.	gene_id "Sox17"; transcript_id "Sox17"; exon_number "2";
-chr1	mm9_refFlat	exon	4483853	4483944	.	-	.	gene_id "Sox17"; transcript_id "Sox17"; exon_number "3";
-chr1	mm9_refFlat	exon	4485217	4486023	.	-	.	gene_id "Sox17"; transcript_id "Sox17"; exon_number "4";
-chr1	mm9_refFlat	exon	4486372	4486494	.	-	.	gene_id "Sox17"; transcript_id "Sox17"; exon_number "5";
-chr1	mm9_refFlat	transcript	4763279	4775807	.	-	.	gene_id "Mrpl15"; transcript_id "Mrpl15"; ref_gene_id "Mrpl15";
-chr1	mm9_refFlat	exon	4763279	4766882	.	-	.	gene_id "Mrpl15"; transcript_id "Mrpl15"; exon_number "1";
-chr1	mm9_refFlat	exon	4767606	4767729	.	-	.	gene_id "Mrpl15"; transcript_id "Mrpl15"; exon_number "2";
-chr1	mm9_refFlat	exon	4772649	4772814	.	-	.	gene_id "Mrpl15"; transcript_id "Mrpl15"; exon_number "3";
-chr1	mm9_refFlat	exon	4774032	4774186	.	-	.	gene_id "Mrpl15"; transcript_id "Mrpl15"; exon_number "4";
-chr1	mm9_refFlat	exon	4775654	4775807	.	-	.	gene_id "Mrpl15"; transcript_id "Mrpl15"; exon_number "5";
-chr1	mm9_refFlat	transcript	4763279	4775807	.	-	.	gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; ref_gene_id "Mrpl15";
-chr1	mm9_refFlat	exon	4763279	4764597	.	-	.	gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; exon_number "1";
-chr1	mm9_refFlat	exon	4767606	4767729	.	-	.	gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; exon_number "2";
-chr1	mm9_refFlat	exon	4772649	4772814	.	-	.	gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; exon_number "3";
-chr1	mm9_refFlat	exon	4774032	4774186	.	-	.	gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; exon_number "4";
-chr1	mm9_refFlat	exon	4775654	4775807	.	-	.	gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; exon_number "5";
-chr1	mm9_refFlat	transcript	4763279	4775807	.	-	.	gene_id "Mrpl15"; transcript_id "Mrpl15_dup2"; ref_gene_id "Mrpl15";
-chr1	mm9_refFlat	exon	4763279	4764597	.	-	.	gene_id "Mrpl15"; transcript_id "Mrpl15_dup2"; exon_number "1";
-chr1	mm9_refFlat	exon	4767606	4767729	.	-	.	gene_id "Mrpl15"; transcript_id "Mrpl15_dup2"; exon_number "2";
-chr1	mm9_refFlat	exon	4772649	4772814	.	-	.	gene_id "Mrpl15"; transcript_id "Mrpl15_dup2"; exon_number "3";
-chr1	mm9_refFlat	exon	4775654	4775807	.	-	.	gene_id "Mrpl15"; transcript_id "Mrpl15_dup2"; exon_number "4";
-chr1	mm9_refFlat	transcript	4797974	4836816	.	+	.	gene_id "Lypla1"; transcript_id "Lypla1"; ref_gene_id "Lypla1";
-chr1	mm9_refFlat	exon	4797974	4798063	.	+	.	gene_id "Lypla1"; transcript_id "Lypla1"; exon_number "1";
-chr1	mm9_refFlat	exon	4798536	4798567	.	+	.	gene_id "Lypla1"; transcript_id "Lypla1"; exon_number "2";
-chr1	mm9_refFlat	exon	4818665	4818730	.	+	.	gene_id "Lypla1"; transcript_id "Lypla1"; exon_number "3";
-chr1	mm9_refFlat	exon	4820349	4820396	.	+	.	gene_id "Lypla1"; transcript_id "Lypla1"; exon_number "4";
-chr1	mm9_refFlat	exon	4822392	4822462	.	+	.	gene_id "Lypla1"; transcript_id "Lypla1"; exon_number "5";
-chr1	mm9_refFlat	exon	4827082	4827155	.	+	.	gene_id "Lypla1"; transcript_id "Lypla1"; exon_number "6";
-chr1	mm9_refFlat	exon	4829468	4829569	.	+	.	gene_id "Lypla1"; transcript_id "Lypla1"; exon_number "7";
-chr1	mm9_refFlat	exon	4831037	4831213	.	+	.	gene_id "Lypla1"; transcript_id "Lypla1"; exon_number "8";
-chr1	mm9_refFlat	exon	4835044	4836816	.	+	.	gene_id "Lypla1"; transcript_id "Lypla1"; exon_number "9";
-chr1	mm9_refFlat	transcript	4847775	4857613	.	+	.	gene_id "Tcea1"; transcript_id "Tcea1_dup1"; ref_gene_id "Tcea1";
-chr1	mm9_refFlat	exon	4847775	4848057	.	+	.	gene_id "Tcea1"; transcript_id "Tcea1_dup1"; exon_number "1";
-chr1	mm9_refFlat	exon	4857551	4857613	.	+	.	gene_id "Tcea1"; transcript_id "Tcea1_dup1"; exon_number "2";
-chr1	mm9_refFlat	transcript	4847775	4887987	.	+	.	gene_id "Tcea1"; transcript_id "Tcea1"; ref_gene_id "Tcea1";
-chr1	mm9_refFlat	exon	4847775	4848057	.	+	.	gene_id "Tcea1"; transcript_id "Tcea1"; exon_number "1";
-chr1	mm9_refFlat	exon	4857551	4857613	.	+	.	gene_id "Tcea1"; transcript_id "Tcea1"; exon_number "2";
-chr1	mm9_refFlat	exon	4868108	4868213	.	+	.	gene_id "Tcea1"; transcript_id "Tcea1"; exon_number "3";
-chr1	mm9_refFlat	exon	4876825	4876912	.	+	.	gene_id "Tcea1"; transcript_id "Tcea1"; exon_number "4";
-chr1	mm9_refFlat	exon	4879538	4879683	.	+	.	gene_id "Tcea1"; transcript_id "Tcea1"; exon_number "5";
-chr1	mm9_refFlat	exon	4880821	4880877	.	+	.	gene_id "Tcea1"; transcript_id "Tcea1"; exon_number "6";
-chr1	mm9_refFlat	exon	4881996	4882150	.	+	.	gene_id "Tcea1"; transcript_id "Tcea1"; exon_number "7";
-chr1	mm9_refFlat	exon	4883498	4883644	.	+	.	gene_id "Tcea1"; transcript_id "Tcea1"; exon_number "8";
-chr1	mm9_refFlat	exon	4885015	4885086	.	+	.	gene_id "Tcea1"; transcript_id "Tcea1"; exon_number "9";
-chr1	mm9_refFlat	exon	4886437	4887987	.	+	.	gene_id "Tcea1"; transcript_id "Tcea1"; exon_number "10";
+# StringTie version 2\.1\.7
+# stringtie --merge -p [0-9]+ -G /[-_/a-zA-Z0-9]+\.dat -m 50 -c 0 -F 1\.0 -T 1\.0 -f 0\.01 -g 250 -o /[-_/a-zA-Z0-9]+\.dat /[-_/a-zA-Z0-9]+\.dat /[-_/a-zA-Z0-9]+\.dat
+chr1\tStringTie\texon\t3189811\t3193042\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; exon_number "[0-9]+"; 
+chr1\tStringTie\texon\t3200023\t3200191\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; exon_number "[0-9]+"; 
+chr1\tStringTie\texon\t3201078\t3201809\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; exon_number "[0-9]+"; 
+chr1\tStringTie\texon\t3204563\t3207049\t1000\t-\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "Xkr4"; exon_number "[0-9]+"; ref_gene_id "Xkr4"; 
+chr1\tStringTie\texon\t3212214\t3212439\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; exon_number "[0-9]+"; 
+chr1\tStringTie\texon\t3212718\t3212801\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; exon_number "[0-9]+"; 
+chr1\tStringTie\texon\t3213096\t3213242\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; exon_number "[0-9]+"; 
+chr1\tStringTie\texon\t3242634\t3243079\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; exon_number "[0-9]+"; 
+chr1\tStringTie\texon\t3243348\t3243401\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; exon_number "[0-9]+"; 
+chr1\tStringTie\texon\t3277914\t3278390\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; exon_number "[0-9]+"; 
+chr1\tStringTie\texon\t3280687\t3280741\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; exon_number "[0-9]+"; 
+chr1\tStringTie\texon\t3282761\t3282832\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; exon_number "[0-9]+"; 
+chr1\tStringTie\texon\t3290489\t3291273\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; exon_number "[0-9]+"; 
+chr1\tStringTie\texon\t3299444\t3299664\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; exon_number "[0-9]+"; 
+chr1\tStringTie\texon\t3319000\t3319051\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; exon_number "[0-9]+"; 
+chr1\tStringTie\texon\t3351241\t3351311\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; exon_number "[0-9]+"; 
+chr1\tStringTie\texon\t3355908\t3356119\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; exon_number "[0-9]+"; 
+chr1\tStringTie\texon\t3363077\t3363446\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; exon_number "[0-9]+"; 
+chr1\tStringTie\texon\t3363754\t3363849\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; exon_number "[0-9]+"; 
+chr1\tStringTie\texon\t3377212\t3377262\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; exon_number "[0-9]+"; 
+chr1\tStringTie\texon\t3386740\t3386836\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; exon_number "[0-9]+"; 
+chr1\tStringTie\texon\t3411783\t3411982\t1000\t-\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "Xkr4"; exon_number "[0-9]+"; ref_gene_id "Xkr4"; 
+chr1\tStringTie\texon\t3450907\t3451109\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; exon_number "[0-9]+"; 
+chr1\tStringTie\texon\t3660633\t3661579\t1000\t-\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "Xkr4"; exon_number "[0-9]+"; ref_gene_id "Xkr4"; 
+chr1\tStringTie\ttranscript\t3189811\t3193042\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; 
