# HG changeset patch
# User iuc
# Date 1579469388 18000
# Node ID 1bfa8c091530db1333ccb55f928839c7656dc3b4

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"

diff -r 000000000000 -r 1bfa8c091530 all_fasta.loc.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/all_fasta.loc.sample	Sun Jan 19 16:29:48 2020 -0500
@@ -0,0 +1,18 @@
+#This file lists the locations and dbkeys of all the fasta files
+#under the "genome" directory (a directory that contains a directory
+#for each build). The script extract_fasta.py will generate the file
+#all_fasta.loc. This file has the format (white space characters are
+#TAB characters):
+#
+#<unique_build_id>	<dbkey>	<display_name>	<file_path>
+#
+#So, all_fasta.loc could look something like this:
+#
+#apiMel3	apiMel3	Honeybee (Apis mellifera): apiMel3	/path/to/genome/apiMel3/apiMel3.fa
+#hg19canon	hg19	Human (Homo sapiens): hg19 Canonical	/path/to/genome/hg19/hg19canon.fa
+#hg19full	hg19	Human (Homo sapiens): hg19 Full	/path/to/genome/hg19/hg19full.fa
+#
+#Your all_fasta.loc file should contain an entry for each individual
+#fasta file. So there will be multiple fasta files for each build,
+#such as with hg19 above.
+#
diff -r 000000000000 -r 1bfa8c091530 chira_quantify.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/chira_quantify.xml	Sun Jan 19 16:29:48 2020 -0500
@@ -0,0 +1,64 @@
+<tool id="chira_quantify" name="ChiRA qauntify" version="@WRAPPER_VERSION@0">
+    <description>quantify aligned loci to score the alignments</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command><![CDATA[
+        chira_quantify.py
+        -b '$segments'
+        -m '$merged'
+        -cs '$crl_share'
+        -ls '$min_locus_size'
+        -e '$em_threshold'
+        '$crl'
+        -o ./
+    ]]></command>
+
+    <inputs>
+        <param format="bed" name="segments" type="data" label="BED file of aligned segments"/>
+        <param format="tabular" name="merged" type="data" label="Tabular file of merged alignments"/>
+        <param name="crl_share" type="float" value="0.7" label="CRL locus fraction" min="0" max="1"
+            help="Minimum fraction of reads of a locus that must overlap with all CRL loci inorder to merge itinto that CRL."/>
+        <param name="min_locus_size" type="integer" value="5" label="Minimum locus size" min="1"
+            help="Minimum number of reads a locus should have in order to participate in CRL creation.
+                 Always set this value relative to your sequencing depth. Setting this to lower leads
+                 CRLs of random multimappings Also consider setting the --crl_share option
+                 along with this"/>
+       <param name="em_threshold" type="float" value="1" label="EM threshold"
+              help="The maximum difference of transcripts expression between two consecutive iterations of EM algorithm to converge."/>
+       <param name="crl" type="boolean" truevalue="-crl" falsevalue="" checked="true"
+              label="Create CRLs" help="Create CRLs and qunatify them or use the loci further without creating the CRLs" />
+    </inputs>
+    <outputs>
+        <data format="tabular" name="loci" from_work_dir="loci.counts" label="ChiRA quantified loci on ${on_string}"/>
+    </outputs>
+
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="segments" value="segments.bed"/>
+            <param name="merged" value="merged.bed"/>
+            <output name="loci" file="loci.counts"/>
+        </test>
+    </tests>
+
+    <help>
+
+.. class:: infomark
+
+**What it does**
+
+This tool first creates CRLS from merged BED file and quantifies them based on the mapped reads.
+
+**Inputs**
+
+  * A BED file containing alignment segments
+  * A BED file containing merged alignments
+
+**Output**
+
+  * Tabular file containing the reads and their CRLs with TPM values.
+
+    </help>
+    <expand macro="citations" />
+  </tool>
diff -r 000000000000 -r 1bfa8c091530 macros.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Sun Jan 19 16:29:48 2020 -0500
@@ -0,0 +1,15 @@
+<macros>
+    <token name="@WRAPPER_VERSION@">@TOOL_VERSION@+galaxy</token>
+    <token name="@TOOL_VERSION@">1.0.2</token>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@TOOL_VERSION@">chira</requirement>
+            <yield/>
+        </requirements>
+    </xml>
+    <xml name="citations">
+        <citations>
+            <yield />
+        </citations>
+    </xml>
+</macros>
diff -r 000000000000 -r 1bfa8c091530 test-data/alignments.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/alignments.bed	Sun Jan 19 16:29:48 2020 -0500
@@ -0,0 +1,337 @@
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+ENSMUST00000182010	446	468	30|4,ENSMUST00000182010,446,468,+,21S22M12S	0	+
+ENSMUST00000064314	967	982	23|1,ENSMUST00000064314,967,982,+,18S15M22S	0	+
diff -r 000000000000 -r 1bfa8c091530 test-data/annotation.gtf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/annotation.gtf	Sun Jan 19 16:29:48 2020 -0500
@@ -0,0 +1,58 @@
