# HG changeset patch
# User iuc
# Date 1564339559 14400
# Node ID d6181de75bdd0077829af905578b957be10f5a4c
# Parent  4afb4a5f09244dfc2070cfc6c24f98aeb53489a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit a972815cbd43dea553b3c0e4ad548f35d0023228-dirty

diff -r 4afb4a5f0924 -r d6181de75bdd macros.xml
--- a/macros.xml	Tue May 09 11:18:00 2017 -0400
+++ b/macros.xml	Sun Jul 28 14:45:59 2019 -0400
@@ -1,11 +1,131 @@
 <macros>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="1.3.1">samtools</requirement>
+            <requirement type="package" version="@TOOL_VERSION@">samtools</requirement>
             <yield/>
         </requirements>
     </xml>
-    <token name="@TOOL_VERSION@">1.3.1</token>
+    <token name="@TOOL_VERSION@">1.9</token>
+    <token name="@FLAGS@">#set $flags = sum(map(int, str($filter).split(',')))</token>
+    <token name="@PREPARE_IDX@"><![CDATA[
+        ##prepare input and indices 
+        ln -s '$input' infile &&
+        #if $input.is_of_type('bam'):
+            #if str( $input.metadata.bam_index ) != "None":
+                ln -s '${input.metadata.bam_index}' infile.bai &&
+            #else:
+                samtools index infile infile.bai &&
+            #end if
+        #elif $input.is_of_type('cram'):
+            #if str( $input.metadata.cram_index ) != "None":
+                ln -s '${input.metadata.cram_index}' infile.crai &&
+            #else:
+                samtools index infile infile.crai &&
+            #end if
+        #end if
+    ]]></token>
+    <token name="@PREPARE_IDX_MULTIPLE@"><![CDATA[
+        ##prepare input and indices 
+        #for $i, $bam in enumerate( $input_bams ):
+            ln -s '$bam' '${i}' &&
+            #if $bam.is_of_type('bam'):
+                #if str( $bam.metadata.bam_index ) != "None":
+                    ln -s '${bam.metadata.bam_index}' '${i}.bai' &&
+                #else:
+                    samtools index '${i}' '${i}.bai' &&
+                #end if
+            #elif $bam.is_of_type('cram'):
+                #if str( $bam.metadata.cram_index ) != "None":
+                    ln -s '${bam.metadata.cram_index}' '${i}.crai' &&
+                #else:
+                    samtools index '${i}' '${i}.crai' &&
+                #end if
+            #end if
+        #end for
+    ]]></token>
+    <token name="@PREPARE_FASTA_IDX@"><![CDATA[
+        ##checks for reference data ($addref_cond.addref_select=="history" or =="cached")
+        ##and sets the -t/-T parameters accordingly:
+        ##- in case of history a symbolic link is used because samtools (view) will generate
+        ##  the index which might not be possible in the directory containing the fasta file
+        ##- in case of cached the absolute path is used which allows to read the cram file
+        ##  without specifying the reference
+        #if $addref_cond.addref_select == "history":
+            ln -s '${addref_cond.ref}' reference.fa &&
+            samtools faidx reference.fa &&
+            #set reffa="reference.fa"
+            #set reffai="reference.fa.fai"
+        #elif $addref_cond.addref_select == "cached":
+            #set reffa=str($addref_cond.ref.fields.path)
+            #set reffai=str($addref_cond.ref.fields.path)+".fai"