+chr1\tStringTie\ttranscript\t3200023\t3200191\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; 
+chr1\tStringTie\ttranscript\t3201078\t3201809\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; 
+chr1\tStringTie\ttranscript\t3204563\t3661579\t1000\t-\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "Xkr4"; ref_gene_id "Xkr4"; 
+chr1\tStringTie\ttranscript\t3212214\t3212439\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; 
+chr1\tStringTie\ttranscript\t3212718\t3212801\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; 
+chr1\tStringTie\ttranscript\t3213096\t3213242\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; 
+chr1\tStringTie\ttranscript\t3242634\t3243079\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; 
+chr1\tStringTie\ttranscript\t3243348\t3243401\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; 
+chr1\tStringTie\ttranscript\t3277914\t3278390\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; 
+chr1\tStringTie\ttranscript\t3280687\t3280741\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; 
+chr1\tStringTie\ttranscript\t3282761\t3282832\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; 
+chr1\tStringTie\ttranscript\t3290489\t3291273\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; 
+chr1\tStringTie\ttranscript\t3299444\t3299664\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; 
+chr1\tStringTie\ttranscript\t3319000\t3319051\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; 
+chr1\tStringTie\ttranscript\t3351241\t3351311\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; 
+chr1\tStringTie\ttranscript\t3355908\t3356119\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; 
+chr1\tStringTie\ttranscript\t3363077\t3363446\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; 
+chr1\tStringTie\ttranscript\t3363754\t3363849\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; 
+chr1\tStringTie\ttranscript\t3377212\t3377262\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; 
+chr1\tStringTie\ttranscript\t3386740\t3386836\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; 
+chr1\tStringTie\ttranscript\t3450907\t3451109\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; 
+chr1\tmm9_refFlat\texon\t4334224\t4340172\t\.\t-\t\.\tgene_id "Rp1"; transcript_id "Rp1"; exon_number "[0-9]+";
+chr1\tmm9_refFlat\texon\t4341991\t4342162\t\.\t-\t\.\tgene_id "Rp1"; transcript_id "Rp1"; exon_number "[0-9]+";
+chr1\tmm9_refFlat\texon\t4342283\t4342918\t\.\t-\t\.\tgene_id "Rp1"; transcript_id "Rp1"; exon_number "[0-9]+";
+chr1\tmm9_refFlat\texon\t4350281\t4350473\t\.\t-\t\.\tgene_id "Rp1"; transcript_id "Rp1"; exon_number "[0-9]+";
+chr1\tmm9_refFlat\texon\t4481009\t4482749\t\.\t-\t\.\tgene_id "Sox17"; transcript_id "Sox17"; exon_number "[0-9]+";
+chr1\tmm9_refFlat\texon\t4483181\t4483547\t\.\t-\t\.\tgene_id "Sox17"; transcript_id "Sox17"; exon_number "[0-9]+";
+chr1\tmm9_refFlat\texon\t4483853\t4483944\t\.\t-\t\.\tgene_id "Sox17"; transcript_id "Sox17"; exon_number "[0-9]+";
+chr1\tmm9_refFlat\texon\t4485217\t4486023\t\.\t-\t\.\tgene_id "Sox17"; transcript_id "Sox17"; exon_number "[0-9]+";
+chr1\tmm9_refFlat\texon\t4486372\t4486494\t\.\t-\t\.\tgene_id "Sox17"; transcript_id "Sox17"; exon_number "[0-9]+";
+chr1\tmm9_refFlat\texon\t4763279\t4764597\t\.\t-\t\.\tgene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; exon_number "[0-9]+";
+chr1\tmm9_refFlat\texon\t4763279\t4764597\t\.\t-\t\.\tgene_id "Mrpl15"; transcript_id "Mrpl15_dup2"; exon_number "[0-9]+";
+chr1\tmm9_refFlat\texon\t4763279\t4766882\t\.\t-\t\.\tgene_id "Mrpl15"; transcript_id "Mrpl15"; exon_number "[0-9]+";
+chr1\tmm9_refFlat\texon\t4767606\t4767729\t\.\t-\t\.\tgene_id "Mrpl15"; transcript_id "Mrpl15"; exon_number "[0-9]+";
+chr1\tmm9_refFlat\texon\t4767606\t4767729\t\.\t-\t\.\tgene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; exon_number "[0-9]+";
+chr1\tmm9_refFlat\texon\t4767606\t4767729\t\.\t-\t\.\tgene_id "Mrpl15"; transcript_id "Mrpl15_dup2"; exon_number "[0-9]+";
+chr1\tmm9_refFlat\texon\t4772649\t4772814\t\.\t-\t\.\tgene_id "Mrpl15"; transcript_id "Mrpl15"; exon_number "[0-9]+";
+chr1\tmm9_refFlat\texon\t4772649\t4772814\t\.\t-\t\.\tgene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; exon_number "[0-9]+";
+chr1\tmm9_refFlat\texon\t4772649\t4772814\t\.\t-\t\.\tgene_id "Mrpl15"; transcript_id "Mrpl15_dup2"; exon_number "[0-9]+";
+chr1\tmm9_refFlat\texon\t4774032\t4774186\t\.\t-\t\.\tgene_id "Mrpl15"; transcript_id "Mrpl15"; exon_number "[0-9]+";
+chr1\tmm9_refFlat\texon\t4774032\t4774186\t\.\t-\t\.\tgene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; exon_number "[0-9]+";
+chr1\tmm9_refFlat\texon\t4775654\t4775807\t\.\t-\t\.\tgene_id "Mrpl15"; transcript_id "Mrpl15"; exon_number "[0-9]+";
+chr1\tmm9_refFlat\texon\t4775654\t4775807\t\.\t-\t\.\tgene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; exon_number "[0-9]+";
+chr1\tmm9_refFlat\texon\t4775654\t4775807\t\.\t-\t\.\tgene_id "Mrpl15"; transcript_id "Mrpl15_dup2"; exon_number "[0-9]+";
+chr1\tmm9_refFlat\texon\t4797974\t4798063\t\.\t\+\t\.\tgene_id "Lypla1"; transcript_id "Lypla1"; exon_number "[0-9]+";
+chr1\tmm9_refFlat\texon\t4798536\t4798567\t\.\t\+\t\.\tgene_id "Lypla1"; transcript_id "Lypla1"; exon_number "[0-9]+";
+chr1\tmm9_refFlat\texon\t4818665\t4818730\t\.\t\+\t\.\tgene_id "Lypla1"; transcript_id "Lypla1"; exon_number "[0-9]+";
+chr1\tmm9_refFlat\texon\t4820349\t4820396\t\.\t\+\t\.\tgene_id "Lypla1"; transcript_id "Lypla1"; exon_number "[0-9]+";
+chr1\tmm9_refFlat\texon\t4822392\t4822462\t\.\t\+\t\.\tgene_id "Lypla1"; transcript_id "Lypla1"; exon_number "[0-9]+";
+chr1\tmm9_refFlat\texon\t4827082\t4827155\t\.\t\+\t\.\tgene_id "Lypla1"; transcript_id "Lypla1"; exon_number "[0-9]+";
+chr1\tmm9_refFlat\texon\t4829468\t4829569\t\.\t\+\t\.\tgene_id "Lypla1"; transcript_id "Lypla1"; exon_number "[0-9]+";
+chr1\tmm9_refFlat\texon\t4831037\t4831213\t\.\t\+\t\.\tgene_id "Lypla1"; transcript_id "Lypla1"; exon_number "[0-9]+";
+chr1\tmm9_refFlat\texon\t4835044\t4836816\t\.\t\+\t\.\tgene_id "Lypla1"; transcript_id "Lypla1"; exon_number "[0-9]+";
+chr1\tmm9_refFlat\texon\t4847775\t4848057\t\.\t\+\t\.\tgene_id "Tcea1"; transcript_id "Tcea1"; exon_number "[0-9]+";
+chr1\tmm9_refFlat\texon\t4847775\t4848057\t\.\t\+\t\.\tgene_id "Tcea1"; transcript_id "Tcea1_dup1"; exon_number "[0-9]+";
+chr1\tmm9_refFlat\texon\t4857551\t4857613\t\.\t\+\t\.\tgene_id "Tcea1"; transcript_id "Tcea1"; exon_number "[0-9]+";
+chr1\tmm9_refFlat\texon\t4857551\t4857613\t\.\t\+\t\.\tgene_id "Tcea1"; transcript_id "Tcea1_dup1"; exon_number "[0-9]+";
+chr1\tmm9_refFlat\texon\t4868108\t4868213\t\.\t\+\t\.\tgene_id "Tcea1"; transcript_id "Tcea1"; exon_number "[0-9]+";
+chr1\tmm9_refFlat\texon\t4876825\t4876912\t\.\t\+\t\.\tgene_id "Tcea1"; transcript_id "Tcea1"; exon_number "[0-9]+";
+chr1\tmm9_refFlat\texon\t4879538\t4879683\t\.\t\+\t\.\tgene_id "Tcea1"; transcript_id "Tcea1"; exon_number "[0-9]+";
+chr1\tmm9_refFlat\texon\t4880821\t4880877\t\.\t\+\t\.\tgene_id "Tcea1"; transcript_id "Tcea1"; exon_number "[0-9]+";
+chr1\tmm9_refFlat\texon\t4881996\t4882150\t\.\t\+\t\.\tgene_id "Tcea1"; transcript_id "Tcea1"; exon_number "[0-9]+";
+chr1\tmm9_refFlat\texon\t4883498\t4883644\t\.\t\+\t\.\tgene_id "Tcea1"; transcript_id "Tcea1"; exon_number "[0-9]+";
+chr1\tmm9_refFlat\texon\t4885015\t4885086\t\.\t\+\t\.\tgene_id "Tcea1"; transcript_id "Tcea1"; exon_number "[0-9]+";
+chr1\tmm9_refFlat\texon\t4886437\t4887987\t\.\t\+\t\.\tgene_id "Tcea1"; transcript_id "Tcea1"; exon_number "[0-9]+";
+chr1\tmm9_refFlat\ttranscript\t4334224\t4350473\t\.\t-\t\.\tgene_id "Rp1"; transcript_id "Rp1"; ref_gene_id "Rp1";
+chr1\tmm9_refFlat\ttranscript\t4481009\t4486494\t\.\t-\t\.\tgene_id "Sox17"; transcript_id "Sox17"; ref_gene_id "Sox17";
+chr1\tmm9_refFlat\ttranscript\t4763279\t4775807\t\.\t-\t\.\tgene_id "Mrpl15"; transcript_id "Mrpl15"; ref_gene_id "Mrpl15";
+chr1\tmm9_refFlat\ttranscript\t4763279\t4775807\t\.\t-\t\.\tgene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; ref_gene_id "Mrpl15";