+14	.	miRNA	115044183	115044205	.	+	.	ID=MIMAT0000529;Alias=MIMAT0000529;Name=mmu-miR-20a-5p;Derives_from=MI0000568
+16	.	miRNA	93369775	93369796	.	+	.	ID=MIMAT0017240;Alias=MIMAT0017240;Name=mmu-miR-802-3p;Derives_from=MI0004249
+1	.	miRNA	36348732	36348753	.	-	.	ID=MIMAT0027696;Alias=MIMAT0027696;Name=mmu-miR-6898-5p;Derives_from=MI0022745
+18	.	miRNA	37854605	37854625	.	-	.	ID=MIMAT0027861;Alias=MIMAT0027861;Name=mmu-miR-6979-3p;Derives_from=MI0022827
+11	havana	transcript	116338339	116347444	.	-	.	gene_id "ENSMUSG00000052949"; gene_version "10"; transcript_id "ENSMUST00000137264"; transcript_version "1"; gene_name "Rnf157"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Rnf157-011"; transcript_source "havana"; transcript_biotype "processed_transcript"; transcript_support_level "3";
+11	havana	exon	116347342	116347444	.	-	.	gene_id "ENSMUSG00000052949"; gene_version "10"; transcript_id "ENSMUST00000137264"; transcript_version "1"; exon_number "1"; gene_name "Rnf157"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Rnf157-011"; transcript_source "havana"; transcript_biotype "processed_transcript"; exon_id "ENSMUSE00000834936"; exon_version "1"; transcript_support_level "3";
+11	havana	exon	116347033	116347098	.	-	.	gene_id "ENSMUSG00000052949"; gene_version "10"; transcript_id "ENSMUST00000137264"; transcript_version "1"; exon_number "2"; gene_name "Rnf157"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Rnf157-011"; transcript_source "havana"; transcript_biotype "processed_transcript"; exon_id "ENSMUSE00001212609"; exon_version "1"; transcript_support_level "3";
+11	havana	exon	116345907	116345955	.	-	.	gene_id "ENSMUSG00000052949"; gene_version "10"; transcript_id "ENSMUST00000137264"; transcript_version "1"; exon_number "3"; gene_name "Rnf157"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Rnf157-011"; transcript_source "havana"; transcript_biotype "processed_transcript"; exon_id "ENSMUSE00001217820"; exon_version "1"; transcript_support_level "3";
+11	havana	exon	116340338	116340378	.	-	.	gene_id "ENSMUSG00000052949"; gene_version "10"; transcript_id "ENSMUST00000137264"; transcript_version "1"; exon_number "4"; gene_name "Rnf157"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Rnf157-011"; transcript_source "havana"; transcript_biotype "processed_transcript"; exon_id "ENSMUSE00001233021"; exon_version "1"; transcript_support_level "3";
+11	havana	exon	116338339	116338830	.	-	.	gene_id "ENSMUSG00000052949"; gene_version "10"; transcript_id "ENSMUST00000137264"; transcript_version "1"; exon_number "5"; gene_name "Rnf157"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Rnf157-011"; transcript_source "havana"; transcript_biotype "processed_transcript"; exon_id "ENSMUSE00000796470"; exon_version "1"; transcript_support_level "3";
+2	havana	transcript	128237693	128239643	.	-	.	gene_id "ENSMUSG00000086879"; gene_version "1"; transcript_id "ENSMUST00000136025"; transcript_version "1"; gene_name "Gm14012"; gene_source "havana"; gene_biotype "lincRNA"; transcript_name "Gm14012-001"; transcript_source "havana"; transcript_biotype "lincRNA"; tag "basic"; transcript_support_level "1";
+2	havana	exon	128239424	128239643	.	-	.	gene_id "ENSMUSG00000086879"; gene_version "1"; transcript_id "ENSMUST00000136025"; transcript_version "1"; exon_number "1"; gene_name "Gm14012"; gene_source "havana"; gene_biotype "lincRNA"; transcript_name "Gm14012-001"; transcript_source "havana"; transcript_biotype "lincRNA"; exon_id "ENSMUSE00000756585"; exon_version "1"; tag "basic"; transcript_support_level "1";
+2	havana	exon	128238858	128239058	.	-	.	gene_id "ENSMUSG00000086879"; gene_version "1"; transcript_id "ENSMUST00000136025"; transcript_version "1"; exon_number "2"; gene_name "Gm14012"; gene_source "havana"; gene_biotype "lincRNA"; transcript_name "Gm14012-001"; transcript_source "havana"; transcript_biotype "lincRNA"; exon_id "ENSMUSE00000805740"; exon_version "1"; tag "basic"; transcript_support_level "1";
+2	havana	exon	128238028	128238200	.	-	.	gene_id "ENSMUSG00000086879"; gene_version "1"; transcript_id "ENSMUST00000136025"; transcript_version "1"; exon_number "3"; gene_name "Gm14012"; gene_source "havana"; gene_biotype "lincRNA"; transcript_name "Gm14012-001"; transcript_source "havana"; transcript_biotype "lincRNA"; exon_id "ENSMUSE00000818254"; exon_version "1"; tag "basic"; transcript_support_level "1";
+2	havana	exon	128237693	128237775	.	-	.	gene_id "ENSMUSG00000086879"; gene_version "1"; transcript_id "ENSMUST00000136025"; transcript_version "1"; exon_number "4"; gene_name "Gm14012"; gene_source "havana"; gene_biotype "lincRNA"; transcript_name "Gm14012-001"; transcript_source "havana"; transcript_biotype "lincRNA"; exon_id "ENSMUSE00000741865"; exon_version "1"; tag "basic"; transcript_support_level "1";
+17	havana	transcript	39846958	39848788	.	+	.	gene_id "ENSMUSG00000098178"; gene_version "1"; transcript_id "ENSMUST00000182010"; transcript_version "1"; gene_name "Yam1"; gene_source "havana"; gene_biotype "lincRNA"; transcript_name "Yam1-001"; transcript_source "havana"; transcript_biotype "lincRNA"; tag "basic"; transcript_support_level "NA";
