# HG changeset patch
# User iuc
# Date 1590009822 14400
# Node ID bc0b40dec7d25a59944a950c86b5f8e344683e1e

"planemo upload for repository https://github.com/nebiolabs/tasmanian-mismatch commit a64a371ca1ed117c9bd8af743d847128fbce461c"

diff -r 000000000000 -r bc0b40dec7d2 README.rst
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.rst	Wed May 20 17:23:42 2020 -0400
@@ -0,0 +1,16 @@
+Galaxy wrappers for tasmanian_mismatch tool
+===========================================
+
+These wrappers are available from the Galaxy Tool Shed at:
+http://toolshed.g2.bx.psu.edu/view/iuc/tasmanian_mismatch
+
+The tasmanian_mismatch repository:
+    - Provides tasmanian-mismatch wrapper
+    - Downloads and builds tasmanian-mismatch and all its dependencies on the Linux or Mac operating system
+
+To collaborate with this project and for more information, please visit https://github.com/nebiolabs/tasmanian-mismatch
+
+
+
+
+
diff -r 000000000000 -r bc0b40dec7d2 Tasmanian.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Tasmanian.xml	Wed May 20 17:23:42 2020 -0400
@@ -0,0 +1,158 @@
+<tool id="tasmanian_mismatch" name="Analysis of artifacts with Tasmanian" version="0.1.3" profile="18.09">
+  <requirements>
+    <requirement type="package" version="0.1.3">tasmanian-mismatch</requirement> 
+    <requirement type="package" version="1.9">samtools</requirement>
+  </requirements>
+  <command detect_errors="exit_code">
+    <![CDATA[
+   
+     #set $reference_fasta_filename = "localref.fa"
+
+     #if str( $reference_source.reference_source_selector ) == "history":
+        ln -s '${reference_source.ref_file}' '${reference_fasta_filename}' &&
+     #else:
+        #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
+     #end if
+
+    samtools view '${bam_input}' | 
+   
+     #if $bed_filename
+        run_intersections -b '$bed_filename' | 
+     #end if  
+ 	   
+     run_tasmanian
+        -q '${basequality}'
+        -s '${softclips}'
+        -m '${mapquality}'
+        -c '${confidence}'
+        -r '${reference_fasta_filename}' > '${output_table}'
+
+  ]]></command>
+  <inputs>
+    <!-- Bam alignment file -->
+    <param type="data" name="bam_input" label="Bam/Sam alignemnt file" format="bam" help="Specify BAM/SAM dataset. If not using a bed file, this file MUST BE SORTED"/>
+    <!-- reference genome upload -->
+    <conditional name="reference_source">
+      <param name="reference_source_selector" type="select" label="Reference genome" help="You can select a reference genome from your history or use a built-in index (Local cache)">
+        <option value="cached">Local cache</option>
+        <option value="history">History</option>
+      </param>
+      <when value="cached">
+        <param name="ref_file" type="select" label="Select the reference genome from the list">
+          <options from_data_table="all_fasta">
+            <filter type="sort_by" column="2" />
+            <validator type="no_options" message="No indexes are available" />
+          </options>
+        </param>
+      </when>
+      <when value="history">
+        <param name="ref_file" type="data" format="fasta" label="Use reference genome from history" help="You can first upload a FASTA sequence to the history" />
+      </when>
+    </conditional>
+            
+    <!-- bed file -->       
+    <param name="bed_filename" type="data" format="bed" optional="true" label="Select a bed file" help="The bed file should contain at least: &quot;chrN&quot;, &quot;start&quot; and &quot;stop&quot;, and is tab separated."/>
+
+    <!-- Additional parameters -->
+    <param name="confidence" label="Boundary" type="integer" value="20" min="0" max="100"
+        help="Number of bases in boundary region, from 0 to length of the read (read help below). Default=20"/> 
+    <param name="softclips" label="Choose an action with softclips" type="select" display="radio"
+        help="How sofclips whould be treated. Values include 0,1 or 2 (read the help below). Default=0">
+      <option value="1">Never use softcliped bases</option>
+      <option value="2">Always use softcliped bases</option>
+      <option value="0" selected="True">Automatic desicion (Default)</option>
+    </param>
+    <param name="mapquality" label="Map quality" type="integer" min="0" max="70" value="20" help="Exclude reads with lower mapQ than this number. Default=20"/>
+    <param name="basequality" label="Base quality" type="integer" min="0" max="70" value="20" help="Exclude bases with lower Base quality than this number. Default=20"/>
+    <param name="keepHTML_conditional" type="select" label="keep HTML output file?">
+      <option value="yes">Yes</option>
+      <option value="no">No</option>
+    </param>    
+  </inputs>
+
+  <outputs>
+    <data name="output_table" format="txt" />
+    <data format="html" name="html_file" from_work_dir="Tasmanian_artifact_report.html" label="tasmanian-mismatch results table">
+      <filter>keepHTML_conditional == "yes"</filter>
+    </data>
+  </outputs>
+
+  <tests>
+    <!-- test when reference from history with bed-->
+    <test>
+      <param name="bam_input" value="test2.bam" ftype="bam"/>
+      <param name="reference_source_selector" value="history"/>
+      <param name="ref_file" value="small_region.fa"/>
+      <param name="bed_filename" value="test2.bed" ftype="bed"/>
+      <output name="output_table" file="test2-bed.output" lines_diff="4"/>
+    </test>
+    <!-- test when reference from history without bed-->
+    <test>
+      <param name="bam_input" value="test2.bam" ftype="bam"/>
+      <param name="reference_source_selector" value="history"/>
+      <param name="ref_file" value="small_region.fa"/>
+      <output name="output_table" file="test2-nobed.output" lines_diff="4"/>
+    </test>
+    <!-- test when reference from cached-->
+    <test>
+      <param name="bam_input" value="test2.bam" ftype="bam" dbkey="hg38"/>
+      <param name="reference_source_selector" value="cached"/>
+      <param name="ref_file" value="hg38"/>
+      <output name="output_table" file="test2-nobed.output" lines_diff="4"/>
+    </test>
+  </tests>
+
+  <help>
+    <![CDATA[
+
+**What it does**
+
+This tool counts the number/proportion of mismatches per position along the read, 
+for each read (see figure below).