+chr1\tmm9_refFlat\ttranscript\t4763279\t4775807\t\.\t-\t\.\tgene_id "Mrpl15"; transcript_id "Mrpl15_dup2"; ref_gene_id "Mrpl15";
+chr1\tmm9_refFlat\ttranscript\t4797974\t4836816\t\.\t\+\t\.\tgene_id "Lypla1"; transcript_id "Lypla1"; ref_gene_id "Lypla1";
+chr1\tmm9_refFlat\ttranscript\t4847775\t4857613\t\.\t\+\t\.\tgene_id "Tcea1"; transcript_id "Tcea1_dup1"; ref_gene_id "Tcea1";
+chr1\tmm9_refFlat\ttranscript\t4847775\t4887987\t\.\t\+\t\.\tgene_id "Tcea1"; transcript_id "Tcea1"; ref_gene_id "Tcea1";
\ No newline at end of file
diff -r 333a6e13b622 -r cef79931dda5 test-data/stringtie_out10.gtf
--- a/test-data/stringtie_out10.gtf	Tue Nov 30 11:01:34 2021 +0000
+++ b/test-data/stringtie_out10.gtf	Wed Jul 27 09:28:15 2022 +0000
@@ -1,6 +1,6 @@
-# stringtie /tmp/tmpgqe071sy/files/8/8/6/dataset_886a7110-225b-4286-8de0-3e630fa369da.dat -L -E 25 -o /tmp/tmpgqe071sy/files/d/5/4/dataset_d54d1211-a9e6-4f03-b0b6-58182b101e8b.dat -p 1 -G guide.gff -b ./special_de_output/sample1/ -f 0.15 -m 200 -a 10 -j 1 -c 2 -g 50 -M 0.95
-# StringTie version 2.1.7
-test_chromosome	StringTie	transcript	53	550	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "45.795303"; FPKM "3354967.250000"; TPM "1000000.000000";
-test_chromosome	StringTie	exon	53	250	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "1"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "49.777779";
-test_chromosome	StringTie	exon	351	400	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "2"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "54.160000";
-test_chromosome	StringTie	exon	501	550	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "3"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "21.660000";
+# StringTie version 2\.1\.7
+# stringtie /[-_/a-zA-Z0-9]+\.dat -L -E 25 -o /[-_/a-zA-Z0-9]+\.dat -p [0-9]+ -G guide\.gff -b \./special_de_output/sample1/ -f 0\.15 -m 200 -a 10 -j 1 -c 2 -g 50 -M 0\.95
+test_chromosome\tStringTie\texon\t351\t400\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "54\.160000";
+test_chromosome\tStringTie\texon\t501\t550\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "21\.660000";
+test_chromosome\tStringTie\texon\t53\t250\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "49\.777779";
+test_chromosome\tStringTie\ttranscript\t53\t550\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "45\.795303"; FPKM "3354967\.250000"; TPM "1000000\.000000";
diff -r 333a6e13b622 -r cef79931dda5 test-data/stringtie_out11.gtf
--- a/test-data/stringtie_out11.gtf	Tue Nov 30 11:01:34 2021 +0000
+++ b/test-data/stringtie_out11.gtf	Wed Jul 27 09:28:15 2022 +0000
@@ -1,58 +1,58 @@
-# stringtie /tmp/tmpgqe071sy/files/5/f/e/dataset_5feb7af0-84a3-4590-975e-97b02b89c256.dat -L -E 30 -o /tmp/tmpgqe071sy/files/d/9/c/dataset_d9c60f6e-5062-4d09-a7e3-05b74adcebca.dat -p 1 -G guide.gff -b ./special_de_output/sample1/ -f 0.15 -m 200 -a 10 -j 1 -c 2 -g 50 -M 0.95
-# StringTie version 2.1.7
-chr19	StringTie	transcript	567221	571736	1000	-	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; cov "5.617600"; FPKM "37220.644531"; TPM "77823.132812";
-chr19	StringTie	exon	567221	567648	1000	-	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "1"; cov "5.815421";
-chr19	StringTie	exon	571440	571596	1000	-	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "2"; cov "5.859873";
-chr19	StringTie	exon	571697	571736	1000	-	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "3"; cov "2.550000";
-chr19	StringTie	transcript	571310	583493	1000	+	.	gene_id "STRG.2"; transcript_id "STRG.2.1"; cov "5.416068"; FPKM "35885.347656"; TPM "75031.218750";
-chr19	StringTie	exon	571310	571579	1000	+	.	gene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "1"; cov "4.559259";
-chr19	StringTie	exon	580379	580461	1000	+	.	gene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "2"; cov "5.556142";
-chr19	StringTie	exon	580646	580782	1000	+	.	gene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "3"; cov "5.689962";
-chr19	StringTie	exon	581315	581610	1000	+	.	gene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "4"; cov "5.556142";
-chr19	StringTie	exon	582514	582582	1000	+	.	gene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "5"; cov "5.556142";
-chr19	StringTie	exon	582750	583493	1000	+	.	gene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "6"; cov "5.592226";
-chr19	StringTie	transcript	572567	583493	1000	+	.	gene_id "STRG.2"; transcript_id "STRG.2.2"; cov "6.175826"; FPKM "40919.292969"; TPM "85556.492188";
-chr19	StringTie	exon	572567	572701	1000	+	.	gene_id "STRG.2"; transcript_id "STRG.2.2"; exon_number "1"; cov "3.325926";
-chr19	StringTie	exon	577774	578121	1000	+	.	gene_id "STRG.2"; transcript_id "STRG.2.2"; exon_number "2"; cov "6.436781";
-chr19	StringTie	exon	579500	579656	1000	+	.	gene_id "STRG.2"; transcript_id "STRG.2.2"; exon_number "3"; cov "7.000000";
-chr19	StringTie	exon	580379	580461	1000	+	.	gene_id "STRG.2"; transcript_id "STRG.2.2"; exon_number "4"; cov "7.443858";
-chr19	StringTie	exon	580646	580782	1000	+	.	gene_id "STRG.2"; transcript_id "STRG.2.2"; exon_number "5"; cov "6.631207";
-chr19	StringTie	exon	581315	581610	1000	+	.	gene_id "STRG.2"; transcript_id "STRG.2.2"; exon_number "6"; cov "6.443858";
-chr19	StringTie	exon	582514	582582	1000	+	.	gene_id "STRG.2"; transcript_id "STRG.2.2"; exon_number "7"; cov "6.443858";
-chr19	StringTie	exon	582750	583493	1000	+	.	gene_id "STRG.2"; transcript_id "STRG.2.2"; exon_number "8"; cov "6.040156";
-chr19	StringTie	transcript	589891	617159	1000	+	.	gene_id "STRG.3"; transcript_id "STRG.3.1"; cov "19.938414"; FPKM "132106.343750"; TPM "276215.781250";
-chr19	StringTie	exon	589891	590577	1000	+	.	gene_id "STRG.3"; transcript_id "STRG.3.1"; exon_number "1"; cov "18.537119";
-chr19	StringTie	exon	603544	603967	1000	+	.	gene_id "STRG.3"; transcript_id "STRG.3.1"; exon_number "2"; cov "21.000000";
-chr19	StringTie	exon	605061	605222	1000	+	.	gene_id "STRG.3"; transcript_id "STRG.3.1"; exon_number "3"; cov "21.000000";
-chr19	StringTie	exon	607964	608182	1000	+	.	gene_id "STRG.3"; transcript_id "STRG.3.1"; exon_number "4"; cov "21.000000";
-chr19	StringTie	exon	610259	610405	1000	+	.	gene_id "STRG.3"; transcript_id "STRG.3.1"; exon_number "5"; cov "21.000000";
-chr19	StringTie	exon	613248	613488	1000	+	.	gene_id "STRG.3"; transcript_id "STRG.3.1"; exon_number "6"; cov "21.000000";
-chr19	StringTie	exon	613852	614016	1000	+	.	gene_id "STRG.3"; transcript_id "STRG.3.1"; exon_number "7"; cov "21.000000";
-chr19	StringTie	exon	615795	617159	1000	+	.	gene_id "STRG.3"; transcript_id "STRG.3.1"; exon_number "8"; cov "19.587545";
-chr19	StringTie	transcript	617224	618760	1000	-	.	gene_id "STRG.4"; transcript_id "STRG.4.1"; cov "29.150192"; FPKM "193141.000000"; TPM "403830.687500";
-chr19	StringTie	exon	617224	617323	1000	-	.	gene_id "STRG.4"; transcript_id "STRG.4.1"; exon_number "1"; cov "20.289286";
-chr19	StringTie	exon	617419	617480	1000	-	.	gene_id "STRG.4"; transcript_id "STRG.4.1"; exon_number "2"; cov "28.788761";
-chr19	StringTie	exon	617570	618586	1000	-	.	gene_id "STRG.4"; transcript_id "STRG.4.1"; exon_number "3"; cov "30.891500";
-chr19	StringTie	exon	618705	618760	1000	-	.	gene_id "STRG.4"; transcript_id "STRG.4.1"; exon_number "4"; cov "13.750000";
-chr19	StringTie	transcript	617224	633601	1000	-	.	gene_id "STRG.4"; transcript_id "STRG.4.2"; cov "5.886094"; FPKM "38999.609375"; TPM "81542.703125";
-chr19	StringTie	exon	617224	617323	1000	-	.	gene_id "STRG.4"; transcript_id "STRG.4.2"; exon_number "1"; cov "1.560714";
-chr19	StringTie	exon	617419	617480	1000	-	.	gene_id "STRG.4"; transcript_id "STRG.4.2"; exon_number "2"; cov "1.985432";
-chr19	StringTie	exon	617570	617655	1000	-	.	gene_id "STRG.4"; transcript_id "STRG.4.2"; exon_number "3"; cov "4.996770";
-chr19	StringTie	exon	617777	617849	1000	-	.	gene_id "STRG.4"; transcript_id "STRG.4.2"; exon_number "4"; cov "5.994817";
-chr19	StringTie	exon	618488	618586	1000	-	.	gene_id "STRG.4"; transcript_id "STRG.4.2"; exon_number "5"; cov "5.525252";