+17	havana	exon	39846958	39848788	.	+	.	gene_id "ENSMUSG00000098178"; gene_version "1"; transcript_id "ENSMUST00000182010"; transcript_version "1"; exon_number "1"; gene_name "Yam1"; gene_source "havana"; gene_biotype "lincRNA"; transcript_name "Yam1-001"; transcript_source "havana"; transcript_biotype "lincRNA"; exon_id "ENSMUSE00001231387"; exon_version "1"; tag "basic"; transcript_support_level "NA";
+5	havana	transcript	137134924	137142413	.	-	.	gene_id "ENSMUSG00000037390"; gene_version "11"; transcript_id "ENSMUST00000160533"; transcript_version "3"; gene_name "Muc3"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Muc3-001"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "cds_start_NF"; tag "mRNA_start_NF"; transcript_support_level "5 (assigned to previous version 2)";
+5	havana	exon	137142259	137142413	.	-	.	gene_id "ENSMUSG00000037390"; gene_version "11"; transcript_id "ENSMUST00000160533"; transcript_version "3"; exon_number "1"; gene_name "Muc3"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Muc3-001"; transcript_source "havana"; transcript_biotype "protein_coding"; exon_id "ENSMUSE00000310616"; exon_version "4"; tag "cds_start_NF"; tag "mRNA_start_NF"; transcript_support_level "5 (assigned to previous version 2)";
+5	havana	CDS	137142259	137142413	.	-	1	gene_id "ENSMUSG00000037390"; gene_version "11"; transcript_id "ENSMUST00000160533"; transcript_version "3"; exon_number "1"; gene_name "Muc3"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Muc3-001"; transcript_source "havana"; transcript_biotype "protein_coding"; protein_id "ENSMUSP00000123755"; protein_version "1"; tag "cds_start_NF"; tag "mRNA_start_NF"; transcript_support_level "5 (assigned to previous version 2)";
+5	havana	exon	137141137	137141205	.	-	.	gene_id "ENSMUSG00000037390"; gene_version "11"; transcript_id "ENSMUST00000160533"; transcript_version "3"; exon_number "2"; gene_name "Muc3"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Muc3-001"; transcript_source "havana"; transcript_biotype "protein_coding"; exon_id "ENSMUSE00000487002"; exon_version "2"; tag "cds_start_NF"; tag "mRNA_start_NF"; transcript_support_level "5 (assigned to previous version 2)";
+5	havana	CDS	137141137	137141205	.	-	2	gene_id "ENSMUSG00000037390"; gene_version "11"; transcript_id "ENSMUST00000160533"; transcript_version "3"; exon_number "2"; gene_name "Muc3"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Muc3-001"; transcript_source "havana"; transcript_biotype "protein_coding"; protein_id "ENSMUSP00000123755"; protein_version "1"; tag "cds_start_NF"; tag "mRNA_start_NF"; transcript_support_level "5 (assigned to previous version 2)";
+5	havana	exon	137140691	137140853	.	-	.	gene_id "ENSMUSG00000037390"; gene_version "11"; transcript_id "ENSMUST00000160533"; transcript_version "3"; exon_number "3"; gene_name "Muc3"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Muc3-001"; transcript_source "havana"; transcript_biotype "protein_coding"; exon_id "ENSMUSE00000488051"; exon_version "2"; tag "cds_start_NF"; tag "mRNA_start_NF"; transcript_support_level "5 (assigned to previous version 2)";
+5	havana	CDS	137140691	137140853	.	-	2	gene_id "ENSMUSG00000037390"; gene_version "11"; transcript_id "ENSMUST00000160533"; transcript_version "3"; exon_number "3"; gene_name "Muc3"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Muc3-001"; transcript_source "havana"; transcript_biotype "protein_coding"; protein_id "ENSMUSP00000123755"; protein_version "1"; tag "cds_start_NF"; tag "mRNA_start_NF"; transcript_support_level "5 (assigned to previous version 2)";
+5	havana	exon	137138188	137138349	.	-	.	gene_id "ENSMUSG00000037390"; gene_version "11"; transcript_id "ENSMUST00000160533"; transcript_version "3"; exon_number "4"; gene_name "Muc3"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Muc3-001"; transcript_source "havana"; transcript_biotype "protein_coding"; exon_id "ENSMUSE00001307390"; exon_version "1"; tag "cds_start_NF"; tag "mRNA_start_NF"; transcript_support_level "5 (assigned to previous version 2)";
+5	havana	CDS	137138188	137138349	.	-	1	gene_id "ENSMUSG00000037390"; gene_version "11"; transcript_id "ENSMUST00000160533"; transcript_version "3"; exon_number "4"; gene_name "Muc3"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Muc3-001"; transcript_source "havana"; transcript_biotype "protein_coding"; protein_id "ENSMUSP00000123755"; protein_version "1"; tag "cds_start_NF"; tag "mRNA_start_NF"; transcript_support_level "5 (assigned to previous version 2)";
+5	havana	exon	137137925	137138022	.	-	.	gene_id "ENSMUSG00000037390"; gene_version "11"; transcript_id "ENSMUST00000160533"; transcript_version "3"; exon_number "5"; gene_name "Muc3"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Muc3-001"; transcript_source "havana"; transcript_biotype "protein_coding"; exon_id "ENSMUSE00001251017"; exon_version "1"; tag "cds_start_NF"; tag "mRNA_start_NF"; transcript_support_level "5 (assigned to previous version 2)";
