# HG changeset patch
# User iuc
# Date 1579469494 18000
# Node ID 5db8946714344078be038e65009f7faa86306f67

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

diff -r 000000000000 -r 5db894671434 all_fasta.loc.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/all_fasta.loc.sample	Sun Jan 19 16:31:34 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 5db894671434 chira_merge.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/chira_merge.xml	Sun Jan 19 16:31:34 2020 -0500
@@ -0,0 +1,97 @@
+<tool id="chira_merge" name="ChiRA merge" version="@WRAPPER_VERSION@0">
+    <description>merge aligned positions</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command><![CDATA[
+        chira_merge.py
+        -b '$alignments'
+        #if str($annotation.choice) == "yes":
+            -g '$annotation.gtf'
+        #end if            
+        -ao '$alignment_overlap'
+        -so '$segment_overlap'
+        -o ./
+    ]]></command>
+
+    <inputs>
+        <param format="bed" name="alignments" type="data" label="Input BED file of alignments"/>
+        <conditional name="annotation">
+            <param name="choice" type="select" label="Hybridize interacting loci?"
+                   help="Hybridization is a time consuming process.">
+                <option value="yes">Yes</option>
+                <option value="no">No</option>
+            </param>
+            <when value="yes">
+                <param format="gtf,gff" name="gtf" type="data" label="Annotations in GTF format"/>
+            </when>
+            <when value="no">
+                <!-- Do nothing -->
+            </when>        
+        </conditional>
+        <param name="alignment_overlap" type="float" value="0.7" label="Overlap fraction for merging alignments" min="0" max="1"
+            help="Minimum fraction of BED entries that must overlap inorder to merge"/>
+        <param name="segment_overlap" type="float" value="0.7" label="Overlap fraction for merging mapped read positions to segments" min="0" max="1"
+            help="Matching read positions with greater than this fraction overlap are merged into a segment"/>
+    </inputs>
+    <outputs>
+        <data format="bed" name="segments_bed" from_work_dir="segments.bed" label="ChiRA aligned read segments on ${on_string}"/>
+        <data format="tabular" name="merged_bed" from_work_dir="merged.bed" label="ChiRA merged alignments on ${on_string}"/>
+    </outputs>
+
+    <tests>
+        <!-- Test: Map without annotation -->
+        <test expect_num_outputs="2">
+            <param name="alignments" value="alignments.bed"/>
+            <param name="choice" value="no" />
+            <output name="segments_bed" >
+                <assert_contents>
+                    <has_text_matching expression="ENSMUST00000160533\t69\t82\t6|1|4,ENSMUST00000160533,69,82,+,42S13M\t0\t+" />
+                </assert_contents>
+            </output>
+            <output name="merged_bed" >
+                <assert_contents>
+                    <has_text_matching expression="ENSMUST00000182010\t19\t74\t+\t6|1|1,ENSMUST00000182010,19,68,+,5S49M1S;7|9|1,ENSMUST00000182010,24,74,+,5S50M" />
+                </assert_contents>
+            </output>
+        </test>
+        <!-- Test: Map with annotation -->
+        <test expect_num_outputs="2">
+            <param name="alignments" value="alignments.bed" />
+            <param name="choice" value="yes" />
+            <param name="gtf" value="annotation.gtf" />
+            <output name="segments_bed" >
+                <assert_contents>
+                    <has_text_matching expression="5\t137142331\t137142344\t6|1|4,ENSMUST00000160533,69,82,+,42S13M\t0\t-" />
+                </assert_contents>
+            </output>
+            <output name="merged_bed" >
+                <assert_contents>
+                    <has_text_matching expression="17\t39846976\t39847031\t+\t6|1|1,ENSMUST00000182010,19,68,+,5S49M1S;7|9|1,ENSMUST00000182010,24,74,+,5S50M" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+
+    <help>
+
+.. class:: infomark
+
+**What it does**
+
+This tool merges the overlapping aligned positions to define the read concentrated loci. If an annotation GTF file produced, the transcriptomic alignment positions are first converted to their corresponding genomic positions.
+
+**Inputs**
+
+* Alignments in BED format
+* An annotation GTF file contaning reference genomic positions.
+
+**Output**
+
+* BED file containing the alignments with reads categorized into segments depending on which part of the read is aligned.
+* Tabular file containing merged alignments. 4th column contains all the alignments merged into that location.