+
+.. image:: ${static_path}/images/snapshot_good.jpg
+    :height: 350                                                            
+    :width: 650   
+
+-----
+
+**What is special**
+
+By providing a bed file, tasmanian-mismatch will count mismatches from all regions depicted in the figure below, 
+and will report them separately. Also, a parameter defined as *"confidence"* allows including reads with >=
+bases in the boundary region in a separate group. This is useful when the bed refers to repeat regions. Since these 
+regions might not have been correctly placed in the assembly or are not the same in different individuals, we can 
+include this *confidence* repeat regions where we have high confidence on the reference genome to which we mapped the reads.
+
+.. image:: ${static_path}/images/intersections_tasmanian.jpg                
+    :height: 150                                                            
+    :width: 650 
+
+Softclips are critical in FFPE (Formalin-fixed paraffin-embedded) experiments as mismatches tend to accumulate at the ends of the reads. Most often, softclips 
+are all accepted during the analysis and many real mismatches are indirectly excluded from the analysis. Hence, this tool 
+provides different ways to deal with this: 
+
+The *softclips* field allows for 3 different ways at treating softclips:    
+0) Exclude these region if there is less than 2/3 identity with the reference genome  
+1) Exclude all softclipped bases  
+2) Include all softclipped bases  
+
+.. class:: warningmark   
+
+BAM/SAM file must be **sorted** if not using a bed file.
+  
+    ]]>
+  </help>
+  <citations>
+    <citation type="bibtex">
+      @misc{githubtasmanian,
+        author = {Langhorst B., Others, Erijman A.},
+        year = {2020},
+        title = {TBD},
+        publisher = {GitHub},
+        journal = {GitHub repository},
+        url = {https://github.com/nebiolabs/tasmanian-mismatch},
+      }
+    </citation>
+  </citations>
+</tool>
diff -r 000000000000 -r bc0b40dec7d2 static/images/intersections_tasmanian.jpg
Binary file static/images/intersections_tasmanian.jpg has changed
diff -r 000000000000 -r bc0b40dec7d2 static/images/snapshot_good.jpg
Binary file static/images/snapshot_good.jpg has changed
diff -r 000000000000 -r bc0b40dec7d2 test-data/all_fasta.loc
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/all_fasta.loc	Wed May 20 17:23:42 2020 -0400
@@ -0,0 +1,2 @@
+#chrM	chrM	ChrM	${__HERE__}/cached_locally/picard_BedToIntervalList_ref.fa
+hg38	hg38	Human hg38	${__HERE__}/cached_locally/small_region.fa
diff -r 000000000000 -r bc0b40dec7d2 test-data/cached_locally/all_fasta.loc
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cached_locally/all_fasta.loc	Wed May 20 17:23:42 2020 -0400
@@ -0,0 +1,1 @@
+hg38	hg38	Human hg38	${__HERE__}/small_region.fa
diff -r 000000000000 -r bc0b40dec7d2 test-data/cached_locally/small_region.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cached_locally/small_region.fa	Wed May 20 17:23:42 2020 -0400
@@ -0,0 +1,102 @@
+>chr1
+TCCTCAGAAAATGGATTTTTCTTTTCTATCACAGTGTCATGCTACAAATTTTCTGAACGTTTATGCTCTG
+TTTTCCTGTTAAAACTGAGTGCTTTTAACACACCCAAGTCACTCTTGAATGATTTGCTGCTTAGAAATTT
+CTTCTGCCAGATACCCTAACTCATCTCCCTCAAGTTCAAAGTTCCACAAATCTCTAGGGCAGGGACAAAA
+TGCTGCCAGTCTCTCTCGATAGCAAGAGACACCTTTACTCCAGTTCCCATTGAGTTCCTCATCTCCATCT
+GAGACCATCTCAGCCTGGATTTCATTGTCTATATCATTATTTGACATTTTAGTCAAAGCCATTCAACAAG
+TCTCTAGGAAGTTCCAAACTTTCCCACATTTTCCTGTCGTTTTCTGAGCCCTCCAAACTGTTTCAACCCC
+TGCCTGTTACCCAGTTCCAAAGTCGCTTCCACATTTTTGGGTTATCTTTACAACAGCACCCCACTCTACC
+AGTACCAATGTACTGTATTAGTCTGTTTTCATGCTGCTGATAAAGACATACCTGAGACTGAGTGATTTAT
+GAAGAAAAAGACACTTAATGGACTCACATTTCCAGGTGGATGGGGAGGCCTCACAATCATGGTGGAAGGC