+5	havana	CDS	137137925	137138022	.	-	1	gene_id "ENSMUSG00000037390"; gene_version "11"; transcript_id "ENSMUST00000160533"; transcript_version "3"; exon_number "5"; gene_name "Muc3"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Muc3-001"; transcript_source "havana"; transcript_biotype "protein_coding"; protein_id "ENSMUSP00000123755"; protein_version "1"; tag "cds_start_NF"; tag "mRNA_start_NF"; transcript_support_level "5 (assigned to previous version 2)";
+5	havana	exon	137137057	137137136	.	-	.	gene_id "ENSMUSG00000037390"; gene_version "11"; transcript_id "ENSMUST00000160533"; transcript_version "3"; exon_number "6"; gene_name "Muc3"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Muc3-001"; transcript_source "havana"; transcript_biotype "protein_coding"; exon_id "ENSMUSE00001259522"; exon_version "1"; tag "cds_start_NF"; tag "mRNA_start_NF"; transcript_support_level "5 (assigned to previous version 2)";
+5	havana	CDS	137137057	137137136	.	-	2	gene_id "ENSMUSG00000037390"; gene_version "11"; transcript_id "ENSMUST00000160533"; transcript_version "3"; exon_number "6"; gene_name "Muc3"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Muc3-001"; transcript_source "havana"; transcript_biotype "protein_coding"; protein_id "ENSMUSP00000123755"; protein_version "1"; tag "cds_start_NF"; tag "mRNA_start_NF"; transcript_support_level "5 (assigned to previous version 2)";
+5	havana	exon	137134924	137135485	.	-	.	gene_id "ENSMUSG00000037390"; gene_version "11"; transcript_id "ENSMUST00000160533"; transcript_version "3"; exon_number "7"; gene_name "Muc3"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Muc3-001"; transcript_source "havana"; transcript_biotype "protein_coding"; exon_id "ENSMUSE00000869736"; exon_version "1"; tag "cds_start_NF"; tag "mRNA_start_NF"; transcript_support_level "5 (assigned to previous version 2)";
+5	havana	CDS	137135444	137135485	.	-	0	gene_id "ENSMUSG00000037390"; gene_version "11"; transcript_id "ENSMUST00000160533"; transcript_version "3"; exon_number "7"; gene_name "Muc3"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Muc3-001"; transcript_source "havana"; transcript_biotype "protein_coding"; protein_id "ENSMUSP00000123755"; protein_version "1"; tag "cds_start_NF"; tag "mRNA_start_NF"; transcript_support_level "5 (assigned to previous version 2)";
+5	havana	UTR	137134924	137135443	.	-	.	gene_id "ENSMUSG00000037390"; gene_version "11"; transcript_id "ENSMUST00000160533"; transcript_version "3"; gene_name "Muc3"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Muc3-001"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "cds_start_NF"; tag "mRNA_start_NF"; transcript_support_level "5 (assigned to previous version 2)";
+17	ensembl_havana	transcript	27655588	27711106	.	+	.	gene_id "ENSMUSG00000040276"; gene_version "10"; transcript_id "ENSMUST00000045896"; transcript_version "5"; gene_name "Pacsin1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Pacsin1-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS28567"; tag "basic"; transcript_support_level "1 (assigned to previous version 4)";
+17	ensembl_havana	exon	27655588	27655759	.	+	.	gene_id "ENSMUSG00000040276"; gene_version "10"; transcript_id "ENSMUST00000045896"; transcript_version "5"; exon_number "1"; gene_name "Pacsin1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Pacsin1-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS28567"; exon_id "ENSMUSE00000460067"; exon_version "2"; tag "basic"; transcript_support_level "1 (assigned to previous version 4)";
+17	ensembl_havana	exon	27701767	27701941	.	+	.	gene_id "ENSMUSG00000040276"; gene_version "10"; transcript_id "ENSMUST00000045896"; transcript_version "5"; exon_number "2"; gene_name "Pacsin1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Pacsin1-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS28567"; exon_id "ENSMUSE00000460051"; exon_version "1"; tag "basic"; transcript_support_level "1 (assigned to previous version 4)";
+17	ensembl_havana	CDS	27701888	27701941	.	+	0	gene_id "ENSMUSG00000040276"; gene_version "10"; transcript_id "ENSMUST00000045896"; transcript_version "5"; exon_number "2"; gene_name "Pacsin1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Pacsin1-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS28567"; protein_id "ENSMUSP00000044168"; protein_version "3"; tag "basic"; transcript_support_level "1 (assigned to previous version 4)";
+17	ensembl_havana	start_codon	27701888	27701890	.	+	0	gene_id "ENSMUSG00000040276"; gene_version "10"; transcript_id "ENSMUST00000045896"; transcript_version "5"; exon_number "2"; gene_name "Pacsin1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Pacsin1-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS28567"; tag "basic"; transcript_support_level "1 (assigned to previous version 4)";