+        #else
+            #set reffa=None
+            #set reffai=None
+        #end if
+    ]]></token>
+    <token name="@ADDTHREADS@"><![CDATA[
+        ##compute the number of ADDITIONAL threads to be used by samtools (-@)
+        addthreads=\${GALAXY_SLOTS:-1} && (( addthreads-- )) &&
+    ]]></token>
+    <token name="@ADDMEMORY@"><![CDATA[
+        ##compute the number of memory available to samtools sort (-m)
+        ##use only 75% of available: https://github.com/samtools/samtools/issues/831
+        addmemory=\${GALAXY_MEMORY_MB_PER_SLOT:-768} && 
+        ((addmemory=addmemory*75/100)) &&
+    ]]></token>
+    <xml name="seed_input">
+       <param name="seed" type="integer" optional="True" label="Seed for random number generator" help="If empty a random seed is used." /> 
+    </xml>
+    <xml name="flag_options">
+        <option value="1">read is paired</option>
+        <option value="2">read is mapped in a proper pair</option>
+        <option value="4">read is unmapped</option>
+        <option value="8">mate is unmapped</option>
+        <option value="16">read reverse strand</option>
+        <option value="32">mate reverse strand</option>
+        <option value="64">read is the first in a pair</option>
+        <option value="128">read is the second in a pair</option>
+        <option value="256">alignment or read is not primary</option>
+        <option value="512">read fails platform/vendor quality checks</option>
+        <option value="1024">read is a PCR or optical duplicate</option>
+        <option value="2048">supplementary alignment</option>
+    </xml>
+
+    <!-- region specification macros and tokens for tools that allow the specification 
+         of region by bed file / space separated list of regions -->
+    <token name="@REGIONS_FILE@"><![CDATA[
+        #if $cond_region.select_region == 'tab':
+            -t '$cond_region.targetregions'
+        #end if
+    ]]></token>
+    <token name="@REGIONS_MANUAL@"><![CDATA[
+        #if $cond_region.select_region == 'text':
+            #for $i, $x in enumerate($cond_region.regions_repeat):
+               '${x.region}'
+            #end for
+        #end if
+    ]]></token>
+    <xml name="regions_macro">
+        <conditional name="cond_region">
+            <param name="select_region" type="select" label="Filter by regions" help="restricts output to only those alignments which overlap the specified region(s)">
+                <option value="no" selected="True">No</option>
+                <option value="text">Manualy specify regions</option>
+                <option value="tab">Regions from tabular file</option>
+            </param>
+            <when value="no"/>
+            <when value="text">
+                <repeat name="regions_repeat" min="1" default="1" title="Regions">
+                    <param name="region" type="text" label="region" help="format chr:from-to">
+                        <validator type="regex" message="Required format: CHR[:FROM[-TO]]; where CHR: string containing any character except quotes, whitespace and colon; FROM and TO: any integer">^[^\s'\":]+(:\d+(-\d+){0,1}){0,1}$</validator>
+                    </param>
+                </repeat>