+AAAAGGCACATCTCTACATGATGGCAGACAAGACAGAATGAGAGCTAAGTGAAAGGGGAACCCCCTTATA
+AAATCATCAGCTCTTGTGAGACTTATTCAAGACCACGAGAACAGTATGGGGGAAATACTCCTGTGATTCA
+GTTATCTCCCGTTGGATCCCTCCCACAAGACACGGAAATTATGGGAGCTACAATTCAAGATGAGATTTGG
+GTGGGGACACATCCAAACCATATTGCTGCTGAATAGATCATGTAGACAGGCTCTCAAACTACACGGAGAG
+CAAGAGAGGCCCACCTTACCACAACATTTCATCCAATCCACTAATAAAACAGGCACATCACTGAAGCCAC
+CTTCAACTCTCCAGACTACCCAGCTGCCAGCTGAATACCACAGATGGCTACAGTTAATACCACATGGAGC
+AGAATCATGTAGCTAAGCCCTGCTTGCGCTAATACAAGTCCACAATTTTTTTTAAGTTTGTTGTTTTAAG
+CTGCTAAGTTTTGAGGTGGTTTGTGGTACGTGGAATAAGATGTCACTCTAATATAATATAAACTTAAACT
+ATGTGGCATTGGCTTTGGAATCAGACAATGGATAGAAGCCAGAAGGATTTCACAAAGACTGTTAGTGAAA
+AGTGAACAGACTTCAAGGAAAATGATAGCAAAACCTGTAAAAGCATTCTGGGAACTGACAGTAAACACTG
+AATGGTCCTTAAGGAGACTGAAAACTTGAAAGAGCTTAAGAAGTCTACTGGAAAGGGCTTTAAGGATAAT
+GAGAAAAAATCATCAGTGGAGGCTGAGGAAAACGCACCAAAGTCATATTCTGATGGGAGAATTAGAAAAC
+GCTTGCCTGGAATGATATAAAAAATAGGAAAAATACCGAAAAAGTTTGTGGATCTGGCTGGGGAGATTTT
+TGGTGTCAACTAAAGAAAAAAATTAAGCTTTTAAGAAATTAAAGTTAGATTTATTTAGGGGTCTGAGAAC
+AAGAGACTGAGGATTACAGCCTAGGAGAAGTCTTCCAGAGAGGTTCTGTCAGACTGCTCTGGTGAAGGTC
+TTTAGCCCACAGTTTATATGCAGGCTGTACATATACACCATGGAATACTATGCCGCCATTAAAAAATGAT
+ATCATGTCTTTTGCTGGAACATGGATGGACCTTCTATTATCCTTAGCAAACTAATGCAGGAACAGAAAAC
+CAAATACAGCATACTCTCAGTTATAAGTGGGAGCTAAATGATGAGAACTCATGAACACAAAGAATAAAAC
+AGACACTGGGGTCTACTTGAGGGTGGAGGGTGAGAAAAGGAAGAGAAGCAGAAAAGATAACTATTGGGTA
+CTAGGTTTAATACCTGGGTGATGAAATGATCTGTACAATAACCCCCTGTGACACCAGTCTACCTATGTAA
+CAAATGCCCCTAAACTTAAAATAAAAGTTAAAAAAAAAGAAAATTAAAATCTCCTTATCATCTACCTGGT
+AATATGAAAAACACAAATCTTTCATTCATTCCTTTCAACTGATGAGGAAAATGAGGCATCGGGAGTTAGT
+AAAAGTCCACATTGAGATATGAGACCCACCACTGGCTGGACGCAGTGGCTCACACCTGTAATCCCAGCAC
+TTTGGGAGGCCGATGCTGGTGGATCACCTAAGGTCAGGAGTTCGGGACCAGGCTGGCCAACATGGTGAAA
+CCCCCATCTCTACTAAAAATACAAAAATTAGCTGGGTGTGGTGGCAGGCACCTGTAATACCAGCTACTAG
+GGAGGCTGAGGCAGGAGAATCGCTTGAACCCAGGAGGTGGAGTTTACAGTGAGCCAAAATCACGCCATTG
+CACTCCAGCCTGGGCAACAAGAGCAAGACTCTGTCGGGGAAAAAAAAGAAAAAAAAAAACCACCGCCATC
+ATTTTGCAAGTGTTACCACTATTGTGTGTTAATATTGTAGAAGTATTCCTAATTATGATTTCTTTGTATT
+CCTAATTGTAATAGCTTTGTATTTGAAAAATTATTGATTCATACTCTATATGTTATTATTTTGTATGTGA
+TGACAACAGAATATATTATCATGCTCCTTTTGTGAATCTCATTCATAATATAAAGTATAAATTTGTGATT
+TTGCTTTAATTTGAAATATTAACTTCAAATATGTTATCACAATTTGATACAAACTATTGACAGTAAATCT
+GTGGATTAAGTAATGTCTTAGTAGGTATTGGGAAAATTTGAAACTAGTAACATGGAGGACTATTGTCATT
+GTTTATTTCAAAGCCAGTTAAAATTCTGCAAAGCAGTGTACATAAAAATAATTTCAAGAAATTTATAAAA
+TACCGAGATTATGGTGTATAAACAACTTTAGATTCTTTGTTTAAGAAATTCTGCCAGTTTGTAATATATG
+CTTCATTCAAAGTAGCTAAGGGCTGTACCTGGCTAATAGTAGGCACCTAATATTTGTTGAAAAGGAATAC
+TGAGTAGCTGGGACCTCCTGAGTAGCTGGGACCACACACATTTAACCTGTATTTATAAAATTACTGTTTA
+GAGAATAACATTTGATGGAATCATGCTTTTACTTTCTGCTTACGACTCAATTGTTTGTACTGACATTAAC
+ATCCCAAATCCTTAGCATGGCCTACAAGGCCCTGAGCAATGTGGCACCTGCTGAAGCCTGCTGCCTCATT
+TAATAACTCTTTGTCTCTTTCCCAGATCCAGCCACTCTAACATTTTTTAGCTCCTGGACCAAGACAAGCT
+CTTCCCAGAACCTGACCTTTGTACCTGTTCTTTATTCCTGGAGTATTTTTCCCCTGACAAATTACTTATC
+ATCTATCATAATTCAGGTTAAATGGCACTAACTCAGGGAAGGCTTCCCTAACTGCCTCCCTTCTCCAACC
+AAATTAGGAACAATTATATGGCCACATAGTATCGAATCAAGTTTATAATTTTAAAATAATTGGGAGATTT
+TGTTGTTTAACACTTGTTTTCACTATAAGACTGTAATTACATGCAAGTAAGAACCATGCCTGTTTGTTCA
+CTCCTGCCACAGTCAGAATAGTGCCTGGAATATGCAGTAAGGGCTGAACAAGCACTAAATAAATGAACAA
+GTGAATAAATGGATATTGTCTCATTTTTAGAACAGAGTACTGAATGGATCATGAACACTATCTGGTATGT
+CACGTAGGTAATTTACAAGGGCTACAATTTCAGCTCAGATTTACCTTTTCCTGGATACAGGTCTTGATAG
+GTCTCTTGATGTCATTTCACTTCAGATTCTTCTTTAGAAAACTTGGACAATAGCATTTGCTGTCTTGTCC
+AAATTGTTACTAAGAATCAAGAGAGATATCTGACATGAAATGACATTGGAAAACATTAAACACGATTGAA
+ATAATGCTAGCCAATATGGTTATTATTAGAAACCAATTACATTTTCAACTTAAAAATAGTAATACTTATT
+GCAGACTCAAATGTGCTTATTCTAAAACAAGTAAATGTTTGCCTATGGTCTGAGATTCTAATCCACGGAG
+TTCATTCTAATCCACATTCAACACTATCATGTACCAGTGGGCCTCATAACCCACCTAGCCCTGTGATTTT
+TCAGGTTCACTTTTCTAAACTTGTGAATTAAATATTTATTTTCTTAGTTCAGAAGAGGAAAAAAACTCTT