+17	ensembl_havana	exon	27702700	27702856	.	+	.	gene_id "ENSMUSG00000040276"; gene_version "10"; transcript_id "ENSMUST00000045896"; transcript_version "5"; exon_number "3"; gene_name "Pacsin1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Pacsin1-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS28567"; exon_id "ENSMUSE00000460033"; exon_version "1"; tag "basic"; transcript_support_level "1 (assigned to previous version 4)";
+17	ensembl_havana	CDS	27702700	27702856	.	+	0	gene_id "ENSMUSG00000040276"; gene_version "10"; transcript_id "ENSMUST00000045896"; transcript_version "5"; exon_number "3"; gene_name "Pacsin1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Pacsin1-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS28567"; protein_id "ENSMUSP00000044168"; protein_version "3"; tag "basic"; transcript_support_level "1 (assigned to previous version 4)";
+17	ensembl_havana	exon	27704845	27705080	.	+	.	gene_id "ENSMUSG00000040276"; gene_version "10"; transcript_id "ENSMUST00000045896"; transcript_version "5"; exon_number "4"; gene_name "Pacsin1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Pacsin1-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS28567"; exon_id "ENSMUSE00000460027"; exon_version "1"; tag "basic"; transcript_support_level "1 (assigned to previous version 4)";
+17	ensembl_havana	CDS	27704845	27705080	.	+	2	gene_id "ENSMUSG00000040276"; gene_version "10"; transcript_id "ENSMUST00000045896"; transcript_version "5"; exon_number "4"; gene_name "Pacsin1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Pacsin1-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS28567"; protein_id "ENSMUSP00000044168"; protein_version "3"; tag "basic"; transcript_support_level "1 (assigned to previous version 4)";
+17	ensembl_havana	exon	27705625	27705780	.	+	.	gene_id "ENSMUSG00000040276"; gene_version "10"; transcript_id "ENSMUST00000045896"; transcript_version "5"; exon_number "5"; gene_name "Pacsin1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Pacsin1-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS28567"; exon_id "ENSMUSE00000460023"; exon_version "1"; tag "basic"; transcript_support_level "1 (assigned to previous version 4)";
+17	ensembl_havana	CDS	27705625	27705780	.	+	0	gene_id "ENSMUSG00000040276"; gene_version "10"; transcript_id "ENSMUST00000045896"; transcript_version "5"; exon_number "5"; gene_name "Pacsin1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Pacsin1-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS28567"; protein_id "ENSMUSP00000044168"; protein_version "3"; tag "basic"; transcript_support_level "1 (assigned to previous version 4)";
+17	ensembl_havana	exon	27705917	27706092	.	+	.	gene_id "ENSMUSG00000040276"; gene_version "10"; transcript_id "ENSMUST00000045896"; transcript_version "5"; exon_number "6"; gene_name "Pacsin1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Pacsin1-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS28567"; exon_id "ENSMUSE00000460015"; exon_version "1"; tag "basic"; transcript_support_level "1 (assigned to previous version 4)";
+17	ensembl_havana	CDS	27705917	27706092	.	+	0	gene_id "ENSMUSG00000040276"; gene_version "10"; transcript_id "ENSMUST00000045896"; transcript_version "5"; exon_number "6"; gene_name "Pacsin1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Pacsin1-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS28567"; protein_id "ENSMUSP00000044168"; protein_version "3"; tag "basic"; transcript_support_level "1 (assigned to previous version 4)";
+17	ensembl_havana	exon	27706994	27707114	.	+	.	gene_id "ENSMUSG00000040276"; gene_version "10"; transcript_id "ENSMUST00000045896"; transcript_version "5"; exon_number "7"; gene_name "Pacsin1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Pacsin1-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS28567"; exon_id "ENSMUSE00000245756"; exon_version "2"; tag "basic"; transcript_support_level "1 (assigned to previous version 4)";
+17	ensembl_havana	CDS	27706994	27707114	.	+	1	gene_id "ENSMUSG00000040276"; gene_version "10"; transcript_id "ENSMUST00000045896"; transcript_version "5"; exon_number "7"; gene_name "Pacsin1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Pacsin1-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS28567"; protein_id "ENSMUSP00000044168"; protein_version "3"; tag "basic"; transcript_support_level "1 (assigned to previous version 4)";
+17	ensembl_havana	exon	27707219	27707346	.	+	.	gene_id "ENSMUSG00000040276"; gene_version "10"; transcript_id "ENSMUST00000045896"; transcript_version "5"; exon_number "8"; gene_name "Pacsin1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Pacsin1-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS28567"; exon_id "ENSMUSE00000245736"; exon_version "1"; tag "basic"; transcript_support_level "1 (assigned to previous version 4)";
+17	ensembl_havana	CDS	27707219	27707346	.	+	0	gene_id "ENSMUSG00000040276"; gene_version "10"; transcript_id "ENSMUST00000045896"; transcript_version "5"; exon_number "8"; gene_name "Pacsin1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Pacsin1-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS28567"; protein_id "ENSMUSP00000044168"; protein_version "3"; tag "basic"; transcript_support_level "1 (assigned to previous version 4)";