+            </when>
+            <when value="tab">
+                <param name="targetregions" argument="-t/--target-regions" type="data" format="tabular" label="Target regions file" help="Do stats in these regions only. Tab-delimited file chr,from,to (1-based, inclusive)" />
+            </when>
+        </conditional>
+    </xml>
+
     <xml name="citations">
         <citations>
             <citation type="bibtex">
@@ -49,21 +169,4 @@
             <exit_code range="1:" level="fatal" description="Error" />
         </stdio>
     </xml>
-    <token name="@no-chrom-options@">
------
-
-.. class:: warningmark
-
-**No options available? How to re-detect metadata**
-
-If you see a &quot;No options available&quot; within the &quot;**Select references (chromosomes and contigs) you would like to restrict bam to**&quot; drop down, you need to re-detect metadata for the dataset you are trying to process. To do this follow these steps:
-
-1. Click on the **pencil** icon adjacent to the dataset in the history
-2. A new menu will appear in the center pane of the interface
-3. Click **Datatype** tab
-4. Set **New Type** to **BAM**
-5. Click **Save**
-
-The medatada will be re-detected and you will be able to see the list of reference sequences in the &quot;**Select references (chromosomes and contigs) you would like to restrict bam to**&quot; drop-down.
-    </token>
 </macros>
diff -r 4afb4a5f0924 -r d6181de75bdd test-data/cached_locally/chr_m.fasta
--- a/test-data/cached_locally/chr_m.fasta	Tue May 09 11:18:00 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,335 +0,0 @@
->chrM
-GTTAATGTAGCTTAATAATATAAAGCAAGGCACTGAAAATGCCTAGATGA
-GTATTCTTACTCCATAAACACATAGGCTTGGTCCTAGCCTTTTTATTAGT
-TATTAATAGAATTACACATGCAAGTATCCGCACCCCAGTGAGAATGCCCT
-CTAAATCACGTCTCTACGATTAAAAGGAGCAGGTATCAAGCACACTAGAA
-AGTAGCTCATAACACCTTGCTCAGCCACACCCCCACGGGACACAGCAGTG
-ATAAAAATTAAGCTATGAACGAAAGTTCGACTAAGTCATATTAAATAAGG
-GTTGGTAAATTTCGTGCCAGCCACCGCGGTCATACGATTAACCCAAATTA
-ATAAATCTCCGGCGTAAAGCGTGTCAAAGACTAATACCAAAATAAAGTTA
-AAACCCAGTTAAGCCGTAAAAAGCTACAACCAAAGTAAAATAGACTACGA
-AAGTGACTTTAATACCTCTGACTACACGATAGCTAAGACCCAAACTGGGA
-TTAGATACCCCACTATGCTTAGCCCTAAACTAAAATAGCTTACCACAACA
-AAGCTATTCGCCAGAGTACTACTAGCAACAGCCTAAAACTCAAAGGACTT
-GGCGGTGCTTTACATCCCTCTAGAGGAGCCTGTTCCATAATCGATAAACC
-CCGATAAACCCCACCATCCCTTGCTAATTCAGCCTATATACCGCCATCTT
-CAGCAAACCCTAAACAAGGTACCGAAGTAAGCACAAATATCCAACATAAA
-AACGTTAGGTCAAGGTGTAGCCCATGGGATGGAGAGAAATGGGCTACATT
-TTCTACCCTAAGAACAAGAACTTTAACCCGGACGAAAGTCTCCATGAAAC
-TGGAGACTAAAGGAGGATTTAGCAGTAAATTAAGAATAGAGAGCTTAATT
-GAATCAGGCCATGAAGCGCGCACACACCGCCCGTCACCCTCCTTAAATAT
-CACAAATCATAACATAACATAAAACCGTGACCCAAACATATGAAAGGAGA
-CAAGTCGTAACAAGGTAAGTATACCGGAAGGTGTACTTGGATAACCAAAG
-TGTAGCTTAAACAAAGCATCCAGCTTACACCTAGAAGATTTCACTCAAAA
-TGAACACTTTGAACTAAAGCTAGCCCAAACAATACCTAATTCAATTACCC
-TTAGTCACTTAACTAAAACATTCACCAAACCATTAAAGTATAGGAGATAG
-AAATTTTAACTTGGCGCTATAGAGAAAGTACCGTAAGGGAACGATGAAAG
-ATGCATTAAAAGTACTAAACAGCAAAGCTTACCCCTTTTACCTTTTGCAT
-AATGATTTAACTAGAATAAACTTAGCAAAGAGAACTTAAGCTAAGCACCC
-CGAAACCAGACGAGCTACCTATGAACAGTTACAAATGAACCAACTCATCT
-ATGTCGCAAAATAGTGAGAAGATTCGTAGGTAGAGGTGAAAAGCCCAACG
-AGCCTGGTGATAGCTGGTTGTCCAGAAACAGAATTTCAGTTCAAATTTAA
-ATTTACCTAAAAACTACTCAATTCTAATGTAAATTTAAATTATAGTCTAA
-AAAGGTACAGCTTTTTAGATACAGGTTACAACCTTCATTAGAGAGTAAGA