-chr19	StringTie	exon	618705	618760	1000	-	.	gene_id "STRG.4"; transcript_id "STRG.4.2"; exon_number "6"; cov "6.875000";
-chr19	StringTie	exon	618997	619110	1000	-	.	gene_id "STRG.4"; transcript_id "STRG.4.2"; exon_number "7"; cov "6.000000";
-chr19	StringTie	exon	619210	619296	1000	-	.	gene_id "STRG.4"; transcript_id "STRG.4.2"; exon_number "8"; cov "6.000000";
-chr19	StringTie	exon	619586	619765	1000	-	.	gene_id "STRG.4"; transcript_id "STRG.4.2"; exon_number "9"; cov "6.000000";
-chr19	StringTie	exon	619958	620080	1000	-	.	gene_id "STRG.4"; transcript_id "STRG.4.2"; exon_number "10"; cov "7.000000";
-chr19	StringTie	exon	620365	620487	1000	-	.	gene_id "STRG.4"; transcript_id "STRG.4.2"; exon_number "11"; cov "7.000000";
-chr19	StringTie	exon	621058	621846	1000	-	.	gene_id "STRG.4"; transcript_id "STRG.4.2"; exon_number "12"; cov "6.751584";
-chr19	StringTie	exon	622149	622373	1000	-	.	gene_id "STRG.4"; transcript_id "STRG.4.2"; exon_number "13"; cov "6.000000";
-chr19	StringTie	exon	622582	622752	1000	-	.	gene_id "STRG.4"; transcript_id "STRG.4.2"; exon_number "14"; cov "6.000000";
-chr19	StringTie	exon	622821	622985	1000	-	.	gene_id "STRG.4"; transcript_id "STRG.4.2"; exon_number "15"; cov "6.000000";
-chr19	StringTie	exon	623454	623603	1000	-	.	gene_id "STRG.4"; transcript_id "STRG.4.2"; exon_number "16"; cov "6.000000";
-chr19	StringTie	exon	624719	624905	1000	-	.	gene_id "STRG.4"; transcript_id "STRG.4.2"; exon_number "17"; cov "6.000000";
-chr19	StringTie	exon	625124	625254	1000	-	.	gene_id "STRG.4"; transcript_id "STRG.4.2"; exon_number "18"; cov "6.000000";
-chr19	StringTie	exon	629540	630168	1000	-	.	gene_id "STRG.4"; transcript_id "STRG.4.2"; exon_number "19"; cov "5.941176";
-chr19	StringTie	exon	632834	632938	1000	-	.	gene_id "STRG.4"; transcript_id "STRG.4.2"; exon_number "20"; cov "5.000000";
-chr19	StringTie	exon	633425	633601	1000	-	.	gene_id "STRG.4"; transcript_id "STRG.4.2"; exon_number "21"; cov "3.988701";
+# StringTie version 2\.1\.7
+# stringtie /[-_/a-zA-Z0-9]+\.dat -L -E 30 -o /[-_/a-zA-Z0-9]+\.dat -p [0-9]+ -G guide\.gff -b \./special_de_output/sample1/ -f 0\.15 -m 200 -a 10 -j 1 -c 2 -g 50 -M 0\.95
+chr19\tStringTie\texon\t567221\t567648\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; cov "5\.815421";
+chr19\tStringTie\texon\t571310\t571579\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; cov "4\.559259";
+chr19\tStringTie\texon\t571440\t571596\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; cov "5\.859873";
+chr19\tStringTie\texon\t571697\t571736\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; cov "2\.550000";
+chr19\tStringTie\texon\t572567\t572701\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.2"; exon_number "[0-9]+"; cov "3\.325926";
+chr19\tStringTie\texon\t577774\t578121\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.2"; exon_number "[0-9]+"; cov "6\.436781";
+chr19\tStringTie\texon\t579500\t579656\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.2"; exon_number "[0-9]+"; cov "7\.000000";
+chr19\tStringTie\texon\t580379\t580461\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; cov "5\.556142";
+chr19\tStringTie\texon\t580379\t580461\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.2"; exon_number "[0-9]+"; cov "7\.443858";
+chr19\tStringTie\texon\t580646\t580782\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; cov "5\.689962";
+chr19\tStringTie\texon\t580646\t580782\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.2"; exon_number "[0-9]+"; cov "6\.631207";
+chr19\tStringTie\texon\t581315\t581610\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; cov "5\.556142";
+chr19\tStringTie\texon\t581315\t581610\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.2"; exon_number "[0-9]+"; cov "6\.443858";
+chr19\tStringTie\texon\t582514\t582582\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; cov "5\.556142";
+chr19\tStringTie\texon\t582514\t582582\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.2"; exon_number "[0-9]+"; cov "6\.443858";
+chr19\tStringTie\texon\t582750\t583493\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; cov "5\.592226";
+chr19\tStringTie\texon\t582750\t583493\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.2"; exon_number "[0-9]+"; cov "6\.040156";
+chr19\tStringTie\texon\t589891\t590577\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; cov "18\.537119";
+chr19\tStringTie\texon\t603544\t603967\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; cov "21\.000000";
+chr19\tStringTie\texon\t605061\t605222\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; cov "21\.000000";
+chr19\tStringTie\texon\t607964\t608182\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; cov "21\.000000";
+chr19\tStringTie\texon\t610259\t610405\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; cov "21\.000000";
+chr19\tStringTie\texon\t613248\t613488\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; cov "21\.000000";
+chr19\tStringTie\texon\t613852\t614016\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; cov "21\.000000";
+chr19\tStringTie\texon\t615795\t617159\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; cov "19\.587545";
+chr19\tStringTie\texon\t617224\t617323\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; cov "20\.289286";
+chr19\tStringTie\texon\t617224\t617323\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.2"; exon_number "[0-9]+"; cov "1\.560714";
+chr19\tStringTie\texon\t617419\t617480\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; cov "28\.788761";
+chr19\tStringTie\texon\t617419\t617480\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.2"; exon_number "[0-9]+"; cov "1\.985432";
+chr19\tStringTie\texon\t617570\t617655\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.2"; exon_number "[0-9]+"; cov "4\.996770";
+chr19\tStringTie\texon\t617570\t618586\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; cov "30\.891500";
+chr19\tStringTie\texon\t617777\t617849\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.2"; exon_number "[0-9]+"; cov "5\.994817";
+chr19\tStringTie\texon\t618488\t618586\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.2"; exon_number "[0-9]+"; cov "5\.525252";
+chr19\tStringTie\texon\t618705\t618760\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; cov "13\.750000";
+chr19\tStringTie\texon\t618705\t618760\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.2"; exon_number "[0-9]+"; cov "6\.875000";
+chr19\tStringTie\texon\t618997\t619110\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.2"; exon_number "[0-9]+"; cov "6\.000000";
+chr19\tStringTie\texon\t619210\t619296\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.2"; exon_number "[0-9]+"; cov "6\.000000";
+chr19\tStringTie\texon\t619586\t619765\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.2"; exon_number "[0-9]+"; cov "6\.000000";
+chr19\tStringTie\texon\t619958\t620080\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.2"; exon_number "[0-9]+"; cov "7\.000000";
+chr19\tStringTie\texon\t620365\t620487\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.2"; exon_number "[0-9]+"; cov "7\.000000";
+chr19\tStringTie\texon\t621058\t621846\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.2"; exon_number "[0-9]+"; cov "6\.751584";
+chr19\tStringTie\texon\t622149\t622373\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.2"; exon_number "[0-9]+"; cov "6\.000000";
+chr19\tStringTie\texon\t622582\t622752\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.2"; exon_number "[0-9]+"; cov "6\.000000";
+chr19\tStringTie\texon\t622821\t622985\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.2"; exon_number "[0-9]+"; cov "6\.000000";
+chr19\tStringTie\texon\t623454\t623603\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.2"; exon_number "[0-9]+"; cov "6\.000000";
+chr19\tStringTie\texon\t624719\t624905\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.2"; exon_number "[0-9]+"; cov "6\.000000";