+GTAATTGTTGCCCATTTCAGGAGAAATCTTGCATATGAAAACAAGAGATAAATATACACAACTGAGGGCT
+GTGGTTTAAACAAAATCTTGAGAATGTTTTTTGACCTTACACATTTGTGCTTTAGTATAACAAAATGATA
+TAGACAAAGGTAACTTTTAATAGAACCAGTCACTAAATTAAAAAAATGACAAATTCTTCTGCTTAGCTAA
+GCAACAGAGAAGGTAAAATACTAATTCAATTCATCAATTTAAGCAATACTCATTAAGAGCCAAGTATGTG
+CTCACTGAATAAGCTGCTAAGGTTTGGTGGTTACAGAGTGTGCGGTGAAATGATGTCTACATCACAGTCC
+AACATTCACAGAGTTTAAAAGCCTACCAAGAATCAAGACAGACACAAATACCTAACATAGACATTTGTAT
+ATGATAAGAGAGCCAGAGTACAATTTAGGAGAAGAAATTGTATGGAAGGAAGGTTCATTTCCATTAGACC
+AGAAAAGACAGCACATTTGAAGGCCTGAATAAGAAATATTCTGGATAAGATATTGTGGCTGCTACCAGAA
+TGGCTCTTGATGATCTCTACCTCTTGGTATTTATACCCTTATATAATCTCTTTCCTATAGTGTAAGCTGG
+TCCCAGGTACTTGTTTCTATTGAATAGAATAGAACAAAAGAAATGAGATGCCACTTCTGAGATTAGATTA
+TAAGATACTGTGAATTTCTTCTTGTGCCCTCTCCCTCTCTCTCTTTCTCTTGCCCTCTCATTTGAATGAA
+GCCAACTGGCATGCTGTCAGTGGCCCAGTGTAAGTCCTGTTACAAGAAATTGATGATTACCTGTAGCCAA
+CCCTAAGTGAAGAACTGAGGTCCTCAGTCCTACAAATGGAGAGAAACTGAATCTAGCTAAGAACCATGTG
+AGTGAGCTGGGAAGAAGATCCACCCTCAGTTGAAATTTAAGATGACATATTGAGCAGACATACTGAGACA
+CACTGAAAGTAAGAGAGCAGGAGGAAACAAAACCAGGGTCATACAAAGAACACAACTGATTTTGAGATTC
+TCACATAAGTATTACACCTTCAGTGAGCACGTGTACTAGAAATTTAAAAAATAAATAAAATAAACCTTCA
+AAGTGAGCTAGCAAATAAATTTCCCTATGGTCTCAGCTCTGAGTGGAGAGAGAAAATGTTCCCTGTGGAG
+TTTATAGCCAGAATCCAGCTCTCAAACAGGTTTCAGCCTGAACTCACACAATCTGTGTGGCTTCCAAATT
+TGCAAGCTGAGAATTTAATTCAAAGTGGTCTCAGGTTGATAGCAGTCCAAAATGCTAGGTAGGAAAAAAA
+ATCCTCTCTGGACAAATAAATCATCAAAGCAAGCTCATAAGAGCAGGTTTCAAAGGTCATGAGCTTCTAA
+CACACACACAAAAATCACACACACAAAATGGGGGTAGCAGCAACATGGGTAGCGTATTCAAACTTGAAAA
+GACTTTAAATATTTGTATTATTAGATGTAGATTATGAAACACATATTTTAATGTGGTTAATTTTTTTAAG
+GAATCAAAACTATGAGTAAAGACCAAGAAAATTGTGCTGGATGGCCACTTCCACCATGGCTCCCCTCCTA
+TTTAAGTCTGGGTACTGTGTCACCCGAAGTCTTCAGGCACATTGTTCCAGGTCTGGGTTTGCCTATGAAA
+GAAACTCATGAGAGCTGGAAATGAGGAGTGAAGAGGAGGTCTTCAAATAAAGCAGGCTTAAGGATTAGAC
+ATAGCAGGTTTGACAGATGTGATGGCTTGCAGAATCCTTTATGAGCTCCCACTGTCCATCTGGATAAGAT
+TTACAGACCTTTCAGAAATTCCTATAAGCTTGGGTTCTGTGCCCACACTCTAGACTGTCAGGCTAAGATC
+TCTGATATAAAACAGACCTCTTCTGATTTTGTCTAGCTGCTTTTCTAATATCTATTCACCAAGCTCTTCC
+AATAATAGCATAAGGCCCTAATTAATATTAAACTTTTATCATTATAATACATAGGATGTCTTCTGTTTTC
+CTGATCAAATTCTGACTACTATTAAAATATAAAGAATTGTCCAGAAATATATAAAAAAAGAATCACACAT
+TGATCTTCTTTAAATGAAAATATAACAATTGTATGGACTAGGATGATTACAGTTGTTCAGTTCTGACTGT
+TATTTGAAGAAAAAAGCAATAAGAAGCCTCAGCAACTTAACAGAAGGAGCTGCCATTTACTAGGAGAAAA
+GATTGTGGATGAGAGTGTAGCAAAGGTCAGAATTCTGTGAAGCTTGAGATGTTTATTATAATGAATTATC
+TTTTATACTCACTACAATTTCCTAACAATTTTGGGGTTTATATTTTTGAAAGAGATATACCTTTAATTTT
+CTTTCTTTGTACTATTGTTAGGTAACTTTGATGTGCAGATTATACTACAGTGAAAGTTGCCAATGACAAG
+GCAAAGTCACTTACATCAGACCCAAAGCAAAGTGGAGCCGGGTCATGAAAAAGGGGATCTTGTGTGTCTG
+TCCACGATAAGCACTATCACAAGGACTTTCTATAAACTCACAAGAAATTTCTGCCCACCCAGCACACTCT
+GTTTGTCCAGCTCATCCTGTAGGTGTCTCTATAATAGGACCTATCATAAAAAATTCCTCAAGACTGCAGC
+ATTTCAGATAAGCCACCCTCACAAGAACACTTGCCTAGCAATGGCTGTTTCTGCCAGTAAGTTAACACCA
+GCTCCTGCATCAGACCCTGTGACCAATGATGTTTGTTTCAAAACAGCTTGCATGGACTTCTTTTTGTCTT
diff -r 000000000000 -r bc0b40dec7d2 test-data/cached_locally/small_region.fa.fai
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cached_locally/small_region.fa.fai	Wed May 20 17:23:42 2020 -0400
@@ -0,0 +1,1 @@
+chr1	7070	7	70	71
diff -r 000000000000 -r bc0b40dec7d2 test-data/small_region.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/small_region.fa	Wed May 20 17:23:42 2020 -0400
@@ -0,0 +1,102 @@
+>chr1
+TCCTCAGAAAATGGATTTTTCTTTTCTATCACAGTGTCATGCTACAAATTTTCTGAACGTTTATGCTCTG
+TTTTCCTGTTAAAACTGAGTGCTTTTAACACACCCAAGTCACTCTTGAATGATTTGCTGCTTAGAAATTT
+CTTCTGCCAGATACCCTAACTCATCTCCCTCAAGTTCAAAGTTCCACAAATCTCTAGGGCAGGGACAAAA
+TGCTGCCAGTCTCTCTCGATAGCAAGAGACACCTTTACTCCAGTTCCCATTGAGTTCCTCATCTCCATCT
+GAGACCATCTCAGCCTGGATTTCATTGTCTATATCATTATTTGACATTTTAGTCAAAGCCATTCAACAAG
+TCTCTAGGAAGTTCCAAACTTTCCCACATTTTCCTGTCGTTTTCTGAGCCCTCCAAACTGTTTCAACCCC