-ACAAGATAAACCCATAGTTGGCTTAAAAGCAGCCATCAATTAAGAAAGCG
-TTCAAGCTCAACGACACATCTATCTTAATCCCAACAATCAACCCAAACTA
-ACTCCTAATCTCATACTGGACTATTCTATCAACACATAGAAGCAATAATG
-TTAATATGAGTAACAAGAATTATTTCTCCTTGCATAAGCTTATATCAGAA
-CGAATACTCACTGATAGTTAACAACAAGATAGGGATAATCCAAAAACTAA
-TCATCTATTTAAACCATTGTTAACCCAACACAGGCATGCATCTATAAGGA
-AAGATTAAAAGAAGTAAAAGGAACTCGGCAAACACAAACCCCGCCTGTTT
-ACCAAAAACATCACCTCTAGCATTTCCAGTATTAGAGGCACTGCCTGCCC
-AGTGACATCTGTTtaaacggccgcggtatcctaaccgtgcaaaggtagca
-taatcacttgttccctaaatagggacttgtatgaatggccacacgagggt
-tttactgtctcttacttccaatcagtgaaattgaccttcccgtgaagagg
-cgggaatgactaaataagacgagaagaccctatggagcttTAATTAACTG
-ATTCACAAAAAACAACACACAAACCTTAACCTTCAGGGACAACAAAACTT
-TTGATTGAATCAGCAATTTCGGTTGGGGTGACCTCGGAGAACAAAACAAC
-CTCCGAGTGATTTAAATCCAGACTAACCAGTCAAAATATATAATCACTTA
-TTGATCCAAACCATTGATCAACGGAACAAGTTACCCTAGGGATAACAGCG
-CAATCCTATTCCAGAGTCCATATCGACAATTAGGGTTTACGACCTCGATG
-TTGGATCAAGACATCCTAATGGTGCAACCGCTATTAAGGGTTCGTTTGTT
-CAACGATTAAAGTCTTACGTGATCTGAGTTCAGACCGGAGTAATCCAGGT
-CGGTTTCTATCTATTCTATACTTTTCCCAGTACGAAAGGACAAGAAAAGT
-AGGGCCCACTTTACAAGAAGCGCCCTCAAACTAATAGATGACATAATCTA
-AATCTAACTAATTTATAACTTCTACCGCCCTAGAACAGGGCTCgttaggg
-tggcagagcccggaaattgcataaaacttaaacctttacactcagaggtt
-caactcctctccctaacaacaTGTTCATAATTAACGTCCTCCTCCTAATT
-GTCCCAATCTTGCTCGCCGTAGCATTCCTCACACTAGTTGAACGAAAAGT
-CTTAGGCTATATGCAACTTCGCAAAGGACCCAACATCGTAGGCCCCTATG
-GCCTACTACAACCTATTGCCGATGCCCTCAAACTATTTATCAAAGAGCCA
-CTACAACCACTAACATCATCGACATCCATATTCATCATCGCACCAATCCT
-AGCCCTAACCCTGGCCTTAACCATATGAATCCCTCTGCCCATACCATACC
-CACTAATCAACATAAACCTAGGAATTCTATTCATACTAGCCATGTCCAGC
-CTAGCTGTCTACTCAATCCTTTGATCAGGATGGGCCTCAAACTCAAAATA
-CGCCCTAATTGGAGCTCTACGAGCAGTAGCACAAACCATCTCATACGAAG
-TAACTCTAGCAATCATCCTACTCTCAGTCCTCCTAATAAGCGGATCATTC
-ACATTATCAACACTTATTATTACCCAAGAATACCTCTGATTAATCTTCCC
-ATCATGACCCTTAGCCATAATGTGATTCATCTCAACATTAGCCGAAACCA
-ACCGAGCTCCATTTGACCTAACAGAAGGAGAATCAGAACTCGTCTCTGGA
-TTCAACGTTGAATACGCAGCCGGCCCATTTGCTCTATTCTTCCTAGCAGA
-ATACGCAAACATCATCATGATAAACATCTTCACAACAACCCTATTTCTAG
-GAGCATTTCACAACCCCTACCTGCCAGAACTCTACTCAATTAATTTCACC
-ATTAAAGCTCTCCTTCTAACATGTTCCTTCCTATGAATCCGAGCATCCTA
-CCCACGATTCCGATATGACCAACTTATACACCTCCTATGAAAGAACTTCC
-TACCACTCACACTAGCCCTCTGCATATGACACGTCTCACTTCCAATCATA
-CTATCCAGCATCCCACCACAAACATAGGAAATATGTCTGACAAAAGAGTT
-ACTTTGATAGAGTAAAACATAGAGGCTCAAACCCTCTTATTTctagaact
-acaggaattgaacctgctcctgagaattcaaaatcctccgtgctaccgaa
-ttacaccatgtcctaCAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCAT
-ACCCCGAAAATGTTGGATTACACCCTTCCCGTACTAATAAATCCCCTTAT
-CTTCACAACTATTCTAATAACAGTTCTTCTAGGAACTATAATCGTTATAA
-TAAGCTCACACTGACTAATAATCTGAATCGGATTTGAAATAAATCTACTA
-GCCATTATCCCTATCCTAATAAAAAAGTACAATCCCCGAACCATAGAAGC
-CTCCACCAAATATTTTCTAACCCAAGCCACCGCATCAATACTCCTCATAA
-TAGCGATCATCATTAACCTCATACACTCAGGCCAATGAACAATCACAAAA
-GTCTTCAACCCCACAGCGTCCATCATTATAACTTCAGCTCTCGCCATAAA
-ACTTGGACTCACACCATTCCACTTCTGAGTACCCGAAGTCACACAGGGCA
-TCTCATTAACATCAGGTCTCATCCTACTTACATGACAAAAACTAGCCCCA
-ATATCAATCCTATATCAAATCTCACCCTCAATTAACCTAAATATCTTATT
-AACTATAGCCGTACTGTCAATCCTAGTAGGAGGCTGAGGCGGTCTCAACC
-AAACCCAACTACGAAAAATCATAGCATACTCGTCAATCGCGCATATAGGA
-TGAATAACAGCTGTCCTAGTATATAACCCAACACTAACAATACTAAACAT
-ATTAATTTACATTATAATAACACTCACAATATTCATACTATTTATCCACA
-GCTCCTCTACTACAACACTATCACTCTCCCACACATGAAACAAAATACCT
-CTAACCACTACACTAATCTTAATTACCTTACTATCCATAGGAGGCCTCCC