+chr19\tStringTie\texon\t625124\t625254\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.2"; exon_number "[0-9]+"; cov "6\.000000";
+chr19\tStringTie\texon\t629540\t630168\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.2"; exon_number "[0-9]+"; cov "5\.941176";
+chr19\tStringTie\texon\t632834\t632938\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.2"; exon_number "[0-9]+"; cov "5\.000000";
+chr19\tStringTie\texon\t633425\t633601\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.2"; exon_number "[0-9]+"; cov "3\.988701";
+chr19\tStringTie\ttranscript\t567221\t571736\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; cov "5\.617600"; FPKM "37220\.644531"; TPM "77823\.132812";
+chr19\tStringTie\ttranscript\t571310\t583493\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; cov "5\.416068"; FPKM "35885\.347656"; TPM "75031\.218750";
+chr19\tStringTie\ttranscript\t572567\t583493\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.2"; cov "6\.175826"; FPKM "40919\.292969"; TPM "85556\.492188";
+chr19\tStringTie\ttranscript\t589891\t617159\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; cov "19\.938414"; FPKM "132106\.343750"; TPM "276215\.781250";
+chr19\tStringTie\ttranscript\t617224\t618760\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; cov "29\.150192"; FPKM "193141\.000000"; TPM "403830\.687500";
+chr19\tStringTie\ttranscript\t617224\t633601\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.2"; cov "5\.886094"; FPKM "38999\.609375"; TPM "81542\.703125";
diff -r 333a6e13b622 -r cef79931dda5 test-data/stringtie_out12.gtf
--- a/test-data/stringtie_out12.gtf	Tue Nov 30 11:01:34 2021 +0000
+++ b/test-data/stringtie_out12.gtf	Wed Jul 27 09:28:15 2022 +0000
@@ -1,73 +1,73 @@
-# stringtie short_sorted.sam long_sorted.sam -E 25 -o /tmp/tmpgqe071sy/files/9/5/b/dataset_95b1ec38-2151-43e7-8584-aa4aff72e957.dat -p 1 -f 0.15 -m 200 -a 10 -j 1 -c 2 -g 50 -M 0.95
-# StringTie version 2.1.7
-chr19	StringTie	transcript	567221	571736	1000	-	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; cov "5.043160"; FPKM "15396.282227"; TPM "50141.804688";
-chr19	StringTie	exon	567221	567648	1000	-	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "1"; cov "5.815421";
-chr19	StringTie	exon	571440	571596	1000	-	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "2"; cov "3.573089";
-chr19	StringTie	exon	571697	571736	1000	-	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "3"; cov "2.550000";
-chr19	StringTie	transcript	571310	583493	1000	+	.	gene_id "STRG.2"; transcript_id "STRG.2.1"; cov "4.701019"; FPKM "14351.757812"; TPM "46740.058594";
-chr19	StringTie	exon	571310	571579	1000	+	.	gene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "1"; cov "5.888981";
-chr19	StringTie	exon	580379	580461	1000	+	.	gene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "2"; cov "4.879346";
-chr19	StringTie	exon	580646	580782	1000	+	.	gene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "3"; cov "4.616338";
-chr19	StringTie	exon	581315	581610	1000	+	.	gene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "4"; cov "4.479919";
-chr19	StringTie	exon	582514	582582	1000	+	.	gene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "5"; cov "4.504012";
-chr19	StringTie	exon	582750	583493	1000	+	.	gene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "6"; cov "4.371838";
-chr19	StringTie	transcript	572567	583493	1000	+	.	gene_id "STRG.2"; transcript_id "STRG.2.2"; cov "6.933517"; FPKM "21167.359375"; TPM "68936.750000";
-chr19	StringTie	exon	572567	572701	1000	+	.	gene_id "STRG.2"; transcript_id "STRG.2.2"; exon_number "1"; cov "3.325926";
-chr19	StringTie	exon	577774	578121	1000	+	.	gene_id "STRG.2"; transcript_id "STRG.2.2"; exon_number "2"; cov "6.436781";
-chr19	StringTie	exon	579500	579656	1000	+	.	gene_id "STRG.2"; transcript_id "STRG.2.2"; exon_number "3"; cov "7.000000";
-chr19	StringTie	exon	580379	580461	1000	+	.	gene_id "STRG.2"; transcript_id "STRG.2.2"; exon_number "4"; cov "8.120653";
-chr19	StringTie	exon	580646	580782	1000	+	.	gene_id "STRG.2"; transcript_id "STRG.2.2"; exon_number "5"; cov "7.682931";
-chr19	StringTie	exon	581315	581610	1000	+	.	gene_id "STRG.2"; transcript_id "STRG.2.2"; exon_number "6"; cov "7.455892";
-chr19	StringTie	exon	582514	582582	1000	+	.	gene_id "STRG.2"; transcript_id "STRG.2.2"; exon_number "7"; cov "7.495987";
-chr19	StringTie	exon	582750	583493	1000	+	.	gene_id "STRG.2"; transcript_id "STRG.2.2"; exon_number "8"; cov "7.276011";
-chr19	StringTie	transcript	589891	617159	1000	+	.	gene_id "STRG.3"; transcript_id "STRG.3.1"; cov "19.937536"; FPKM "60867.378906"; TPM "198229.687500";
-chr19	StringTie	exon	589891	590577	1000	+	.	gene_id "STRG.3"; transcript_id "STRG.3.1"; exon_number "1"; cov "18.537117";
-chr19	StringTie	exon	603544	603967	1000	+	.	gene_id "STRG.3"; transcript_id "STRG.3.1"; exon_number "2"; cov "21.000000";
-chr19	StringTie	exon	605061	605222	1000	+	.	gene_id "STRG.3"; transcript_id "STRG.3.1"; exon_number "3"; cov "20.981482";
-chr19	StringTie	exon	607964	608182	1000	+	.	gene_id "STRG.3"; transcript_id "STRG.3.1"; exon_number "4"; cov "21.000000";
-chr19	StringTie	exon	610259	610405	1000	+	.	gene_id "STRG.3"; transcript_id "STRG.3.1"; exon_number "5"; cov "21.000000";
-chr19	StringTie	exon	613248	613488	1000	+	.	gene_id "STRG.3"; transcript_id "STRG.3.1"; exon_number "6"; cov "21.000000";
-chr19	StringTie	exon	613852	614016	1000	+	.	gene_id "STRG.3"; transcript_id "STRG.3.1"; exon_number "7"; cov "21.000000";
-chr19	StringTie	exon	615795	617159	1000	+	.	gene_id "STRG.3"; transcript_id "STRG.3.1"; exon_number "8"; cov "19.587545";
-chr16	StringTie	transcript	784986	788300	1000	-	.	gene_id "STRG.4"; transcript_id "STRG.4.1"; cov "30.393349"; FPKM "92787.968750"; TPM "302187.000000";
-chr16	StringTie	exon	784986	786377	1000	-	.	gene_id "STRG.4"; transcript_id "STRG.4.1"; exon_number "1"; cov "33.698273";
-chr16	StringTie	exon	786827	786928	1000	-	.	gene_id "STRG.4"; transcript_id "STRG.4.1"; exon_number "2"; cov "24.970589";
-chr16	StringTie	exon	787077	787179	1000	-	.	gene_id "STRG.4"; transcript_id "STRG.4.1"; exon_number "3"; cov "24.747572";
-chr16	StringTie	exon	787354	787477	1000	-	.	gene_id "STRG.4"; transcript_id "STRG.4.1"; exon_number "4"; cov "25.967739";
-chr16	StringTie	exon	787556	787744	1000	-	.	gene_id "STRG.4"; transcript_id "STRG.4.1"; exon_number "5"; cov "21.576719";
-chr16	StringTie	exon	788256	788300	1000	-	.	gene_id "STRG.4"; transcript_id "STRG.4.1"; exon_number "6"; cov "2.600000";
-chr16	StringTie	transcript	789075	798048	1000	+	.	gene_id "STRG.5"; transcript_id "STRG.5.1"; cov "24.152929"; FPKM "73736.570312"; TPM "240141.406250";
-chr16	StringTie	exon	789075	789125	1000	+	.	gene_id "STRG.5"; transcript_id "STRG.5.1"; exon_number "1"; cov "2.764706";
-chr16	StringTie	exon	789210	789360	1000	+	.	gene_id "STRG.5"; transcript_id "STRG.5.1"; exon_number "2"; cov "12.516557";
-chr16	StringTie	exon	789547	789715	1000	+	.	gene_id "STRG.5"; transcript_id "STRG.5.1"; exon_number "3"; cov "20.360947";
-chr16	StringTie	exon	790177	790269	1000	+	.	gene_id "STRG.5"; transcript_id "STRG.5.1"; exon_number "4"; cov "18.048386";
-chr16	StringTie	exon	790347	790399	1000	+	.	gene_id "STRG.5"; transcript_id "STRG.5.1"; exon_number "5"; cov "21.396227";
-chr16	StringTie	exon	790525	790666	1000	+	.	gene_id "STRG.5"; transcript_id "STRG.5.1"; exon_number "6"; cov "19.359156";
-chr16	StringTie	exon	791161	791370	1000	+	.	gene_id "STRG.5"; transcript_id "STRG.5.1"; exon_number "7"; cov "22.309525";
-chr16	StringTie	exon	791851	791948	1000	+	.	gene_id "STRG.5"; transcript_id "STRG.5.1"; exon_number "8"; cov "16.336735";
-chr16	StringTie	exon	792224	792347	1000	+	.	gene_id "STRG.5"; transcript_id "STRG.5.1"; exon_number "9"; cov "19.322580";
-chr16	StringTie	exon	792439	792590	1000	+	.	gene_id "STRG.5"; transcript_id "STRG.5.1"; exon_number "10"; cov "8.835526";
-chr16	StringTie	exon	792718	792811	1000	+	.	gene_id "STRG.5"; transcript_id "STRG.5.1"; exon_number "11"; cov "21.244680";