+TGCCTGTTACCCAGTTCCAAAGTCGCTTCCACATTTTTGGGTTATCTTTACAACAGCACCCCACTCTACC
+AGTACCAATGTACTGTATTAGTCTGTTTTCATGCTGCTGATAAAGACATACCTGAGACTGAGTGATTTAT
+GAAGAAAAAGACACTTAATGGACTCACATTTCCAGGTGGATGGGGAGGCCTCACAATCATGGTGGAAGGC
+AAAAGGCACATCTCTACATGATGGCAGACAAGACAGAATGAGAGCTAAGTGAAAGGGGAACCCCCTTATA
+AAATCATCAGCTCTTGTGAGACTTATTCAAGACCACGAGAACAGTATGGGGGAAATACTCCTGTGATTCA
+GTTATCTCCCGTTGGATCCCTCCCACAAGACACGGAAATTATGGGAGCTACAATTCAAGATGAGATTTGG
+GTGGGGACACATCCAAACCATATTGCTGCTGAATAGATCATGTAGACAGGCTCTCAAACTACACGGAGAG
+CAAGAGAGGCCCACCTTACCACAACATTTCATCCAATCCACTAATAAAACAGGCACATCACTGAAGCCAC
+CTTCAACTCTCCAGACTACCCAGCTGCCAGCTGAATACCACAGATGGCTACAGTTAATACCACATGGAGC
+AGAATCATGTAGCTAAGCCCTGCTTGCGCTAATACAAGTCCACAATTTTTTTTAAGTTTGTTGTTTTAAG
+CTGCTAAGTTTTGAGGTGGTTTGTGGTACGTGGAATAAGATGTCACTCTAATATAATATAAACTTAAACT
+ATGTGGCATTGGCTTTGGAATCAGACAATGGATAGAAGCCAGAAGGATTTCACAAAGACTGTTAGTGAAA
+AGTGAACAGACTTCAAGGAAAATGATAGCAAAACCTGTAAAAGCATTCTGGGAACTGACAGTAAACACTG
+AATGGTCCTTAAGGAGACTGAAAACTTGAAAGAGCTTAAGAAGTCTACTGGAAAGGGCTTTAAGGATAAT
+GAGAAAAAATCATCAGTGGAGGCTGAGGAAAACGCACCAAAGTCATATTCTGATGGGAGAATTAGAAAAC
+GCTTGCCTGGAATGATATAAAAAATAGGAAAAATACCGAAAAAGTTTGTGGATCTGGCTGGGGAGATTTT
+TGGTGTCAACTAAAGAAAAAAATTAAGCTTTTAAGAAATTAAAGTTAGATTTATTTAGGGGTCTGAGAAC
+AAGAGACTGAGGATTACAGCCTAGGAGAAGTCTTCCAGAGAGGTTCTGTCAGACTGCTCTGGTGAAGGTC
+TTTAGCCCACAGTTTATATGCAGGCTGTACATATACACCATGGAATACTATGCCGCCATTAAAAAATGAT
+ATCATGTCTTTTGCTGGAACATGGATGGACCTTCTATTATCCTTAGCAAACTAATGCAGGAACAGAAAAC
+CAAATACAGCATACTCTCAGTTATAAGTGGGAGCTAAATGATGAGAACTCATGAACACAAAGAATAAAAC
+AGACACTGGGGTCTACTTGAGGGTGGAGGGTGAGAAAAGGAAGAGAAGCAGAAAAGATAACTATTGGGTA
+CTAGGTTTAATACCTGGGTGATGAAATGATCTGTACAATAACCCCCTGTGACACCAGTCTACCTATGTAA
+CAAATGCCCCTAAACTTAAAATAAAAGTTAAAAAAAAAGAAAATTAAAATCTCCTTATCATCTACCTGGT
+AATATGAAAAACACAAATCTTTCATTCATTCCTTTCAACTGATGAGGAAAATGAGGCATCGGGAGTTAGT
+AAAAGTCCACATTGAGATATGAGACCCACCACTGGCTGGACGCAGTGGCTCACACCTGTAATCCCAGCAC
+TTTGGGAGGCCGATGCTGGTGGATCACCTAAGGTCAGGAGTTCGGGACCAGGCTGGCCAACATGGTGAAA
+CCCCCATCTCTACTAAAAATACAAAAATTAGCTGGGTGTGGTGGCAGGCACCTGTAATACCAGCTACTAG
+GGAGGCTGAGGCAGGAGAATCGCTTGAACCCAGGAGGTGGAGTTTACAGTGAGCCAAAATCACGCCATTG
+CACTCCAGCCTGGGCAACAAGAGCAAGACTCTGTCGGGGAAAAAAAAGAAAAAAAAAAACCACCGCCATC
+ATTTTGCAAGTGTTACCACTATTGTGTGTTAATATTGTAGAAGTATTCCTAATTATGATTTCTTTGTATT
+CCTAATTGTAATAGCTTTGTATTTGAAAAATTATTGATTCATACTCTATATGTTATTATTTTGTATGTGA
+TGACAACAGAATATATTATCATGCTCCTTTTGTGAATCTCATTCATAATATAAAGTATAAATTTGTGATT
+TTGCTTTAATTTGAAATATTAACTTCAAATATGTTATCACAATTTGATACAAACTATTGACAGTAAATCT
+GTGGATTAAGTAATGTCTTAGTAGGTATTGGGAAAATTTGAAACTAGTAACATGGAGGACTATTGTCATT
+GTTTATTTCAAAGCCAGTTAAAATTCTGCAAAGCAGTGTACATAAAAATAATTTCAAGAAATTTATAAAA
+TACCGAGATTATGGTGTATAAACAACTTTAGATTCTTTGTTTAAGAAATTCTGCCAGTTTGTAATATATG
+CTTCATTCAAAGTAGCTAAGGGCTGTACCTGGCTAATAGTAGGCACCTAATATTTGTTGAAAAGGAATAC
+TGAGTAGCTGGGACCTCCTGAGTAGCTGGGACCACACACATTTAACCTGTATTTATAAAATTACTGTTTA
+GAGAATAACATTTGATGGAATCATGCTTTTACTTTCTGCTTACGACTCAATTGTTTGTACTGACATTAAC
+ATCCCAAATCCTTAGCATGGCCTACAAGGCCCTGAGCAATGTGGCACCTGCTGAAGCCTGCTGCCTCATT
+TAATAACTCTTTGTCTCTTTCCCAGATCCAGCCACTCTAACATTTTTTAGCTCCTGGACCAAGACAAGCT
+CTTCCCAGAACCTGACCTTTGTACCTGTTCTTTATTCCTGGAGTATTTTTCCCCTGACAAATTACTTATC
+ATCTATCATAATTCAGGTTAAATGGCACTAACTCAGGGAAGGCTTCCCTAACTGCCTCCCTTCTCCAACC
+AAATTAGGAACAATTATATGGCCACATAGTATCGAATCAAGTTTATAATTTTAAAATAATTGGGAGATTT
+TGTTGTTTAACACTTGTTTTCACTATAAGACTGTAATTACATGCAAGTAAGAACCATGCCTGTTTGTTCA
+CTCCTGCCACAGTCAGAATAGTGCCTGGAATATGCAGTAAGGGCTGAACAAGCACTAAATAAATGAACAA
+GTGAATAAATGGATATTGTCTCATTTTTAGAACAGAGTACTGAATGGATCATGAACACTATCTGGTATGT
+CACGTAGGTAATTTACAAGGGCTACAATTTCAGCTCAGATTTACCTTTTCCTGGATACAGGTCTTGATAG
+GTCTCTTGATGTCATTTCACTTCAGATTCTTCTTTAGAAAACTTGGACAATAGCATTTGCTGTCTTGTCC
+AAATTGTTACTAAGAATCAAGAGAGATATCTGACATGAAATGACATTGGAAAACATTAAACACGATTGAA