-CCCACTATCAGGATTCATACCCAAATGAATAATCATTCAAGAGCTCACCA
-AAAATAGCAGCATCATCCTCCCCACACTAATAGCCATTATAGCACTACTC
-AACCTCTACTTCTACATACGACTAACCTATTCCACCTCACTGACCATATT
-CCCATCCACAAACAACATAAAAATAAAATGACAATTCGAAACCAAACGAA
-TTACTCTCTTACCCCCGTTAATTGTTATATCCTCCCTACTCCTCCCCCTA
-ACCCCCATACTATCAATTTTGGACTAGGAATTTAGGTTAACATCCCAGAC
-CAAGAGCCTTCAAAGCTCTAAGCAAGTGAATCCACTTAATTCCTGCATAC
-TAAGGACTGCGAGACTCTATCTCACATCAATTGAACGCAAATCAAACTCT
-TTTATTAAGCTAAGCCCTTACTAGATTGGTGGGCTACCATCCCACGAAAT
-TTTAGTTAACAGCTAAATACCCTAATCAACTGGCTTCAATCTACTTCTCC
-CGCCGCCTAGAAAAAAAGGCGGGAGAAGCCCCGGCAGAAATTGAAGCTGC
-TCCTTTGAATTTGCAATTCAATGTGAAAATTCACCACGGGACTTGATAAG
-AAGAGGATTCCAACCCCTGTCTTTAGATTTACAGTCTAATGCTTACTCAG
-CCATCTTACCTATGTTCATCAACCGCTGACTATTTTCAACTAACCACAAA
-GACATCGGCACTCTGTACCTCCTATTCGGCGCTTGAGCTGGAATAGTAGG
-AACTGCCCTAAGCCTCCTAATCCGTGCTGAATTAGGCCAACCTGGGACCC
-TACTAGGAGATGATCAGATCTACAATGTCATTGTAACCGCCCATGCATTC
-GTAATAATTTTCTTTATGGTCATACCCATTATAATCGGAGGATTCGGAAA
-CTGATTAGTCCCCCTGATAATTGGAGCACCTGATATAGCTTTCCCCCGAA
-TAAACAACATAAGCTTCTGATTACTTCCCCCATCATTCCTACTTCTTCTC
-GCTTCCTCAATAATTGAAGCAGGTGCCGGAACAGGCTGAACCGTATATCC
-TCCTCTAGCTGGAAATCTGGCGCATGCAGGAGCCTCTGTTGACTTAACCA
-TTTTCTCTCTCCACCTAGCTGGGGTGTCCTCGATTTTAGGTGCCATCAAC
-TTTATTACCACAATCATTAACATAAAACCACCAGCCCTATCCCAATATCA
-AACCCCCCTATTCGTTTGATCTGTCCTTATTACGGCAGTACTCCTTCTCC
-TAGCCCTCCCGGTCCTAGCAGCAGGCATTACCATGCTTCTCACAGACCGT
-AACCTGAACACTACTTTCTTCGACCCCGCAGGAGGAGGGGATCCAATCCT
-TTATCAACACCTATTCTGATTCTTCGGACACCCCGAAGTCTATATTCTTA
-TCCTACCAGGCTTCGGTATAATCTCACACATCGTCACATACTACTCAGGT
-AAAAAGGAACCTTTTGGCTACATGGGTATAGTGTGAGCTATAATATCCAT
-TGGCTTTCTAGGCTTCATCGTATGGGCTCACCACATGTTTACAGTAGGGA
-TAGACGTTGACACACGAGCATACTTCACATCAGCTACCATAATCATCGCT
-ATCCCTACTGGTGTAAAAGTATTCAGCTGACTAGCCACCCTGCACGGAGG
-AAATATCAAATGATCTCCAGCTATACTCTGAGCTCTAGGCTTCATCTTCT
-TATTCACAGTAGGAGGTCTAACAGGAATCGTCCTAGCTAACTCATCCCTA
-GATATTGTTCTCCACGATACTTATTATGTAGTAGCACATTTCCATTATGT
-CCTGTCTATAGGAGCAGTCTTCGCCATTATGGGGGGATTTGTACACTGAT
-TCCCTCTATTCTCAGGATACACACTCAACCAAACCTGAGCAAAAATCCAC
-TTTACAATTATATTCGTAGGGGTAAATATAACCTTCTTCCCACAACATTT
-CCTTGGCCTCTCAGGAATGCCACGACGCTATTCTGATTATCCAGACGCAT
-ATACAACATGAAATACCATCTCATCCATAGGATCTTTTATCTCACTTACA
-GCAGTGATACTAATAATTTTCATAATTTGAGAAGCGTTCGCATCCAAACG
-AGAAGTGTCTACAGTAGAATTAACCTCAACTAATCTGGAATGACTACACG
-GATGCCCCCCACCATACCACACATTTGAAGAACCCACCTACGTAAACCTA
-AAAtaagaaaggaaggaatcgaaccccctctaactggtttcaagccaata
-tcataaccactatgtctttctcCATCAATTGAGGTATTAGTAAAAATTAC
-ATGACTTTGTCAAAGTTAAATTATAGGTTAAACCCCTATATACCTCTATG
-GCCTACCCCTTCCAACTAGGATTCCAAGACGCAACATCCCCTATTATAGA
-AGAACTCCTACACTTCCACGACCACACACTAATAATCGTATTCCTAATTA
-GCTCTCTAGTATTATATATTATCTCATCAATACTAACAACTAAATTAACC
-CATACCAGCACCATAGATGCTCAAGAAGTAGAGACAATTTGAACGATTTT
-ACCAGCCATCATCCTTATTCTAATCGCCCTCCCATCCCTACGAATTCTAT
-ATATAATAGATGAAATCAATAATCCGTCCCTCACAGTCAAAACAATAGGC
-CACCAATGATACTGAAGCTACGAGTATACCGATTACGAAGACTTGACCTT
-TGACTCCTACATGATCCCCACATCAGACCTAAAACCAGGAGAATTACGTC
-TTCTAGAAGTCGACAATCGAGTGGTTCTCCCCATAGAAATAACCATCCGA
-ATGCTAATTTCATCCGAAGACGTCCTACACTCATGAGCTGTGCCCTCCCT
-AGGCCTAAAAACAGACGCTATCCCTGGGCGCCTAAATCAGACAACTCTCG
-TGGCCTCTCGACCAGGACTTTACTACGGTCAATGCTCAGAGATCTGCGGA
-TCAAACCACAGCTTTATACCAATTGTCCTTGAACTAGTTCCACTGAAACA
-CTTCGAAGAATGATCTGCATCAATATTATAAAGTCACTAAGAAGCTATTA
-TAGCATTAACCTTTTAAGTTAAAGATTGAGGGTTCAACCCCCTCCCTAGT