-chr16	StringTie	exon	792966	793064	1000	+	.	gene_id "STRG.5"; transcript_id "STRG.5.1"; exon_number "12"; cov "19.494951";
-chr16	StringTie	exon	793144	793274	1000	+	.	gene_id "STRG.5"; transcript_id "STRG.5.1"; exon_number "13"; cov "16.229008";
-chr16	StringTie	exon	794054	794201	1000	+	.	gene_id "STRG.5"; transcript_id "STRG.5.1"; exon_number "14"; cov "22.121622";
-chr16	StringTie	exon	795132	795356	1000	+	.	gene_id "STRG.5"; transcript_id "STRG.5.1"; exon_number "15"; cov "30.586666";
-chr16	StringTie	exon	795685	795834	1000	+	.	gene_id "STRG.5"; transcript_id "STRG.5.1"; exon_number "16"; cov "14.393333";
-chr16	StringTie	exon	795947	796077	1000	+	.	gene_id "STRG.5"; transcript_id "STRG.5.1"; exon_number "17"; cov "27.061069";
-chr16	StringTie	exon	796717	796861	1000	+	.	gene_id "STRG.5"; transcript_id "STRG.5.1"; exon_number "18"; cov "39.082760";
-chr16	StringTie	exon	796961	797092	1000	+	.	gene_id "STRG.5"; transcript_id "STRG.5.1"; exon_number "19"; cov "43.295456";
-chr16	StringTie	exon	797694	797751	1000	+	.	gene_id "STRG.5"; transcript_id "STRG.5.1"; exon_number "20"; cov "53.689655";
-chr16	StringTie	exon	797839	798048	1000	+	.	gene_id "STRG.5"; transcript_id "STRG.5.1"; exon_number "21"; cov "44.473808";
-chr16	StringTie	transcript	854482	911074	1000	-	.	gene_id "STRG.6"; transcript_id "STRG.6.1"; cov "5.773279"; FPKM "17625.265625"; TPM "57401.042969";
-chr16	StringTie	exon	854482	854706	1000	-	.	gene_id "STRG.6"; transcript_id "STRG.6.1"; exon_number "1"; cov "3.262222";
-chr16	StringTie	exon	868944	869056	1000	-	.	gene_id "STRG.6"; transcript_id "STRG.6.1"; exon_number "2"; cov "9.176991";
-chr16	StringTie	exon	869883	870066	1000	-	.	gene_id "STRG.6"; transcript_id "STRG.6.1"; exon_number "3"; cov "11.130435";
-chr16	StringTie	exon	870729	870882	1000	-	.	gene_id "STRG.6"; transcript_id "STRG.6.1"; exon_number "4"; cov "10.467532";
-chr16	StringTie	exon	871161	871341	1000	-	.	gene_id "STRG.6"; transcript_id "STRG.6.1"; exon_number "5"; cov "3.563536";
-chr16	StringTie	exon	879570	879737	1000	-	.	gene_id "STRG.6"; transcript_id "STRG.6.1"; exon_number "6"; cov "2.625000";
-chr16	StringTie	exon	893007	893072	1000	-	.	gene_id "STRG.6"; transcript_id "STRG.6.1"; exon_number "7"; cov "3.242424";
-chr16	StringTie	exon	910931	911074	1000	-	.	gene_id "STRG.6"; transcript_id "STRG.6.1"; exon_number "8"; cov "2.770833";
-chr16	StringTie	transcript	934126	970901	1000	-	.	gene_id "STRG.7"; transcript_id "STRG.7.1"; cov "3.068716"; FPKM "9368.495117"; TPM "30510.824219";
-chr16	StringTie	exon	934126	934254	1000	-	.	gene_id "STRG.7"; transcript_id "STRG.7.1"; exon_number "1"; cov "1.131783";
-chr16	StringTie	exon	954357	954666	1000	-	.	gene_id "STRG.7"; transcript_id "STRG.7.1"; exon_number "2"; cov "4.341936";
-chr16	StringTie	exon	970788	970901	1000	-	.	gene_id "STRG.7"; transcript_id "STRG.7.1"; exon_number "3"; cov "1.798246";
+# StringTie version 2\.1\.7
+# stringtie short_sorted\.sam long_sorted\.sam -E 25 -o /[/.\-_A-Za-z0-9]+\.dat -p 2 -f 0\.15 -m 200 -a 10 -j 1 -c 2 -g 50 -M 0\.95
+chr16\tStringTie\texon\t784986\t786377\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.[0-9+]"; exon_number "1"; cov "33\.698273";
+chr16\tStringTie\texon\t786827\t786928\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.[0-9+]"; exon_number "2"; cov "24\.970589";
+chr16\tStringTie\texon\t787077\t787179\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.[0-9+]"; exon_number "3"; cov "24\.747572";
+chr16\tStringTie\texon\t787354\t787477\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.[0-9+]"; exon_number "4"; cov "25\.967739";
+chr16\tStringTie\texon\t787556\t787744\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.[0-9+]"; exon_number "5"; cov "21\.576719";
+chr16\tStringTie\texon\t788256\t788300\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.[0-9+]"; exon_number "6"; cov "2\.600000";
+chr16\tStringTie\texon\t789075\t789125\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.[0-9+]"; exon_number "1"; cov "2\.764706";
+chr16\tStringTie\texon\t789210\t789360\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.[0-9+]"; exon_number "2"; cov "12\.516557";
+chr16\tStringTie\texon\t789547\t789715\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.[0-9+]"; exon_number "3"; cov "20\.360947";
+chr16\tStringTie\texon\t790177\t790269\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.[0-9+]"; exon_number "4"; cov "18\.048386";
+chr16\tStringTie\texon\t790347\t790399\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.[0-9+]"; exon_number "5"; cov "21\.396227";
+chr16\tStringTie\texon\t790525\t790666\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.[0-9+]"; exon_number "6"; cov "19\.359156";
+chr16\tStringTie\texon\t791161\t791370\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.[0-9+]"; exon_number "7"; cov "22\.309525";
+chr16\tStringTie\texon\t791851\t791948\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.[0-9+]"; exon_number "8"; cov "16\.336735";
+chr16\tStringTie\texon\t792224\t792347\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.[0-9+]"; exon_number "9"; cov "19\.322580";
+chr16\tStringTie\texon\t792439\t792590\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.[0-9+]"; exon_number "10"; cov "8\.835526";
+chr16\tStringTie\texon\t792718\t792811\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.[0-9+]"; exon_number "11"; cov "21\.244680";
+chr16\tStringTie\texon\t792966\t793064\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.[0-9+]"; exon_number "12"; cov "19\.494951";
+chr16\tStringTie\texon\t793144\t793274\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.[0-9+]"; exon_number "13"; cov "16\.229008";
+chr16\tStringTie\texon\t794054\t794201\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.[0-9+]"; exon_number "14"; cov "22\.121622";
+chr16\tStringTie\texon\t795132\t795356\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.[0-9+]"; exon_number "15"; cov "30\.586666";
+chr16\tStringTie\texon\t795685\t795834\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.[0-9+]"; exon_number "16"; cov "14\.393333";
+chr16\tStringTie\texon\t795947\t796077\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.[0-9+]"; exon_number "17"; cov "27\.061069";
+chr16\tStringTie\texon\t796717\t796861\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.[0-9+]"; exon_number "18"; cov "39\.082760";
+chr16\tStringTie\texon\t796961\t797092\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.[0-9+]"; exon_number "19"; cov "43\.295456";
+chr16\tStringTie\texon\t797694\t797751\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.[0-9+]"; exon_number "20"; cov "53\.689655";
+chr16\tStringTie\texon\t797839\t798048\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.[0-9+]"; exon_number "21"; cov "44\.473808";
+chr16\tStringTie\texon\t854482\t854706\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.[0-9+]"; exon_number "1"; cov "3\.262222";
+chr16\tStringTie\texon\t868944\t869056\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.[0-9+]"; exon_number "2"; cov "9\.176991";
+chr16\tStringTie\texon\t869883\t870066\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.[0-9+]"; exon_number "3"; cov "11\.130435";
+chr16\tStringTie\texon\t870729\t870882\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.[0-9+]"; exon_number "4"; cov "10\.467532";
+chr16\tStringTie\texon\t871161\t871341\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.[0-9+]"; exon_number "5"; cov "3\.563536";
+chr16\tStringTie\texon\t879570\t879737\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.[0-9+]"; exon_number "6"; cov "2\.625000";
+chr16\tStringTie\texon\t893007\t893072\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.[0-9+]"; exon_number "7"; cov "3\.242424";
+chr16\tStringTie\texon\t910931\t911074\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.[0-9+]"; exon_number "8"; cov "2\.770833";
+chr16\tStringTie\texon\t934126\t934254\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.[0-9+]"; exon_number "1"; cov "1\.131783";