+ATAATGCTAGCCAATATGGTTATTATTAGAAACCAATTACATTTTCAACTTAAAAATAGTAATACTTATT
+GCAGACTCAAATGTGCTTATTCTAAAACAAGTAAATGTTTGCCTATGGTCTGAGATTCTAATCCACGGAG
+TTCATTCTAATCCACATTCAACACTATCATGTACCAGTGGGCCTCATAACCCACCTAGCCCTGTGATTTT
+TCAGGTTCACTTTTCTAAACTTGTGAATTAAATATTTATTTTCTTAGTTCAGAAGAGGAAAAAAACTCTT
+GTAATTGTTGCCCATTTCAGGAGAAATCTTGCATATGAAAACAAGAGATAAATATACACAACTGAGGGCT
+GTGGTTTAAACAAAATCTTGAGAATGTTTTTTGACCTTACACATTTGTGCTTTAGTATAACAAAATGATA
+TAGACAAAGGTAACTTTTAATAGAACCAGTCACTAAATTAAAAAAATGACAAATTCTTCTGCTTAGCTAA
+GCAACAGAGAAGGTAAAATACTAATTCAATTCATCAATTTAAGCAATACTCATTAAGAGCCAAGTATGTG
+CTCACTGAATAAGCTGCTAAGGTTTGGTGGTTACAGAGTGTGCGGTGAAATGATGTCTACATCACAGTCC
+AACATTCACAGAGTTTAAAAGCCTACCAAGAATCAAGACAGACACAAATACCTAACATAGACATTTGTAT
+ATGATAAGAGAGCCAGAGTACAATTTAGGAGAAGAAATTGTATGGAAGGAAGGTTCATTTCCATTAGACC
+AGAAAAGACAGCACATTTGAAGGCCTGAATAAGAAATATTCTGGATAAGATATTGTGGCTGCTACCAGAA
+TGGCTCTTGATGATCTCTACCTCTTGGTATTTATACCCTTATATAATCTCTTTCCTATAGTGTAAGCTGG
+TCCCAGGTACTTGTTTCTATTGAATAGAATAGAACAAAAGAAATGAGATGCCACTTCTGAGATTAGATTA
+TAAGATACTGTGAATTTCTTCTTGTGCCCTCTCCCTCTCTCTCTTTCTCTTGCCCTCTCATTTGAATGAA
+GCCAACTGGCATGCTGTCAGTGGCCCAGTGTAAGTCCTGTTACAAGAAATTGATGATTACCTGTAGCCAA
+CCCTAAGTGAAGAACTGAGGTCCTCAGTCCTACAAATGGAGAGAAACTGAATCTAGCTAAGAACCATGTG
+AGTGAGCTGGGAAGAAGATCCACCCTCAGTTGAAATTTAAGATGACATATTGAGCAGACATACTGAGACA
+CACTGAAAGTAAGAGAGCAGGAGGAAACAAAACCAGGGTCATACAAAGAACACAACTGATTTTGAGATTC
+TCACATAAGTATTACACCTTCAGTGAGCACGTGTACTAGAAATTTAAAAAATAAATAAAATAAACCTTCA
+AAGTGAGCTAGCAAATAAATTTCCCTATGGTCTCAGCTCTGAGTGGAGAGAGAAAATGTTCCCTGTGGAG
+TTTATAGCCAGAATCCAGCTCTCAAACAGGTTTCAGCCTGAACTCACACAATCTGTGTGGCTTCCAAATT
+TGCAAGCTGAGAATTTAATTCAAAGTGGTCTCAGGTTGATAGCAGTCCAAAATGCTAGGTAGGAAAAAAA
+ATCCTCTCTGGACAAATAAATCATCAAAGCAAGCTCATAAGAGCAGGTTTCAAAGGTCATGAGCTTCTAA
+CACACACACAAAAATCACACACACAAAATGGGGGTAGCAGCAACATGGGTAGCGTATTCAAACTTGAAAA
+GACTTTAAATATTTGTATTATTAGATGTAGATTATGAAACACATATTTTAATGTGGTTAATTTTTTTAAG
+GAATCAAAACTATGAGTAAAGACCAAGAAAATTGTGCTGGATGGCCACTTCCACCATGGCTCCCCTCCTA
+TTTAAGTCTGGGTACTGTGTCACCCGAAGTCTTCAGGCACATTGTTCCAGGTCTGGGTTTGCCTATGAAA
+GAAACTCATGAGAGCTGGAAATGAGGAGTGAAGAGGAGGTCTTCAAATAAAGCAGGCTTAAGGATTAGAC
+ATAGCAGGTTTGACAGATGTGATGGCTTGCAGAATCCTTTATGAGCTCCCACTGTCCATCTGGATAAGAT
+TTACAGACCTTTCAGAAATTCCTATAAGCTTGGGTTCTGTGCCCACACTCTAGACTGTCAGGCTAAGATC
+TCTGATATAAAACAGACCTCTTCTGATTTTGTCTAGCTGCTTTTCTAATATCTATTCACCAAGCTCTTCC
+AATAATAGCATAAGGCCCTAATTAATATTAAACTTTTATCATTATAATACATAGGATGTCTTCTGTTTTC
+CTGATCAAATTCTGACTACTATTAAAATATAAAGAATTGTCCAGAAATATATAAAAAAAGAATCACACAT
+TGATCTTCTTTAAATGAAAATATAACAATTGTATGGACTAGGATGATTACAGTTGTTCAGTTCTGACTGT
+TATTTGAAGAAAAAAGCAATAAGAAGCCTCAGCAACTTAACAGAAGGAGCTGCCATTTACTAGGAGAAAA
+GATTGTGGATGAGAGTGTAGCAAAGGTCAGAATTCTGTGAAGCTTGAGATGTTTATTATAATGAATTATC
+TTTTATACTCACTACAATTTCCTAACAATTTTGGGGTTTATATTTTTGAAAGAGATATACCTTTAATTTT
+CTTTCTTTGTACTATTGTTAGGTAACTTTGATGTGCAGATTATACTACAGTGAAAGTTGCCAATGACAAG
+GCAAAGTCACTTACATCAGACCCAAAGCAAAGTGGAGCCGGGTCATGAAAAAGGGGATCTTGTGTGTCTG
+TCCACGATAAGCACTATCACAAGGACTTTCTATAAACTCACAAGAAATTTCTGCCCACCCAGCACACTCT
+GTTTGTCCAGCTCATCCTGTAGGTGTCTCTATAATAGGACCTATCATAAAAAATTCCTCAAGACTGCAGC
+ATTTCAGATAAGCCACCCTCACAAGAACACTTGCCTAGCAATGGCTGTTTCTGCCAGTAAGTTAACACCA
+GCTCCTGCATCAGACCCTGTGACCAATGATGTTTGTTTCAAAACAGCTTGCATGGACTTCTTTTTGTCTT
diff -r 000000000000 -r bc0b40dec7d2 test-data/small_region.fa.fai
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/small_region.fa.fai	Wed May 20 17:23:42 2020 -0400
@@ -0,0 +1,1 @@
+chr1	7070	7	70	71
diff -r 000000000000 -r bc0b40dec7d2 test-data/test2-bed.output
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test2-bed.output	Wed May 20 17:23:42 2020 -0400
@@ -0,0 +1,153 @@