-GATATGCCACAGTTGGATACATCAACATGATTTATTAATATCGTCTCAAT
-AATCCTAACTCTATTTATTGTATTTCAACTAAAAATCTCAAAGCACTCCT
-ATCCGACACACCCAGAAGTAAAGACAACCAAAATAACAAAACACTCTGCC
-CCTTGAGAATCAAAATGAACGAAAATCTATTCGCCTCTTTCGCTACCCCA
-ACAATAGTAGGCCTCCCTATTGTAATTCTGATCATCATATTTCCCAGCAT
-CCTATTCCCCTCACCCAACCGACTAATCAACAATCGCCTAATCTCAATTC
-AACAATGGCTAGTCCAACTTACATCAAAACAAATAATAGCTATCCATAAC
-AGCAAAGGACAAACCTGAACTCTTATACTCATATCACTGATCCTATTCAT
-TGGCTCAACAAACTTATTAGGCCTACTACCTCACTCATTTACACCAACAA
-CACAACTATCAATAAACCTAGGCATAGCTATTCCCCTATGGGCAGGGACA
-GTATTCATAGGCTTTCGTCACAAAACAAAAGCAGCCCTAGCCCACTTTCT
-ACCTCAAGGGACGCCCATTTTCCTCATCCCCATACTAGTAATTATCGAGA
-CTATCAGCCTATTTATTCAACCTGTAGCCCTAGCCGTGCGGCTAACCGCT
-AACATTACCGCCGGACACCTCCTAATACACCTCATCGGAGGGGCAACACT
-AGCCCTCATAAGCATCAGCCCCTCAACAGCCCTTATTACGTTTATCATCC
-TAATTCTACTAACTATCCTCGAATTCGCAGTAGCTATAATCCAAGCCTAC
-GTATTCACTCTCCTGGTAAGCCTTTACTTACACGACAACACCTAATGACC
-CACCAAACCCACGCTTACCACATAGTAAACCCCAGCCCATGACCACTTAC
-AGGAGCCCTATCAGCCCTCCTGATAACATCAGGACTAGCCATGTGATTTC
-ACTTTAACTCAACCTTACTTCTAGCTATAGGGCTATTAACTAACATCCTT
-ACCATATATCAATGATGACGAGACATCATCCGAGAAAGCACATTCCAAGG
-CCATCACACATCAATCGTTCAAAAGGGACTCCGATATGGCATAATCCTTT
-TTATTATCTCAGAAGTCTTCTTCTTCTCTGGCTTCTTCTGAGCCTTTTAC
-CACTCAAGCCTAGCCCCCACACCCGAACTAGGCGGCTGCTGACCACCCAC
-AGGTATCCACCCCTTAAACCCCCTAGAAGTCCCCTTACTCAACACCTCAG
-TGCTCCTAGCATCTGGAGTCTCTATCACCTGAGCCCACCATAGCCTAATA
-GAAGGAAACCGTAAAAATATGCTCCAAGGCCTATTCATCACAATTTCACT
-AGGCGTATACTTCACCCTTCTCCAAGCCTCAGAATACTATGAAGCCTCAT
-TTACTATTTCAGATGGAGTATACGGATCAACATTTTTCGTAGCAACAGGG
-TTCCACGGACTACACGTAATTATCGGATCTACCTTCCTCATTGTATGTTT
-CCTACGCCAACTAAAATTCCACTTTACATCCAGCCACCACTTCGGATTCG
-AAGCAGCCGCTTGATACTGACACTTCGTCGACGTAGTCTGACTATTCTTG
-TACGTCTCTATTTATTGATGAGGATCCTATTCTTTTAGTATTGACCAGTA
-CAATTGACTTCCAATCAATCAGCTTCGGTATAACCCGAAAAAGAATAATA
-AACCTCATACTGACACTCCTCACTAACACATTACTAGCCTCGCTACTCGT
-ACTCATCGCATTCTGACTACCACAACTAAACATCTATGCAGAAAAAACCA
-GCCCATATGAATGCGGATTTGACCCTATAGGGTCAGCACGCCTCCCCTTC
-TCAATAAAATTTTTCTTAGTGGCCATTACATTTCTGCTATTCGACTTAGA
-AATTGCCCTCCTATTACCCCTTCCATGAGCATCCCAAACAACTAACCTAA
-ACACTATACTTATCATAGCACTAGTCCTAATCTCTCTTCTAGCCATCAGC
-CTAGCCTACGAATGAACCCAAAAAGGACTAGAATGAACTGAGTATGGTAA
-TTAGTTTAAACCAAAACAAATGATTTCGACTCATTAAACTATGATTAACT
-TCATAATTACCAACATGTCACTAGTCCATATTAATATCTTCCTAGCATTC
-ACAGTATCCCTCGTAGGCCTACTAATGTACCGATCCCACCTAATATCCTC
-ACTCCTATGCCTAGAAGGAATAATACTATCACTATTCGTCATAGCAACCA
-TAATAGTCCTAAACACCCACTTCACACTAGCTAGTATAATACCTATCATC
-TTACTAGTATTTGCTGCCTGCGAACGAGCTCTAGGATTATCCCTACTAGT
-CATAGTCTCCAATACTTATGGAGTAGACCACGTACAAAACCTTAACCTCC
-TCCAATGCTAAAAATTATCATTCCCACAATCATACTTATGCCCCTTACAT
-GACTATCAAAAAAGAATATAATCTGAATCAACACTACAACCTATAGTCTA
-TTAATCAGCCTTATCAGCCTATCCCTCCTAAACCAACCTAGCAACAATAG
-CCTAAACTTCTCACTAATATTCTTCTCCGATCCCCTATCAGCCCCACTTC
-TGGTGTTGACAACATGACTACTGCCACTAATACTCATAGCCAGCCAACAC
-CATCTATCTAAGGAACCACTAATCCGAAAAAAACTCTACATCACCATGCT
-AACCATACTTCAAACTTTCCTAATCATGACTTTTACCGCCACAGAACTAA
-TCTCCTTCTACATCCTATTTGAAGCCACATTAGTTCCAACACTAATTATC
-ATCACCCGCTGAGGCAACCAAACAGAACGCCTGAACGCAGGCCTCTACTT
-CCTATTCTACACACTAATAGGTTCCCTCCCACTCTTAGTTGCACTAATCT
-CTATCCAAAACCTAACAGGCTCACTAAACTTCCTATTAATTCAATACTGA
-AACCAAGCACTACCCGACTCTTGATCCAATATTTTCCTATGACTAGCATG
-TATAATAGCATTCATAGTCAAAATACCGGTATATGGTCTTCACCTCTGAC
-TCCCAAAAGCCCATGTAGAAGCCCCAATTGCCGGATCCATAGTGCTAGCA