+chr16\tStringTie\texon\t954357\t954666\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.[0-9+]"; exon_number "2"; cov "4\.341936";
+chr16\tStringTie\texon\t970788\t970901\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.[0-9+]"; exon_number "3"; cov "1\.798246";
+chr16\tStringTie\ttranscript\t784986\t788300\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.[0-9+]"; cov "30\.393349"; FPKM "92787\.968750"; TPM "302187\.000000";
+chr16\tStringTie\ttranscript\t789075\t798048\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.[0-9+]"; cov "24\.152929"; FPKM "73736\.570312"; TPM "240141\.406250";
+chr16\tStringTie\ttranscript\t854482\t911074\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.[0-9+]"; cov "5\.773279"; FPKM "17625\.265625"; TPM "57401\.042969";
+chr16\tStringTie\ttranscript\t934126\t970901\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.[0-9+]"; cov "3\.068716"; FPKM "9368\.495117"; TPM "30510\.824219";
+chr19\tStringTie\texon\t567221\t567648\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.[0-9+]"; exon_number "1"; cov "5\.815421";
+chr19\tStringTie\texon\t571310\t571579\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.[0-9+]"; exon_number "1"; cov "5\.888981";
+chr19\tStringTie\texon\t571440\t571596\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.[0-9+]"; exon_number "2"; cov "3\.573089";
+chr19\tStringTie\texon\t571697\t571736\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.[0-9+]"; exon_number "3"; cov "2\.550000";
+chr19\tStringTie\texon\t572567\t572701\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.[0-9+]"; exon_number "1"; cov "3\.325926";
+chr19\tStringTie\texon\t577774\t578121\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.[0-9+]"; exon_number "2"; cov "6\.436781";
+chr19\tStringTie\texon\t579500\t579656\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.[0-9+]"; exon_number "3"; cov "7\.000000";
+chr19\tStringTie\texon\t580379\t580461\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.[0-9+]"; exon_number "2"; cov "4\.879346";
+chr19\tStringTie\texon\t580379\t580461\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.[0-9+]"; exon_number "4"; cov "8\.120653";
+chr19\tStringTie\texon\t580646\t580782\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.[0-9+]"; exon_number "3"; cov "4\.616338";
+chr19\tStringTie\texon\t580646\t580782\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.[0-9+]"; exon_number "5"; cov "7\.682931";
+chr19\tStringTie\texon\t581315\t581610\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.[0-9+]"; exon_number "4"; cov "4\.479919";
+chr19\tStringTie\texon\t581315\t581610\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.[0-9+]"; exon_number "6"; cov "7\.455892";
+chr19\tStringTie\texon\t582514\t582582\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.[0-9+]"; exon_number "5"; cov "4\.504012";
+chr19\tStringTie\texon\t582514\t582582\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.[0-9+]"; exon_number "7"; cov "7\.495987";
+chr19\tStringTie\texon\t582750\t583493\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.[0-9+]"; exon_number "6"; cov "4\.371838";
+chr19\tStringTie\texon\t582750\t583493\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.[0-9+]"; exon_number "8"; cov "7\.276011";
+chr19\tStringTie\texon\t589891\t590577\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.[0-9+]"; exon_number "1"; cov "18\.537117";
+chr19\tStringTie\texon\t603544\t603967\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.[0-9+]"; exon_number "2"; cov "21\.000000";
+chr19\tStringTie\texon\t605061\t605222\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.[0-9+]"; exon_number "3"; cov "20\.981482";
+chr19\tStringTie\texon\t607964\t608182\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.[0-9+]"; exon_number "4"; cov "21\.000000";
+chr19\tStringTie\texon\t610259\t610405\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.[0-9+]"; exon_number "5"; cov "21\.000000";
+chr19\tStringTie\texon\t613248\t613488\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.[0-9+]"; exon_number "6"; cov "21\.000000";
+chr19\tStringTie\texon\t613852\t614016\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.[0-9+]"; exon_number "7"; cov "21\.000000";
+chr19\tStringTie\texon\t615795\t617159\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.[0-9+]"; exon_number "8"; cov "19\.587545";
+chr19\tStringTie\ttranscript\t567221\t571736\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.[0-9+]"; cov "5\.043160"; FPKM "15396\.282227"; TPM "50141\.804688";
+chr19\tStringTie\ttranscript\t571310\t583493\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.[0-9+]"; cov "4\.701019"; FPKM "14351\.757812"; TPM "46740\.058594";
+chr19\tStringTie\ttranscript\t572567\t583493\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.[0-9+]"; cov "6\.933517"; FPKM "21167\.359375"; TPM "68936\.750000";
+chr19\tStringTie\ttranscript\t589891\t617159\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.[0-9+]"; cov "19\.937536"; FPKM "60867\.378906"; TPM "198229\.687500";
diff -r 333a6e13b622 -r cef79931dda5 test-data/stringtie_out1_re.gtf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/stringtie_out1_re.gtf	Wed Jul 27 09:28:15 2022 +0000
@@ -0,0 +1,6 @@
+# StringTie version 2\.1\.7
+# stringtie /[-_/a-zA-Z0-9]+\.dat -o /[-_/a-zA-Z0-9]+\.dat -p [0-9]+ -f 0\.15 -m 200 -a 10 -j 1 -c 2 -g 50 -M 0\.95
+test_chromosome\tStringTie\texon\t351\t400\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; cov "53\.000004";
+test_chromosome\tStringTie\texon\t501\t550\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; cov "21\.660000";
+test_chromosome\tStringTie\texon\t53\t250\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; cov "49\.237373";
+test_chromosome\tStringTie\ttranscript\t53\t550\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; cov "45\.241611"; FPKM "3314403\.750000"; TPM "1000000\.000000";
diff -r 333a6e13b622 -r cef79931dda5 test-data/stringtie_out2_re.gtf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/stringtie_out2_re.gtf	Wed Jul 27 09:28:15 2022 +0000
@@ -0,0 +1,6 @@
+# StringTie version 2\.1\.7
+# stringtie /[-_/a-zA-Z0-9]+\.dat -o /[-_/a-zA-Z0-9]+\.dat -p [0-9]+ -f 0\.17 -m 200 -a 10 -j 1 -c 2 -g 50 -M 0\.95
+test_chromosome\tStringTie\texon\t351\t400\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; cov "53\.000004";
+test_chromosome\tStringTie\texon\t501\t550\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; cov "21\.660000";
+test_chromosome\tStringTie\texon\t53\t250\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; cov "49\.237373";
+test_chromosome\tStringTie\ttranscript\t53\t550\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; cov "45\.241611"; FPKM "3314403\.750000"; TPM "1000000\.000000";
diff -r 333a6e13b622 -r cef79931dda5 test-data/stringtie_out3_re.gtf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/stringtie_out3_re.gtf	Wed Jul 27 09:28:15 2022 +0000
@@ -0,0 +1,6 @@
+# StringTie version 2\.1\.7
+# stringtie /[-_/a-zA-Z0-9]+\.dat -o /[-_/a-zA-Z0-9]+\.dat -p [0-9]+ -G guide\.gff -b \./special_de_output/sample1/ -f 0\.15 -m 200 -a 10 -j 1 -c 2 -g 50 -M 0\.95
+test_chromosome\tStringTie\texon\t351\t400\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "53\.000004";
+test_chromosome\tStringTie\texon\t501\t550\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "21\.660000";
+test_chromosome\tStringTie\texon\t53\t250\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "49\.237373";
+test_chromosome\tStringTie\ttranscript\t53\t550\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "45\.241611"; FPKM "3314403\.750000"; TPM "1000000\.000000";
diff -r 333a6e13b622 -r cef79931dda5 test-data/stringtie_out4_re.gtf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/stringtie_out4_re.gtf	Wed Jul 27 09:28:15 2022 +0000
@@ -0,0 +1,6 @@
+# StringTie version 2\.1\.7
+# stringtie /[-_/a-zA-Z0-9]+\.dat -o /[-_/a-zA-Z0-9]+\.dat -p [0-9]+ -G guide\.gff -b \./special_de_output/sample1/ -f 0\.17 -m 200 -a 10 -j 1 -c 2 -g 50 -M 0\.95( -A /[-_/a-zA-Z0-9]+\.dat)?