+17	ensembl_havana	exon	27707880	27708067	.	+	.	gene_id "ENSMUSG00000040276"; gene_version "10"; transcript_id "ENSMUST00000045896"; transcript_version "5"; exon_number "9"; gene_name "Pacsin1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Pacsin1-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS28567"; exon_id "ENSMUSE00000459997"; exon_version "1"; tag "basic"; transcript_support_level "1 (assigned to previous version 4)";
+17	ensembl_havana	CDS	27707880	27708067	.	+	1	gene_id "ENSMUSG00000040276"; gene_version "10"; transcript_id "ENSMUST00000045896"; transcript_version "5"; exon_number "9"; gene_name "Pacsin1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Pacsin1-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS28567"; protein_id "ENSMUSP00000044168"; protein_version "3"; tag "basic"; transcript_support_level "1 (assigned to previous version 4)";
+17	ensembl_havana	exon	27708426	27711106	.	+	.	gene_id "ENSMUSG00000040276"; gene_version "10"; transcript_id "ENSMUST00000045896"; transcript_version "5"; exon_number "10"; gene_name "Pacsin1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Pacsin1-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS28567"; exon_id "ENSMUSE00000348638"; exon_version "2"; tag "basic"; transcript_support_level "1 (assigned to previous version 4)";
+17	ensembl_havana	CDS	27708426	27708532	.	+	2	gene_id "ENSMUSG00000040276"; gene_version "10"; transcript_id "ENSMUST00000045896"; transcript_version "5"; exon_number "10"; gene_name "Pacsin1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Pacsin1-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS28567"; protein_id "ENSMUSP00000044168"; protein_version "3"; tag "basic"; transcript_support_level "1 (assigned to previous version 4)";
+17	ensembl_havana	stop_codon	27708533	27708535	.	+	0	gene_id "ENSMUSG00000040276"; gene_version "10"; transcript_id "ENSMUST00000045896"; transcript_version "5"; exon_number "10"; gene_name "Pacsin1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Pacsin1-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS28567"; tag "basic"; transcript_support_level "1 (assigned to previous version 4)";
+17	ensembl_havana	UTR	27655588	27655759	.	+	.	gene_id "ENSMUSG00000040276"; gene_version "10"; transcript_id "ENSMUST00000045896"; transcript_version "5"; gene_name "Pacsin1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Pacsin1-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS28567"; tag "basic"; transcript_support_level "1 (assigned to previous version 4)";
+17	ensembl_havana	UTR	27701767	27701887	.	+	.	gene_id "ENSMUSG00000040276"; gene_version "10"; transcript_id "ENSMUST00000045896"; transcript_version "5"; gene_name "Pacsin1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Pacsin1-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS28567"; tag "basic"; transcript_support_level "1 (assigned to previous version 4)";
+17	ensembl_havana	UTR	27708536	27711106	.	+	.	gene_id "ENSMUSG00000040276"; gene_version "10"; transcript_id "ENSMUST00000045896"; transcript_version "5"; gene_name "Pacsin1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Pacsin1-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS28567"; tag "basic"; transcript_support_level "1 (assigned to previous version 4)";
diff -r 000000000000 -r 1bfa8c091530 test-data/chimeras
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/chimeras	Sun Jan 19 16:29:48 2020 -0500
@@ -0,0 +1,3 @@
+tagid	txid1	txid2	geneid1	geneid2	symbol1	symbol2	region1	region2	tx_pos_start1	tx_pos_end1	tx_pos_strand1	length1	tx_pos_start2	tx_pos_end2	tx_pos_strand2	length2	read_info	genomic_pos1	genomic_pos2	locus1	locus2	groupid1	groupid2	tpm1	tpm2	score1	score2	score	sequences	hybrid	hybrid_pos	mfe
+4|1	ENSMUST00000136025	mmu-miR-6979-3p	NA	NA	NA	NA	NA	NA	32	46	+	NA	2	12	+	NA	2,15,30,39,54	ENSMUST00000136025:32:46:+	mmu-miR-6979-3p:2:12:+	ENSMUST00000136025:32:46:+	mmu-miR-6979-3p:2:12:+	1	7	121100.0	165100.0	1.0	1.0	2.0	CAGGACUCUUGGCU&GUGUCUGUCU	NA	NA	NA
+3|2	mmu-miR-20a-5p	ENSMUST00000136025	NA	NA	NA	NA	NA	NA	0	23	+	NA	132	142	+	NA	6,28,35,44,55	mmu-miR-20a-5p:0:23:+	ENSMUST00000136025:132:142:+	mmu-miR-20a-5p:0:23:+	ENSMUST00000136025:132:142:+	5	2	75660.0	165100.0	1.0	1.0	2.0	UAAAGUGCUUAUAGUGCAGGUAG&CUGCCUGCCU	((.((((((((&))))))))))	13&1	-10.88
diff -r 000000000000 -r 1bfa8c091530 test-data/loci.counts
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/loci.counts	Sun Jan 19 16:29:48 2020 -0500
@@ -0,0 +1,9 @@
+6|1|1	ENSMUST00000182010	4	0	19	68	+	5S49M1S	ENSMUST00000182010:19:68:+	ENSMUST00000182010:19:74:+	1	1	6.485e+04
+7|9|1	ENSMUST00000182010	4	0	24	74	+	5S50M	ENSMUST00000182010:24:74:+	ENSMUST00000182010:19:74:+	1	1	6.485e+04
+4|1|2	ENSMUST00000136025	0	1	32	46	+	1S14M39S	ENSMUST00000136025:32:46:+	ENSMUST00000136025:32:46:+	1	1	1.211e+05