-GCCATTCTACTAAAACTAGGAGGCTACGGAATACTACGAATTACAACAAT
-ACTAAACCCCCAAACTAGCTTTATAGCCTACCCCTTCCTCATACTATCCC
-TGTGAGGAATAATCATAACTAGTTCCATCTGCTTGCGACAAACCGATCTA
-AAATCACTTATTGCATACTCCTCTGTCAGCCACATAGCCCTAGTAATCGT
-AGCCGTCCTCATCCAAACACCATGAAGTTATATAGGAGCTACAGCCCTAA
-TAATCGCTCACGGCCTTACATCATCAATACTATTCTGCCTGGCAAACTCA
-AATTACGAACGTACCCATAGCCGAACTATAATCCTAGCCCGCGGGCTTCA
-AACACTTCTTCCCCTTATAGCAGCCTGATGACTATTAGCCAGCCTAACCA
-ACCTGGCCCTCCCTCCCAGCATTAACCTAATTGGAGAGCTATTCGTAGTA
-ATATCATCATTCTCATGATCAAATATTACCATTATCCTAATAGGAGCCAA
-TATCACCATCACCGCCCTCTACTCCCTATACATACTAATCACAACACAAC
-GAGGGAAATACACACACCATATCAACAGCATTAAACCTTCATTTACACGA
-GAAAACGCACTCATGGCCCTCCACATGACTCCCCTACTACTCCTATCACT
-TAACCCTAAAATTATCCTAGGCTTTACGTACTGTAAATATAGTTTAACAA
-AAACACTAGATTGTGGATCTAGAAACAGAAACTTAATATTTCTTATTTAC
-CGAGAAAGTATGCAAGAACTGCTAATTCATGCCCCCATGTCCAACAAACA
-TGGCTCTCTCAAACTTTTAAAGGATAGGAGCTATCCGTTGGTCTTAGGAA
-CCAAAAAATTGGTGCAACTCCAAATAAAAGTAATCAACATGTTCTCCTCC
-CTCATACTAGTTTCACTATTAGTACTAACCCTCCCAATCATATTATCAAT
-CTTCAATACCTACAAAAACAGCACGTTCCCGCATCATGTAAAAAACACTA
-TCTCATATGCCTTCATTACTAGCCTAATTCCCACTATAATATTTATTCAC
-TCTGGACAAGAAACAATTATCTCAAACTGACACTGAATAACCATACAAAC
-CCTCAAACTATCCCTAAGCTTCAAACTAGATTACTTCTCAATAATTTTCG
-TACCAGTAGCCCTATTCGTAACATGATCTATTATGGAATTCTCCCTATGA
-TACATGCACTCAGATCCTTACATTACTCGATTTTTTAAATACTTACTTAC
-ATTCCTCATCACTATAATAATTCTAGTCACAGCTAACAACCTTTTCCAAC
-TGTTCATCGGATGGGAGGGAGTAGGCATCATGTCATTCTTACTAATCGGA
-TGATGATACGGCCGAACAGATGCCAACACCGCGGCCCTTCAAGCAATCCT
-TTATAACCGCATCGGGGATATCGGCTTCATCATGGCCATAGCCTGATTCC
-TATTCAACACCAACACATGAGACCTCCAACAAATCTTCATACTCGACCCC
-AACCTTACCAACCTCCCGCTCCTAGGCCTCCTCCTAGCCGCAACTGGCAA
-ATCCGCTCAATTTGGACTCCACCCATGACTTCCTTCAGCCATAGAGGGCC
-CTACACCAGTCTCAGCCCTACTCCACTCCAGCACAATAGTTGTAGCAGGC
-GTCTTCCTGCTAATCCGCTTCCATCCACTAATAGAAAACAACAAAACAAT
-CCAGTCACTTACCCTATGCCTAGGAGCCATCACCACACTATTCACAGCAA
-TCTGCGCACTCACTCAAAACGATATCAAAAAAATCATTGCTTTCTCCACC
-TCCAGCCAACTAGGCCTGATAATCGTAACCATCGGTATCAATCAACCCTA
-CCTAGCATTCCTCCACATTTGCACTCACGCATTCTTCAAAGCTATACTAT
-TTATATGTTCCGGATCCATTATCCACAGCCTAAATGACGAGCAAGATATC
-CGAAAAATAGGCGGACTATTTAATGCAATACCCTTCACCACCACATCTCT
-AATTATTGGCAGCCTTGCACTCACCGGAATTCCTTTCCTCACAGGCTTCT
-ACTCCAAAGACCTCATCATCGAAACCGCCAACACATCGTACACCAACGCC
-TGAGCCCTACTAATAACTCTCATTGCCACATCCCTCACAGCTGTCTACAG
-TACCCGAATCATCTTCTTTGCACTCCTAGGGCAACCCCGCTTCCTCCCTC
-TGACCTCAATCAACGAAAATAACCCCTTTCTAATTAACTCCATCAAACGC
-CTCTTAATTGGCAGCATTTTTGCCGGATTCTTCATCTCCAACAATATCTA
-CCCCACAACCGTCCCAGAAATAACCATACCTACTTACATAAAACTCACCG
-CCCTCGCAGTAACCATCCTAGGATTTACACTAGCCCTAGAACTAAGCTTG
-ATAACCCATAACTTAAAACTAGAACACTCCACCAACGTATTCAAATTCTC
-CAACCTCCTAGGATACTACCCAACAATTATACACCGACTCCCACCGCTCG
-CTAACCTATCAATAAGCCAAAAATCAGCATCACTTCTACTAGACTCAATC
-TGACTAGAAAACATCCTGCCAAAATCTATCTCCCAGTTCCAAATAAAAAC
-CTCGATCCTAATTTCCACCCAAAAAGGACAAATCAAATTATATTTCCTCT
-CATTCCTCATCACCCTTACCCTAAGCATACTACTTTTTAATCTCCACGAG
-TAACCTCTAAAATTACCAAGACCCCAACAAGCAACGATCAACCAGTCACA
-ATCACAACCCAAGCCCCATAACTATACAATGCAGCAGCCCCTATAATTTC
-CTCACTAAACGCCCCAGAATCTCCAGTATCATAAATAGCTCAAGCCCCCA
-CACCACTAAACTTAAACACTACCCCCACTTCCTCACTCTTCAGAACATAT
-AAAACCAACATAACCTCCATCAACAACCCTAAAAGAAATACCCCCATAAC
-AGTCGTATTAGACACCCATACCTCAGGATACTGCTCAGTAGCCATAGCCG
-TTGTATAACCAAAAACAACCAACATTCCTCCCAAATAAATCAAAAACACC
-ATCAACCCCAAAAAGGACCCTCCAAAATTCATAATAATACCACAACCTAC
-CCCTCCACTTACAATCAGCACTAAACCCCCATAAATAGGTGAAGGTTTTG