+read,position,Ia_a,Ia_t,Ia_c,Ia_g,It_a,It_t,It_c,It_g,Ic_a,Ic_t,Ic_c,Ic_g,Ig_a,Ig_t,Ig_c,Ig_g,Ca_a,Ca_t,Ca_c,Ca_g,Ct_a,Ct_t,Ct_c,Ct_g,Cc_a,Cc_t,Cc_c,Cc_g,Cg_a,Cg_t,Cg_c,Cg_g,Na_a,Na_t,Na_c,Na_g,Nt_a,Nt_t,Nt_c,Nt_g,Nc_a,Nc_t,Nc_c,Nc_g,Ng_a,Ng_t,Ng_c,Ng_g,cIa_a,cIa_t,cIa_c,cIa_g,cIt_a,cIt_t,cIt_c,cIt_g,cIc_a,cIc_t,cIc_c,cIc_g,cIg_a,cIg_t,cIg_c,cIg_g,cCa_a,cCa_t,cCa_c,cCa_g,cCt_a,cCt_t,cCt_c,cCt_g,cCc_a,cCc_t,cCc_c,cCc_g,cCg_a,cCg_t,cCg_c,cCg_g
+1,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,4,0,0,0,0,2,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,3,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+1,2,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,3,0,0,0,0,2,0,0,0,0,1,0,0,0,0,1,1,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1
+1,3,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2,0,0,0,0,0,0,0,0,0,2,0,0,0,0,3,0,0,0,0,0,2,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+1,4,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,5,0,0,0,0,1,0,0,0,0,0,1,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+1,5,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2,0,0,0,0,2,0,0,0,0,2,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,1,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+1,6,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2,0,0,0,0,2,0,0,0,0,1,0,0,0,0,2,1,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+1,7,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2,0,0,0,0,2,0,0,0,0,1,0,0,0,0,2,1,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1
+1,8,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,3,0,0,0,0,1,0,0,0,0,2,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,1,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+1,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2,0,0,0,0,1,0,0,0,0,3,0,0,0,0,1,1,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0
+1,10,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,3,0,0,0,0,2,0,0,0,0,1,0,0,0,0,1,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0
+1,11,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2,0,0,0,0,1,0,0,0,0,1,0,0,0,0,3,0,0,0,0,0,0,0,0,0,0,1,0,0,1,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0
+1,12,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,4,0,0,0,0,0,0,0,0,0,2,0,0,0,0,1,2,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0
+1,13,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,2,0,0,0,0,2,0,0,0,0,2,1,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+1,14,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,4,0,0,0,0,0,0,0,0,0,3,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,1,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+1,15,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2,0,0,0,0,3,0,0,0,0,1,0,0,0,0,1,1,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+1,16,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2,0,0,0,0,1,0,0,0,0,2,0,0,0,0,2,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,1,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0
+1,17,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2,0,0,0,0,2,0,0,0,0,1,0,0,0,0,2,2,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+1,18,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,3,0,0,0,0,2,0,0,0,0,0,0,0,0,0,2,0,0,0,0,0,1,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0
+1,19,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,3,0,0,0,0,1,0,0,0,0,0,0,0,0,0,3,0,0,0,0,0,1,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0
+1,20,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,4,0,0,0,0,1,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,1,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0
+1,21,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2,0,0,0,0,2,0,0,0,0,1,0,0,0,0,2,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,1