+3|2|2	ENSMUST00000136025	1	2	132	142	+	34S10M11S	ENSMUST00000136025:132:142:+	ENSMUST00000136025:132:142:+	1	1	1.651e+05
+2|2|2	ENSMUST00000137264	2	3	12	27	+	4S15M30S	ENSMUST00000137264:12:27:+	ENSMUST00000137264:12:27:+	1	1	1.135e+05
+6|1|4	ENSMUST00000160533	3	4	69	82	+	42S13M	ENSMUST00000160533:69:82:+	ENSMUST00000160533:69:82:+	1	1	1.297e+05
+3|2|1	mmu-miR-20a-5p	5	5	0	23	+	5S23M27S	mmu-miR-20a-5p:0:23:+	mmu-miR-20a-5p:0:23:+	1	1	7.566e+04
+2|2|1	mmu-miR-6898-5p	6	6	11	21	+	10M39S	mmu-miR-6898-5p:11:21:+	mmu-miR-6898-5p:11:21:+	1	1	1.651e+05
+4|1|1	mmu-miR-6979-3p	7	7	2	12	+	29S10M15S	mmu-miR-6979-3p:2:12:+	mmu-miR-6979-3p:2:12:+	1	1	1.651e+05
diff -r 000000000000 -r 1bfa8c091530 test-data/merged.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/merged.bed	Sun Jan 19 16:29:48 2020 -0500
@@ -0,0 +1,8 @@
+ENSMUST00000136025	32	46	+	4|1|2,ENSMUST00000136025,32,46,+,1S14M39S
+ENSMUST00000136025	132	142	+	3|2|2,ENSMUST00000136025,132,142,+,34S10M11S
+ENSMUST00000137264	12	27	+	2|2|2,ENSMUST00000137264,12,27,+,4S15M30S
+ENSMUST00000160533	69	82	+	6|1|4,ENSMUST00000160533,69,82,+,42S13M
+ENSMUST00000182010	19	74	+	6|1|1,ENSMUST00000182010,19,68,+,5S49M1S;7|9|1,ENSMUST00000182010,24,74,+,5S50M
+mmu-miR-20a-5p	0	23	+	3|2|1,mmu-miR-20a-5p,0,23,+,5S23M27S
+mmu-miR-6898-5p	11	21	+	2|2|1,mmu-miR-6898-5p,11,21,+,10M39S
+mmu-miR-6979-3p	2	12	+	4|1|1,mmu-miR-6979-3p,2,12,+,29S10M15S
diff -r 000000000000 -r 1bfa8c091530 test-data/reads.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/reads.fasta	Sun Jan 19 16:29:48 2020 -0500
@@ -0,0 +1,14 @@
+>1|1
+AAAAGACTCTGTAGACATGGCTGGTCTTGAACTCACAGAGATTTGTCTGCCTTTC
+>2|2
+ATGCAGGGAGGACGATGCGAATGGGGAATCAGGCTAAACAGTTTGAATA
+>3|2
+CGCGGTAAAGTGCTTATAGTGCAGGTAGACAGTACTGCCTGCCTTAATGAATGAA
+>4|1
+TCAGGACTCTTGGCTGTATCCTTTCCTAAGTGTCTGTCTTCCTTACCACTAACA
+>5|8
+TGTAGACACAAGGTACACCAATGCCTCTCTGACCACCCATGAGTCTTTGACCTA
+>6|1
+TGTGGTCATTAATCAAGAACGAAAGTCGGAGGTTCGAAGACGATTAGATACCGTC
+>7|9
+TGTTGAATCAAGAACGAAAGTCGGAGGTTCGAAGACGATCAGATACCGTCGTAGT
diff -r 000000000000 -r 1bfa8c091530 test-data/reads.fastq
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/reads.fastq	Sun Jan 19 16:29:48 2020 -0500
@@ -0,0 +1,96 @@
+@183438/1
+TGTTGAATCAAGAACGAAAGTCGGAGGTTCGAAGACGATCAGATACCGTCGTAGT
++
+GGGGHHHHHHHHHHHGGGGGHHGGGGGGHHGHHGGHGGGHGHHHHHHGGGGGHGG
+@397634/1
+TGTTGAATCAAGAACGAAAGTCGGAGGTTCGAAGACGATCAGATACCGTCGTAGT
++
+GGGGHHGHHHHHHHHGGGGGHHGGGGGGHHGHHGGHGGGHGHHHHHHGGGGGHGG
+@701890/1
+TGTTGAATCAAGAACGAAAGTCGGAGGTTCGAAGACGATCAGATACCGTCGTAGT
++
+EEGGHGHHHHHHHHHGGGGGGHGGCGGFGHGHHGGHGGGHGHHHHHHGGGGGGFG
+@745414/1
+TGTTGAATCAAGAACGAAAGTCGGAGGTTCGAAGACGATCAGATACCGTCGTAGT
++
+GGGGHHHHHHHHHHHGGGGGHHGGGGGGHHGHHGGHGGGHGHHHHHHGGGGGHGF
+@753363/1
+TGTTGAATCAAGAACGAAAGTCGGAGGTTCGAAGACGATCAGATACCGTCGTAGT
++
+EEEGHHHFHHHHHHHGGFEEFGGGGGGGHHGHHGGHGGFHGHHHHHHGFGGGGGG
+@881071/1
+TGTTGAATCAAGAACGAAAGTCGGAGGTTCGAAGACGATCAGATACCGTCGTAGT
++
+GGGGHHHHHHHHHHHGGGGGHHGGFGGGHHGHHGGHGGGHGHHHHHHGFGGFHGG
+@1059959/1
+TGTTGAATCAAGAACGAAAGTCGGAGGTTCGAAGACGATCAGATACCGTCGTAGT
++
+GGGGHHHHHHHHHHHGGGGGHHGGGGGEHHGHHGGHGGGHGHHHHHHGGGGGHGG
+@1157152/1
+TGTTGAATCAAGAACGAAAGTCGGAGGTTCGAAGACGATCAGATACCGTCGTAGT
++
+GGGGHHHHHHHHHHHGGGGGHHGGGGGEHHGHHGGHGGGHGHHHHHHGGGGGHGG
+@1295751/1
+TGTTGAATCAAGAACGAAAGTCGGAGGTTCGAAGACGATCAGATACCGTCGTAGT
++
+GGGGHHHHHHHHHHHGGGGGHHGGGGGGHHGHHGGHGGGHGHHHHHHGGGGGHGG
+@585749/1
+TGTGGTCATTAATCAAGAACGAAAGTCGGAGGTTCGAAGACGATTAGATACCGTC
++
+GGEGGHHHHHHHHHHHFHHHG?FGEHHGGGFEEHHGHHGGFF?FHGHHHHHGEGG
+@1209323/1
+ATGCAGGGAGGACGATGCGAATGGGGAATCAGGCTAAACAGTTTGAATA
++
+3AAABFFBBBBBGGEFGGG2AAGHHGGAGHHHHHHHHCHGHHHHHH5GF
+@1248864/1
+ATGCAGGGAGGACGATGCGAATGGGGAATCAGGCTAAACAGTTTGAATA
++
+ABBBAF4DAB?BGGEFEFG2AAF3CEGGHHGGFCG33FHFHFHHHHHHH
+@475998/1
+CGCGGTAAAGTGCTTATAGTGCAGGTAGACAGTACTGCCTGCCTTAATGAATGAA
++
+GGEEGB1FFFDGGGFHHHDDFGGHFHEFHHHHFDGGGE?GHFHHHHFHHHDEDHD
+@478112/1
+CGCGGTAAAGTGCTTATAGTGCAGGTAGACAGTACTGCCTGCCTTAATGAATGAA
++
+EEFGGFGEHHFGHBBFHHHFGHHHHAGHHHFHFFGEF@BFGGAEHFFHHHGHGHF
+@74093/1
+TGTAGACACAAGGTACACCAATGCCTCTCTGACCACCCATGAGTCTTTGACCTA
++
+G?FHHFFHFEFHH3FBAGGC2AAFEEGHFGFDEGGGFEAGFGE5AFF5@@BE5G
+@448633/1
+TGTAGACACAAGGTACACCAATGCCTCTCTGACCACCCATGAGTCTTTGACCTA
++
+EFGGFHH5BAFA23AAFFHHDGGHHFGHHHEGHCFGFAFGH3FGGBBG@E@FGF
+@849624/1
+TGTAGACACAAGGTACACCAATGCCTCTCTGACCACCCATGAGTCTTTGACCTA
++
+AABFBFFFF2CGDBADEFB2FAFFFHBGHFHDFGHAEGCFFEFDD5GGG@BBFE
+@1076923/1
+TGTAGACACAAGGTACACCAATGCCTCTCTGACCACCCATGAGTCTTTGACCTA
++
+GCEFGHHHFEFH23DB553A2BGFFDBBA35FGFFGGGEECGH5DD@@@EBEGF
+@1278542/1
+TGTAGACACAAGGTACACCAATGCCTCTCTGACCACCCATGAGTCTTTGACCTA
++
+EGGFHGHHHHGHGEGFHHHHHHFHHHFHGFGHHHHHGGEE3GHGGHGFDBGHHE
+@1290525/1
+TGTAGACACAAGGTACACCAATGCCTCTCTGACCACCCATGAGTCTTTGACCTA
++
+CEFFDHH5B2AE2F555532AGF3EGH3AFAEHHFHGD133335DFGH5D@3FF
+@1379287/1
+TGTAGACACAAGGTACACCAATGCCTCTCTGACCACCCATGAGTCTTTGACCTA
++
+AEEF1FGHHHGHHFGHHHGG/E1EHHHHGHHFDGGEG?CFGBGEGHHGHHHHHH
+@1490590/1
+TGTAGACACAAGGTACACCAATGCCTCTCTGACCACCCATGAGTCTTTGACCTA
++
+GEA3BD5DF2EGCGEDF5EGH3AGHHHFHGFBFHBGGGGH33BFFD555D53FG
+@854752/1
+AAAAGACTCTGTAGACATGGCTGGTCTTGAACTCACAGAGATTTGTCTGCCTTTC