-AAGAAAACCCCACAAAACTAACAACAAAAATAACACTCAAAATAAACACA
-ATATATGTCATCATTATTCCCACGTGGAATCTAACCACGACCAATGACAT
-GAAAAATCATCGTTGTATTTCAACTATAAGAACACCAATGACAAACATCC
-GGAAATCTCACCCACTAATTAAAATCATCAATCACTCTTTTATTGACCTA
-CCAGCCCCCTCAAACATTTCATCATGATGAAACTTCGGCTCCCTCCTAGG
-AATCTGCCTAATCCTCCAAATCTTAACAGGCCTATTCCTAGCCATACACT
-ACACATCAGACACGACAACTGCCTTCTCATCCGTCACTCACATCTGCCGA
-GACGTTAACTACGGATGAATTATTCGCTACCTCCATGCCAACGGAGCATC
-AATATTTTTTATCTGCCTCTTCATTCACGTAGGACGCGGCCTCTACTACG
-GCTCTTACACATTCCTAGAGACATGAAACATTGGAATCATCCTACTTTTC
-ACAGTTATAGCTACAGCATTCATGGGCTATGTCCTACCATGAGGCCAAAT
-ATCCTTTTGAGGAGCAACAGTCATCACGAACCTCCTATCAGCAATTCCCT
-ACATCGGTACTACCCTCGTCGAGTGAATCTGAGGTGGATTCTCAGTAGAC
-AAAGCCACCCTTACCCGATTTTTTGCTTTCCACTTCATCCTACCCTTCAT
-CATCACAGCCCTGGTAGTCGTACATTTACTATTTCTTCACGAAACAGGAT
-CTAATAACCCCTCAGGAATCCCATCCGATATGGACAAAATCCCATTCCAC
-CCATATTATACAATTAAAGACATCCTAGGACTCCTCCTCCTGATCTTGCT
-CCTACTAACTCTAGTATTATTCTCCCCCGACCTCCTAGGAGACCCAGACA
-ACTACACCCCAGCTAACCCTCTCAGCACTCCCCCTCATATTAAACCAGAA
-TGGTACTTCCTGTTTGCCTACGCCATCCTACGCTCCATTCCCAACAAACT
-AGGCGGCGTATTAGCCCTAATCCTCTCCATCCTGATCCTAGCACTCATCC
-CCACCCTCCACATATCAAAACAACGAAGCATAATATTCCGGCCTCTCAGC
-CAATGCGTATTCTGACTCTTAGTGGCAGACTTACTGACACTAACATGAAT
-CGGCGGACAGCCAGTGGAACACCCATACGTAATTATCGGCCAACTGGCCT
-CAATCCTCTACTTCTCCCTAATTCTCATTTTTATACCACTCGCAAGCACC
-ATCGAAAACAATCTTCTAAAATGAAGAGTCCCTGTAGTATATCGCACATT
-ACCCTGGTCTTGTAAACCAGAAAAGGGGGAAAACGTTTCCTCCCAAGGAC
-TATCAAGGAAGAAGCTCTAGCTCCACCATCAACACCCAAAGCTGAAATTC
-TACTTAAACTATTCCTTGATTTCTTCCCCTAAACGACAACAATTTACCCT
-CATGTGCTATGTCAGTATCAGATTATACCCCCACATAACACCATACCCAC
-CTGACATGCAATATCTTATGAATGGCCTATGTACGTCGTGCATTAAATTG
-TCTGCCCCATGAATAATAAGCATGTACATAATATCATTTATCTTACATAA
-GTACATTATATTATTGATCGTGCATACCCCATCCAAGTCAAATCATTTCC
-AGTCAACACGCATATCACAGCCCATGTTCCACGAGCTTAATCACCAAGCC
-GCGGGAAATCAGCAACCCTCCCAACTACGTGTCCCAATCCTCGCTCCGGG
-CCCATCCAAACGTGGGGGTTTCTACAATGAAACTATACCTGGCATCTGGT
-TCTTTCTTCAGGGCCATTCCCACCCAACCTCGCCCATTCTTTCCCCTTAA
-ATAAGACATCTCGATGGACTAATGACTAATCAGCCCATGCTCACACATAA
-CTGTGATTTCATGCATTTGGTATCTTTTTATATTTGGGGATGCTATGACT
-CAGCTATGGCCGTCAAAGGCCTCGACGCAGTCAATTAAATTGAAGCTGGA
-CTTAAATTGAACGTTATTCCTCCGCATCAGCAACCATAAGGTGTTATTCA
-GTCCATGGTAGCGGGACATAGGAAACAAgtgcacctgtgcacctgtgcac
-ctgtgcacctgtgcacctgtgcacctgtgcacctgtgcacctgtgcacct
-gtgcacctgtgcacctgtgcacctgtgcacctgtgcacctgtgcacctgt
-gcacctgtgcacctgtgcacctgtgcacctgtgcacctgtgcacctgtgc
-acctgtgcacctgtgcacctgtgcacctgtgcacctgtgcacctgtgcac
-ctgtgcacctACCCGCGCAGTAAGCAAGTAATATAGCTTTCTTAATCAAA
-CCCCCCCTACCCCCCATTAAACTCCACATATGTACATTCAACACAATCTT
-GCCAAACCCCAAAAACAAGACTAAACAATGCACAATACTTCATGAAGCTT
-AACCCTCGCATGCCAACCATAATAACTCAACACACCTAACAATCTTAACA
-GAACTTTCCCCCCGCCATTAATACCAACATGCTACTTTAATCAATAAAAT
-TTCCATAGACAGGCATCCCCCTAGATCTAATTTTCTAAATCTGTCAACCC
-TTCTTCCCCC
diff -r 4afb4a5f0924 -r d6181de75bdd test-data/cached_locally/chr_m.fasta.fai
--- a/test-data/cached_locally/chr_m.fasta.fai	Tue May 09 11:18:00 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-chrM	16660	6	50	51
diff -r 4afb4a5f0924 -r d6181de75bdd test-data/cached_locally/fasta_indexes.loc
--- a/test-data/cached_locally/fasta_indexes.loc	Tue May 09 11:18:00 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-equCab2chrM	equCab2	Horse (Equus caballus): equCab2 chrM	${__HERE__}/chr_m.fasta