+1,22,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,3,0,0,0,0,3,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,1,0,0,0,0,0,0,0,0,0,1
+1,23,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2,0,0,0,0,1,0,0,0,0,3,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,1,0,0,0,0,1,0,0,0,0,0
+1,24,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,4,0,0,0,0,1,0,0,0,0,2,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,1,0,0,0,0,1,0,0,0,0,0
+1,25,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,1,0,0,0,0,4,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,1,0,0,0,0,0,0,0,0,0,1
+1,26,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,4,0,0,0,0,3,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1
+1,27,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2,0,0,0,0,2,0,0,0,0,2,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2,0,0,0,0,1,0,0,0,0,0
+1,28,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,3,0,0,0,0,2,0,0,0,0,1,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0
+1,29,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,3,0,0,0,0,0,0,0,0,0,3,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,1,0,0,0,0,1
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\ No newline at end of file
diff -r 000000000000 -r bc0b40dec7d2 test-data/test2-nobed.output
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test2-nobed.output	Wed May 20 17:23:42 2020 -0400
@@ -0,0 +1,153 @@
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\ No newline at end of file
diff -r 000000000000 -r bc0b40dec7d2 test-data/test2.bam
Binary file test-data/test2.bam has changed
diff -r 000000000000 -r bc0b40dec7d2 test-data/test2.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test2.bed	Wed May 20 17:23:42 2020 -0400
@@ -0,0 +1,4 @@
+chr1	850	879	+	L1P5	LINE	L1
+chr1	1019	1200	+	L1P5	LINE	L1
+chr1	5728	5735	+	L1P5	LINE	L1
+chr1	465	487	+	L1P5	LINE	L1
diff -r 000000000000 -r bc0b40dec7d2 test-data/test2.output
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test2.output	Wed May 20 17:23:42 2020 -0400
@@ -0,0 +1,153 @@
+read,position,Ia_a,Ia_t,Ia_c,Ia_g,It_a,It_t,It_c,It_g,Ic_a,Ic_t,Ic_c,Ic_g,Ig_a,Ig_t,Ig_c,Ig_g,Ca_a,Ca_t,Ca_c,Ca_g,Ct_a,Ct_t,Ct_c,Ct_g,Cc_a,Cc_t,Cc_c,Cc_g,Cg_a,Cg_t,Cg_c,Cg_g,Na_a,Na_t,Na_c,Na_g,Nt_a,Nt_t,Nt_c,Nt_g,Nc_a,Nc_t,Nc_c,Nc_g,Ng_a,Ng_t,Ng_c,Ng_g,cIa_a,cIa_t,cIa_c,cIa_g,cIt_a,cIt_t,cIt_c,cIt_g,cIc_a,cIc_t,cIc_c,cIc_g,cIg_a,cIg_t,cIg_c,cIg_g,cCa_a,cCa_t,cCa_c,cCa_g,cCt_a,cCt_t,cCt_c,cCt_g,cCc_a,cCc_t,cCc_c,cCc_g,cCg_a,cCg_t,cCg_c,cCg_g
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\ No newline at end of file
diff -r 000000000000 -r bc0b40dec7d2 test-data/test2.output2
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test2.output2	Wed May 20 17:23:42 2020 -0400
@@ -0,0 +1,153 @@
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\ No newline at end of file
diff -r 000000000000 -r bc0b40dec7d2 tool-data/all_fasta.loc.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/all_fasta.loc.sample	Wed May 20 17:23:42 2020 -0400
@@ -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 bc0b40dec7d2 tool_data_table_conf.xml.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample	Wed May 20 17:23:42 2020 -0400
@@ -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="tool-data/all_fasta.loc" />
+    </table>
+</tables>
diff -r 000000000000 -r bc0b40dec7d2 tool_data_table_conf.xml.test
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.test	Wed May 20 17:23:42 2020 -0400
@@ -0,0 +1,8 @@
+<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc-->
+<tables>
+    <!-- Location of Picard dict file and other files -->
+    <table name="all_fasta" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="${__HERE__}/test-data/all_fasta.loc" />
+    </table>
+</tables>