# HG changeset patch
# User iuc
# Date 1564404391 14400
# Node ID 3e15f2544a5cece7ad51cb219a52735fcce8380c
# Parent  4190f6830fe0964a6e4f65f628c1da59ebe3bec6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_cram commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6

diff -r 4190f6830fe0 -r 3e15f2544a5c samtools_bam_to_cram.xml
--- a/samtools_bam_to_cram.xml	Sun Oct 14 12:00:54 2018 -0400
+++ b/samtools_bam_to_cram.xml	Mon Jul 29 08:46:31 2019 -0400
@@ -9,33 +9,23 @@
     <expand macro="version_command"/>
 
     <command><![CDATA[
-        #if str( $input_alignment.metadata.bam_index ) != "None":
-            ln
-                -f
-                -s
-                '${input_alignment.metadata.bam_index}'
-                '${input_alignment}.bai'
-                &&
-        #end if
-
-        #if $reference_source.reference_source_selector == 'history':
-            #set ref_fa = 'ref.fa'
-            ln -s '${reference_source.input_reference}' ref.fa &&
-        #else:
-            #set ref_fa = str( $reference_source.input_reference.fields.path )
-        #end if
+        @ADDTHREADS@
+        @PREPARE_FASTA_IDX@
+        @PREPARE_IDX@
 
         samtools view
             #if $parameter_regions.target_region == "regions_bed_file"
                 -L '${parameter_regions.regions_bed_file}'
             #end if
 
-            -@\${GALAXY_SLOTS:-1}
-            -C
-            -T '$ref_fa'
+            -@ \$addthreads
+	    -C
+	    -h 
             -o '${output_alignment}'
-
-            '${input_alignment}'
+            -T '$reffa'
+            -t '$reffai'
+            --output-fmt-option no_ref
+            infile
 
             #if $parameter_regions.target_region == "region"
                 '${parameter_regions.region_string}'
@@ -43,22 +33,22 @@
     ]]></command>
 
     <inputs>
-        <param name="input_alignment" type="data" format="bam,sam" label="BAM (or SAM) alignment file"/>
-        <conditional name="reference_source">
-            <param name="reference_source_selector" type="select" label="Load reference genome from">
+        <param name="input" type="data" format="bam,sam" label="BAM (or SAM) alignment file"/>
+        <conditional name="addref_cond">
+            <param name="addref_select" type="select" label="Load reference genome from">
                 <option value="cached">Local cache</option>
                 <option value="history">History</option>
             </param>
             <when value="cached">
-                <param name="input_reference" type="select" label="Reference genome">
+                <param name="ref" type="select" label="Reference genome">
                     <options from_data_table="fasta_indexes">
-                        <filter type="data_meta" ref="input_alignment" key="dbkey" column="1" />
+                        <filter type="data_meta" ref="input" key="dbkey" column="1" />
                     </options>
                     <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
                 </param>
             </when>
             <when value="history">
-                <param name="input_reference" type="data" format="fasta" label="Reference FASTA file"/>
+                <param name="ref" type="data" format="fasta" label="Reference FASTA file"/>
             </when>
         </conditional>
         <conditional name="parameter_regions">
@@ -84,43 +74,43 @@
 
     <tests>
         <test>
-            <param name="input_alignment" value="test.bam" ftype="bam" />
-            <param name="reference_source_selector" value="history" />
-            <param name="input_reference" value="test.fa" />
+            <param name="input" value="test.bam" ftype="bam" />
+            <param name="addref_select" value="history" />
+            <param name="ref" value="test.fa" />
             <param name="target_region" value="entire_input_file" />
 
             <output name="output_alignment" file="test.cram" compare="sim_size" delta="250" />
         </test>
         <test>
-            <param name="input_alignment" value="test.sam" ftype="sam" />
-            <param name="reference_source_selector" value="history" />
-            <param name="input_reference" value="test.fa" />
+            <param name="input" value="test.sam" ftype="sam" />
+            <param name="addref_select" value="history" />
+            <param name="ref" value="test.fa" />
             <param name="target_region" value="entire_input_file" />
 
             <output name="output_alignment" file="test.cram" compare="sim_size" delta="250" />
         </test>
         <test>
-            <param name="input_alignment" value="test.bam" ftype="bam" />
-            <param name="reference_source_selector" value="history" />
-            <param name="input_reference" value="test.fa" />
+            <param name="input" value="test.bam" ftype="bam" />
+            <param name="addref_select" value="history" />
+            <param name="ref" value="test.fa" />
             <param name="target_region" value="region" />
             <param name="region_string" value="CHROMOSOME_I" />
 
             <output name="output_alignment" file="test.cram" compare="sim_size" delta="250" />
         </test>
         <test>
-            <param name="input_alignment" value="test.bam" ftype="bam" />
-            <param name="reference_source_selector" value="history" />
-            <param name="input_reference" value="test.fa" />
+            <param name="input" value="test.bam" ftype="bam" />
+            <param name="addref_select" value="history" />
+            <param name="ref" value="test.fa" />
             <param name="target_region" value="regions_bed_file" />
             <param name="regions_bed_file" value="test.bed" ftype="bed" />
 
             <output name="output_alignment" file="test.cram" compare="sim_size" delta="250" />
         </test>
         <test>
-            <param name="input_alignment" ftype="bam" dbkey="equCab2" value="sam_to_bam_out2.bam" />
-            <param name="reference_source_selector" value="cached" />
-            <param name="input_reference" value="equCab2chrM" />
+            <param name="input" ftype="bam" dbkey="equCab2" value="sam_to_bam_out2.bam" />
+            <param name="addref_select" value="cached" />
+            <param name="ref" value="equCab2chrM" />
             <param name="target_region" value="entire_input_file" />
             <output name="output_alignment" file="test2.cram" compare="sim_size" delta="250" />
         </test>
diff -r 4190f6830fe0 -r 3e15f2544a5c test-data/cached_locally/chr_m.fasta
--- a/test-data/cached_locally/chr_m.fasta	Sun Oct 14 12:00:54 2018 -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 4190f6830fe0 -r 3e15f2544a5c test-data/cached_locally/chr_m.fasta.fai
--- a/test-data/cached_locally/chr_m.fasta.fai	Sun Oct 14 12:00:54 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-chrM	16660	6	50	51
diff -r 4190f6830fe0 -r 3e15f2544a5c test-data/cached_locally/fasta_indexes.loc
--- a/test-data/cached_locally/fasta_indexes.loc	Sun Oct 14 12:00:54 2018 -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
diff -r 4190f6830fe0 -r 3e15f2544a5c test-data/test.cram
Binary file test-data/test.cram has changed