++
+G?EFFAF5335DD5B5553222B1A55AFAGHHE33BAF325555A5DF5B3F3B
+@1180232/1
+TCAGGACTCTTGGCTGTATCCTTTCCTAAGTGTCTGTCTTCCTTACCACTAACA
++
+EGE0F10B01DDBGC/0BFFGGHHHFE21BA2D221DGHH2DBAGHBDFBG1GF
diff -r 000000000000 -r 1bfa8c091530 test-data/ref.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ref.fasta	Sun Jan 19 16:29:48 2020 -0500
@@ -0,0 +1,18 @@
+>mmu-miR-20a-5p
+TAAAGTGCTTATAGTGCAGGTAG
+>mmu-miR-802-3p
+ACGGAGAGTCTTTGTCACTCAG
+>mmu-miR-6898-5p
+TGTAAGGGGAGATGCAGGGAGC
+>mmu-miR-6979-3p
+TTGTGTCTGTCTGGCTCCCAG
+>ENSMUST00000137264
+CTACTCACATGAAGGGAGGACGATGCGCAACCCTCCACCCACCTGCCTCATCGCCTGTAACCGCGATTCTTACCCTCTCAGAAAGAACCAGAAGCCTTCCCTCTGTGGGCTAATACGTGCCAGCCAAACCTGTGGGCCAGCTGAGCTGAGGGTCAGGGCTGGTTGTTTCTGTAGGCTTTCTCTTCTGAGTGGAGACCAAGAAGACTGAAGAGTTTGGCAGCCTTGTTAGACGCCCATGGACAGGTTTTGGTCTCTGGCACTC
+>ENSMUST00000136025
+GATCTGATTGAGTCACAGCTGAGATGTGGCACCAGGACTCTTGGCTACACTCAGTTCTCTCAGTTTGACTGAGTACTCTGGGATCACAGAAGTGACTACATGATGCAGCCCAGAGGTCTGAACTCAAAGCTTCTGCCTGCCTACCTTATCTCACTGCTGGCAAATGCATCCCCTCTGCTCCACCCATC
+>ENSMUST00000182010
+GCATTTGCCAAGAATGTTTTCATTAATCAAGAACGAAAGTCGGAGTTTCGAAGACGATCAGATACCGTTGTAGTTCCAACCATAAACGATGCCGACTGGC
+>ENSMUST00000160533
+CAAAGGCAGTATCGTGGTGGATTATGATGTCATCCTGAAGGCCAAGTACACCCCAGGATTTGAAAACACATTAGATACCGTCGTCAAAAACCTGGAGACA
+>ENSMUST00000045896
+GAGGCCAATGGTGGCGCCAACCCCTTCGAGGATGATGCCAAGGGAGTTCGTGTACGGGCACTCTATGACTACGACGGTCAGGAGCAGGATGAGCTCAGCT
diff -r 000000000000 -r 1bfa8c091530 test-data/ref1.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ref1.fasta	Sun Jan 19 16:29:48 2020 -0500
@@ -0,0 +1,8 @@
+>mmu-miR-20a-5p
+TAAAGTGCTTATAGTGCAGGTAG
+>mmu-miR-802-3p
+ACGGAGAGTCTTTGTCACTCAG
+>mmu-miR-6898-5p
+TGTAAGGGGAGATGCAGGGAGC
+>mmu-miR-6979-3p
+TTGTGTCTGTCTGGCTCCCAG
diff -r 000000000000 -r 1bfa8c091530 test-data/ref2.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ref2.fasta	Sun Jan 19 16:29:48 2020 -0500
@@ -0,0 +1,10 @@
+>ENSMUST00000137264
+CTACTCACATGAAGGGAGGACGATGCGCAACCCTCCACCCACCTGCCTCATCGCCTGTAACCGCGATTCTTACCCTCTCAGAAAGAACCAGAAGCCTTCCCTCTGTGGGCTAATACGTGCCAGCCAAACCTGTGGGCCAGCTGAGCTGAGGGTCAGGGCTGGTTGTTTCTGTAGGCTTTCTCTTCTGAGTGGAGACCAAGAAGACTGAAGAGTTTGGCAGCCTTGTTAGACGCCCATGGACAGGTTTTGGTCTCTGGCACTC
+>ENSMUST00000136025
+GATCTGATTGAGTCACAGCTGAGATGTGGCACCAGGACTCTTGGCTACACTCAGTTCTCTCAGTTTGACTGAGTACTCTGGGATCACAGAAGTGACTACATGATGCAGCCCAGAGGTCTGAACTCAAAGCTTCTGCCTGCCTACCTTATCTCACTGCTGGCAAATGCATCCCCTCTGCTCCACCCATC
+>ENSMUST00000182010
+GCATTTGCCAAGAATGTTTTCATTAATCAAGAACGAAAGTCGGAGTTTCGAAGACGATCAGATACCGTTGTAGTTCCAACCATAAACGATGCCGACTGGC
+>ENSMUST00000160533
+CAAAGGCAGTATCGTGGTGGATTATGATGTCATCCTGAAGGCCAAGTACACCCCAGGATTTGAAAACACATTAGATACCGTCGTCAAAAACCTGGAGACA
+>ENSMUST00000045896
+GAGGCCAATGGTGGCGCCAACCCCTTCGAGGATGATGCCAAGGGAGTTCGTGTACGGGCACTCTATGACTACGACGGTCAGGAGCAGGATGAGCTCAGCT
diff -r 000000000000 -r 1bfa8c091530 test-data/segments.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/segments.bed	Sun Jan 19 16:29:48 2020 -0500
@@ -0,0 +1,13 @@
+ENSMUST00000182010	19	68	6|1|1,ENSMUST00000182010,19,68,+,5S49M1S	0	+
+ENSMUST00000182010	24	74	7|9|1,ENSMUST00000182010,24,74,+,5S50M	0	+
+mmu-miR-20a-5p	0	23	3|2|1,mmu-miR-20a-5p,0,23,+,5S23M27S	0	+
+mmu-miR-6898-5p	11	21	2|2|1,mmu-miR-6898-5p,11,21,+,10M39S	0	+
+mmu-miR-6979-3p	2	12	4|1|1,mmu-miR-6979-3p,2,12,+,29S10M15S	0	+
+ENSMUST00000137264	12	27	2|2|2,ENSMUST00000137264,12,27,+,4S15M30S	0	+
+ENSMUST00000136025	32	46	4|1|2,ENSMUST00000136025,32,46,+,1S14M39S	0	+
+ENSMUST00000136025	132	142	3|2|2,ENSMUST00000136025,132,142,+,34S10M11S	0	+
+ENSMUST00000182010	19	45	6|1|2,ENSMUST00000182010,19,45,+,5S26M24S	0	+
+ENSMUST00000182010	24	45	7|9|2,ENSMUST00000182010,24,45,+,5S21M29S	0	+
+ENSMUST00000182010	46	58	6|1|3,ENSMUST00000182010,46,58,+,32S12M11S	0	+
+ENSMUST00000182010	46	68	7|9|3,ENSMUST00000182010,46,68,+,27S22M6S	0	+
+ENSMUST00000160533	69	82	6|1|4,ENSMUST00000160533,69,82,+,42S13M	0	+
diff -r 000000000000 -r 1bfa8c091530 test-data/singletons
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/singletons	Sun Jan 19 16:29:48 2020 -0500
@@ -0,0 +1,4 @@
+tagid	txid	geneid	symbol	region	tx_pos_start	tx_pos_end	tx_pos_strand	length	read_info	genomic_pos	locus	groupid	tpm	score	score	sequences
+6|1	ENSMUST00000182010	NA	NA	NA	19	68	+	NA	6,54,55	ENSMUST00000182010:19:68:+	ENSMUST00000182010:19:74:+	0	64850.0	1.0	1.0	UCAUUAAUCAAGAACGAAAGUCGGAGUUUCGAAGACGAUCAGAUACCGUUGUAGU
+7|9	ENSMUST00000182010	NA	NA	NA	24	74	+	NA	6,55,55	ENSMUST00000182010:24:74:+	ENSMUST00000182010:19:74:+	0	64850.0	1.0	1.0	UCAUUAAUCAAGAACGAAAGUCGGAGUUUCGAAGACGAUCAGAUACCGUUGUAGU
+2|2	ENSMUST00000137264	NA	NA	NA	12	27	+	NA	5,19,49	ENSMUST00000137264:12:27:+	ENSMUST00000137264:12:27:+	3	113500.0	1.0	1.0	AGGGAGGACGAUGCG
diff -r 000000000000 -r 1bfa8c091530 tool_data_table_conf.xml.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample	Sun Jan 19 16:29:48 2020 -0500
@@ -0,0 +1,7 @@
+<tables>
+    <!-- Locations of all fasta files under genome directory -->
+    <table name="all_fasta" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="all_fasta.loc" />
+    </table>
+</tables>