+test_chromosome\tStringTie\texon\t351\t400\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "53\.000004";
+test_chromosome\tStringTie\texon\t501\t550\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "21\.660000";
+test_chromosome\tStringTie\texon\t53\t250\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "49\.237373";
+test_chromosome\tStringTie\ttranscript\t53\t550\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "45\.241611"; FPKM "3314403\.750000"; TPM "1000000\.000000";
diff -r 333a6e13b622 -r cef79931dda5 test-data/stringtie_out5.gtf
--- a/test-data/stringtie_out5.gtf	Tue Nov 30 11:01:34 2021 +0000
+++ b/test-data/stringtie_out5.gtf	Wed Jul 27 09:28:15 2022 +0000
@@ -1,6 +1,6 @@
-# stringtie /tmp/tmpgqe071sy/files/0/e/1/dataset_0e10eba1-035e-4481-9311-22277f50cd38.dat -o /tmp/tmpgqe071sy/files/d/a/a/dataset_daa0c96d-9176-476d-82fc-e2b7ef2dcd8e.dat -p 1 -G guide.gff -C /tmp/tmpgqe071sy/files/9/6/1/dataset_9614085c-99c8-4957-9b89-2391d231ddb8.dat -b ./special_de_output/sample1/ -f 0.15 -m 200 -a 10 -j 1 -c 2 -g 50 -M 0.95
-# StringTie version 2.1.7
-test_chromosome	StringTie	transcript	53	550	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "45.241611"; FPKM "3314403.750000"; TPM "1000000.000000";
-test_chromosome	StringTie	exon	53	250	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "1"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "49.237373";
-test_chromosome	StringTie	exon	351	400	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "2"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "53.000004";
-test_chromosome	StringTie	exon	501	550	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "3"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "21.660000";
+# StringTie version 2\.1\.7
+# stringtie /[-_/a-zA-Z0-9]+\.dat -o /[-_/a-zA-Z0-9]+\.dat -p [0-9]+ -G guide\.gff -C /[-_/a-zA-Z0-9]+\.dat -b \./special_de_output/sample1/ -f 0\.15 -m 200 -a 10 -j 1 -c 2 -g 50 -M 0\.95
+test_chromosome\tStringTie\texon\t351\t400\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "53\.000004";
+test_chromosome\tStringTie\texon\t501\t550\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "21\.660000";
+test_chromosome\tStringTie\texon\t53\t250\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "49\.237373";
+test_chromosome\tStringTie\ttranscript\t53\t550\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "45\.241611"; FPKM "3314403\.750000"; TPM "1000000\.000000";
diff -r 333a6e13b622 -r cef79931dda5 test-data/stringtie_out6.gtf
--- a/test-data/stringtie_out6.gtf	Tue Nov 30 11:01:34 2021 +0000
+++ b/test-data/stringtie_out6.gtf	Wed Jul 27 09:28:15 2022 +0000
@@ -1,6 +1,6 @@
-# stringtie /tmp/tmpgqe071sy/files/a/7/3/dataset_a739b50f-5870-4fab-becb-e667dfdfd00e.dat -o /tmp/tmpgqe071sy/files/8/3/6/dataset_8365f524-36d5-4bce-89dd-0c362b90be45.dat -p 1 -G guide.gff -C /tmp/tmpgqe071sy/files/3/9/6/dataset_39649d2b-5fe0-4cbe-8d5a-cd4c8b2663c9.dat -e -b ./special_de_output/sample1/ -f 0.15 -m 200 -a 10 -j 1 -c 2 -g 50 -M 0.95
-# StringTie version 2.1.7
-test_chromosome	StringTie	transcript	53	550	1000	+	.	gene_id "CUFF.1"; transcript_id "CUFF.1.1"; cov "45.241611"; FPKM "3314403.750000"; TPM "1000000.000000";
-test_chromosome	StringTie	exon	53	250	1000	+	.	gene_id "CUFF.1"; transcript_id "CUFF.1.1"; exon_number "1"; cov "49.237373";
-test_chromosome	StringTie	exon	351	400	1000	+	.	gene_id "CUFF.1"; transcript_id "CUFF.1.1"; exon_number "2"; cov "53.000004";
-test_chromosome	StringTie	exon	501	550	1000	+	.	gene_id "CUFF.1"; transcript_id "CUFF.1.1"; exon_number "3"; cov "21.660000";
+# StringTie version 2\.1\.7
+# stringtie /[-_/a-zA-Z0-9]+\.dat -o /[-_/a-zA-Z0-9]+\.dat -p [0-9]+ -G guide\.gff -C /[-_/a-zA-Z0-9]+\.dat -e -b \./special_de_output/sample1/ -f 0\.15 -m 200 -a 10 -j 1 -c 2 -g 50 -M 0\.95
+test_chromosome\tStringTie\texon\t351\t400\t1000\t\+\t\.\tgene_id "CUFF\.[0-9]+"; transcript_id "CUFF\.[0-9]+\.1"; exon_number "[0-9]+"; cov "53\.000004";
+test_chromosome\tStringTie\texon\t501\t550\t1000\t\+\t\.\tgene_id "CUFF\.[0-9]+"; transcript_id "CUFF\.[0-9]+\.1"; exon_number "[0-9]+"; cov "21\.660000";
+test_chromosome\tStringTie\texon\t53\t250\t1000\t\+\t\.\tgene_id "CUFF\.[0-9]+"; transcript_id "CUFF\.[0-9]+\.1"; exon_number "[0-9]+"; cov "49\.237373";
+test_chromosome\tStringTie\ttranscript\t53\t550\t1000\t\+\t\.\tgene_id "CUFF\.[0-9]+"; transcript_id "CUFF\.[0-9]+\.1"; cov "45\.241611"; FPKM "3314403\.750000"; TPM "1000000\.000000";
diff -r 333a6e13b622 -r cef79931dda5 test-data/stringtie_out8.gtf
--- a/test-data/stringtie_out8.gtf	Tue Nov 30 11:01:34 2021 +0000
+++ b/test-data/stringtie_out8.gtf	Wed Jul 27 09:28:15 2022 +0000
@@ -1,6 +1,6 @@
-# stringtie /tmp/tmpgqe071sy/files/d/e/8/dataset_de884427-d510-47bf-acb3-4375c0ce2337.dat -o /tmp/tmpgqe071sy/files/2/7/e/dataset_27e677d1-ed55-49db-bfb2-a38c2c6bf911.dat -p 1 -G guide.gff -b ./special_de_output/sample1/ -f 0.15 -m 200 -a 10 -j 1 -c 2 -g 50 -M 0.95
-# StringTie version 2.1.7
-test_chromosome	StringTie	transcript	53	550	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "45.241611"; FPKM "3314403.750000"; TPM "1000000.000000";
-test_chromosome	StringTie	exon	53	250	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "1"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "49.237373";
-test_chromosome	StringTie	exon	351	400	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "2"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "53.000004";
-test_chromosome	StringTie	exon	501	550	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "3"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "21.660000";
+# StringTie version 2\.1\.7
+# stringtie /[-_/a-zA-Z0-9]+\.dat -o /[-_/a-zA-Z0-9]+\.dat -p [0-9]+ -G guide\.gff -b \./special_de_output/sample1/ -f 0\.15 -m 200 -a 10 -j 1 -c 2 -g 50 -M 0\.95
+test_chromosome\tStringTie\texon\t351\t400\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "53\.000004";
+test_chromosome\tStringTie\texon\t501\t550\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "21\.660000";
+test_chromosome\tStringTie\texon\t53\t250\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "49\.237373";
+test_chromosome\tStringTie\ttranscript\t53\t550\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "45\.241611"; FPKM "3314403\.750000"; TPM "1000000\.000000";
diff -r 333a6e13b622 -r cef79931dda5 test-data/stringtie_out9.gtf
--- a/test-data/stringtie_out9.gtf	Tue Nov 30 11:01:34 2021 +0000
+++ b/test-data/stringtie_out9.gtf	Wed Jul 27 09:28:15 2022 +0000
@@ -1,6 +1,6 @@
-# stringtie /tmp/tmpgqe071sy/files/a/3/b/dataset_a3ba39e7-c812-41eb-a15c-e039ad42a33a.dat -o /tmp/tmpgqe071sy/files/7/4/7/dataset_74713e40-e879-4efa-b57e-f3d95a82284f.dat -p 1 -G guide.gff -b ./special_de_output/sample1/ -f 0.15 -m 200 -a 10 -j 1 -c 2 -g 50 -M 0.95
-# StringTie version 2.1.7
-test_chromosome	StringTie	transcript	53	550	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "45.241611"; FPKM "3314403.750000"; TPM "1000000.000000";
-test_chromosome	StringTie	exon	53	250	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "1"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "49.237373";
-test_chromosome	StringTie	exon	351	400	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "2"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "53.000004";
-test_chromosome	StringTie	exon	501	550	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "3"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "21.660000";
+# StringTie version 2\.1\.7
+# stringtie /[-_/a-zA-Z0-9]+\.dat -o /[-_/a-zA-Z0-9]+\.dat -p [0-9]+ -G guide\.gff -b \./special_de_output/sample1/ -f 0\.15 -m 200 -a 10 -j 1 -c 2 -g 50 -M 0\.95
+test_chromosome\tStringTie\texon\t351\t400\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "53\.000004";
+test_chromosome\tStringTie\texon\t501\t550\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "21\.660000";
+test_chromosome\tStringTie\texon\t53\t250\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "49\.237373";
+test_chromosome\tStringTie\ttranscript\t53\t550\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "45\.241611"; FPKM "3314403\.750000"; TPM "1000000\.000000";
diff -r 333a6e13b622 -r cef79931dda5 test-data/stringtie_out_coverage.gtf
--- a/test-data/stringtie_out_coverage.gtf	Tue Nov 30 11:01:34 2021 +0000
+++ b/test-data/stringtie_out_coverage.gtf	Wed Jul 27 09:28:15 2022 +0000
@@ -1,4 +1,4 @@
-test_chromosome	Cufflinks	transcript	53	550	1000	+	.	ID=CUFF.1.1;geneID=CUFF.1;coverage=60.97
-test_chromosome	Cufflinks	exon	53	250	1000	+	.	Parent=CUFF.1.1
-test_chromosome	Cufflinks	exon	351	400	1000	+	.	Parent=CUFF.1.1
-test_chromosome	Cufflinks	exon	501	550	1000	+	.	Parent=CUFF.1.1
+test_chromosome\tCufflinks\texon\t351\t400\t1000\t\+\t\.\tParent=CUFF\.[0-9]+\.1
+test_chromosome\tCufflinks\texon\t501\t550\t1000\t\+\t\.\tParent=CUFF\.[0-9]+\.1
+test_chromosome\tCufflinks\texon\t53\t250\t1000\t\+\t\.\tParent=CUFF\.[0-9]+\.1
+test_chromosome\tCufflinks\ttranscript\t53\t550\t1000\t\+\t\.\tID=CUFF\.[0-9]+\.1;geneID=CUFF\.[0-9]+;coverage=60\.97