+
+    </help>
+    <expand macro="citations" />
+</tool>
diff -r 000000000000 -r 5db894671434 macros.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Sun Jan 19 16:31:34 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 5db894671434 test-data/alignments.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/alignments.bed	Sun Jan 19 16:31:34 2020 -0500
@@ -0,0 +1,337 @@
+mmu-miR-124-3p	0	20	3|2,mmu-miR-124-3p,0,20,+,5S20M30S	0	+
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+mmu-miR-3098-3p	3	14	16|3,mmu-miR-3098-3p,3,14,+,39S11M5S	0	+
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+mmu-miR-7651-3p	6	16	24|1,mmu-miR-7651-3p,6,16,+,6S10M39S	0	+
+mmu-miR-742-3p	7	16	16|3,mmu-miR-742-3p,7,16,+,35S9M11S	0	+
+mmu-miR-6936-3p	2	11	20|1,mmu-miR-6936-3p,2,11,+,31S9M14S	0	+
+mmu-miR-6936-3p	2	11	20|1,mmu-miR-6936-3p,2,11,+,33S9M12S	0	+
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+mmu-miR-7016-3p	10	20	23|1,mmu-miR-7016-3p,10,20,+,34S10M11S	0	+
+mmu-miR-7019-5p	6	16	4|2,mmu-miR-7019-5p,6,16,+,30S10M15S	0	+
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+ENSMUST00000182010	408	445	22|1,ENSMUST00000182010,408,445,+,5S37M13S	0	+
+ENSMUST00000182010	409	445	12|3,ENSMUST00000182010,409,445,+,5S36M14S	0	+
+ENSMUST00000182010	419	445	34|1,ENSMUST00000182010,419,445,+,5S26M24S	0	+
+ENSMUST00000182010	424	445	35|9,ENSMUST00000182010,424,445,+,5S21M29S	0	+
+ENSMUST00000182010	426	445	15|2,ENSMUST00000182010,426,445,+,5S19M31S	0	+
+ENSMUST00000182010	428	445	36|10,ENSMUST00000182010,428,445,+,5S17M33S	0	+
+ENSMUST00000182010	430	445	30|4,ENSMUST00000182010,430,445,+,5S15M35S	0	+
+ENSMUST00000182010	446	458	22|1,ENSMUST00000182010,446,458,+,43S12M	0	+
+ENSMUST00000182010	446	459	12|3,ENSMUST00000182010,446,459,+,42S13M	0	+
+ENSMUST00000182010	446	458	34|1,ENSMUST00000182010,446,458,+,32S12M11S	0	+
+ENSMUST00000182010	446	468	35|9,ENSMUST00000182010,446,468,+,27S22M6S	0	+
+ENSMUST00000182010	446	468	15|2,ENSMUST00000182010,446,468,+,25S22M8S	0	+
+ENSMUST00000182010	446	468	36|10,ENSMUST00000182010,446,468,+,23S22M10S	0	+
+ENSMUST00000182010	446	468	30|4,ENSMUST00000182010,446,468,+,21S22M12S	0	+
+ENSMUST00000064314	967	982	23|1,ENSMUST00000064314,967,982,+,18S15M22S	0	+
diff -r 000000000000 -r 5db894671434 test-data/annotation.gtf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/annotation.gtf	Sun Jan 19 16:31:34 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 5db894671434 test-data/chimeras
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/chimeras	Sun Jan 19 16:31:34 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 5db894671434 test-data/loci.counts
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/loci.counts	Sun Jan 19 16:31:34 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 5db894671434 test-data/merged.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/merged.bed	Sun Jan 19 16:31:34 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 5db894671434 test-data/reads.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/reads.fasta	Sun Jan 19 16:31:34 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 5db894671434 test-data/reads.fastq
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/reads.fastq	Sun Jan 19 16:31:34 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 5db894671434 test-data/ref.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ref.fasta	Sun Jan 19 16:31:34 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 5db894671434 test-data/ref1.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ref1.fasta	Sun Jan 19 16:31:34 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 5db894671434 test-data/ref2.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ref2.fasta	Sun Jan 19 16:31:34 2020 -0500
@@ -0,0 +1,10 @@
+>ENSMUST00000137264
+CTACTCACATGAAGGGAGGACGATGCGCAACCCTCCACCCACCTGCCTCATCGCCTGTAACCGCGATTCTTACCCTCTCAGAAAGAACCAGAAGCCTTCCCTCTGTGGGCTAATACGTGCCAGCCAAACCTGTGGGCCAGCTGAGCTGAGGGTCAGGGCTGGTTGTTTCTGTAGGCTTTCTCTTCTGAGTGGAGACCAAGAAGACTGAAGAGTTTGGCAGCCTTGTTAGACGCCCATGGACAGGTTTTGGTCTCTGGCACTC
+>ENSMUST00000136025
+GATCTGATTGAGTCACAGCTGAGATGTGGCACCAGGACTCTTGGCTACACTCAGTTCTCTCAGTTTGACTGAGTACTCTGGGATCACAGAAGTGACTACATGATGCAGCCCAGAGGTCTGAACTCAAAGCTTCTGCCTGCCTACCTTATCTCACTGCTGGCAAATGCATCCCCTCTGCTCCACCCATC
+>ENSMUST00000182010
+GCATTTGCCAAGAATGTTTTCATTAATCAAGAACGAAAGTCGGAGTTTCGAAGACGATCAGATACCGTTGTAGTTCCAACCATAAACGATGCCGACTGGC
+>ENSMUST00000160533
+CAAAGGCAGTATCGTGGTGGATTATGATGTCATCCTGAAGGCCAAGTACACCCCAGGATTTGAAAACACATTAGATACCGTCGTCAAAAACCTGGAGACA
+>ENSMUST00000045896
+GAGGCCAATGGTGGCGCCAACCCCTTCGAGGATGATGCCAAGGGAGTTCGTGTACGGGCACTCTATGACTACGACGGTCAGGAGCAGGATGAGCTCAGCT
diff -r 000000000000 -r 5db894671434 test-data/segments.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/segments.bed	Sun Jan 19 16:31:34 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 5db894671434 test-data/singletons
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/singletons	Sun Jan 19 16:31:34 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 5db894671434 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 16:31:34 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>