# HG changeset patch
# User iuc
# Date 1537359711 14400
# Node ID 00d1f08bdcdc6366f471be1598a37829b01a1d46
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
diff -r 000000000000 -r 00d1f08bdcdc macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Wed Sep 19 08:21:51 2018 -0400
@@ -0,0 +1,127 @@
+
+
+
+ samtools
+
+
+
+ 1.9
+ #set $flags = sum(map(int, str($filter).split(',')))
+
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+ @misc{SAM_def,
+ title={Definition of SAM/BAM format},
+ url = {https://samtools.github.io/hts-specs/},}
+
+ 10.1093/bioinformatics/btp352
+ 10.1093/bioinformatics/btr076
+ 10.1093/bioinformatics/btr509
+
+ @misc{Danecek_et_al,
+ Author={Danecek, P., Schiffels, S., Durbin, R.},
+ title={Multiallelic calling model in bcftools (-m)},
+ url = {http://samtools.github.io/bcftools/call-m.pdf},}
+
+
+ @misc{Durbin_VCQC,
+ Author={Durbin, R.},
+ title={Segregation based metric for variant call QC},
+ url = {http://samtools.github.io/bcftools/rd-SegBias.pdf},}
+
+
+ @misc{Li_SamMath,
+ Author={Li, H.},
+ title={Mathematical Notes on SAMtools Algorithms},
+ url = {http://www.broadinstitute.org/gatk/media/docs/Samtools.pdf},}
+
+
+ @misc{SamTools_github,
+ title={SAMTools GitHub page},
+ url = {https://github.com/samtools/samtools},}
+
+
+
+
+ &1 | grep Version]]>
+
+
+
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+
+
diff -r 000000000000 -r 00d1f08bdcdc samtools_view.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/samtools_view.xml Wed Sep 19 08:21:51 2018 -0400
@@ -0,0 +1,439 @@
+
+ reformat, filter, or subsample
+
+ macros.xml
+
+
+
+
+ 0
+ -q $cond_filter.quality
+ #end if
+ #if str( $cond_filter.library ) != ''
+ -l '$cond_filter.library'
+ #end if
+ #if str( $cond_filter.cigarcons ) != ''
+ -m $cond_filter.cigarcons
+ #end if
+ #if str($cond_filter.inclusive_filter) != 'None':
+ #set $filter = $cond_filter.inclusive_filter
+ @FLAGS@
+ -f $flags
+ #end if
+ #if str($cond_filter.exclusive_filter) != 'None':
+ #set $filter = $cond_filter.exclusive_filter
+ @FLAGS@
+ -F $flags
+ #end if
+ #if str($cond_filter.exclusive_filter_all) != 'None':
+ #set $filter = $cond_filter.exclusive_filter_all
+ @FLAGS@
+ -G $flags
+ #end if
+ #for $i, $s in enumerate($cond_filter.readtags)
+ -x '${s.readtag}'
+ #end for
+ #end if
+ #if $cond_subsample.select_subsample == 'yes':
+ #set fraction=str($cond_subsample.subsample).split('.')[1]
+ #if str($cond_subsample.seed) == '':
+ -s "\${RANDOM}".$fraction
+ #else
+ -s $cond_subsample.seed.$fraction
+ #end if
+ #end if
+
+ ## output options
+ $adv_output.header
+ $adv_output.collapsecigar
+ #if $adv_output.outputpassing == 'yes'
+ -U inv_outfile
+ #end if
+ -o outfile
+
+ ## additional reference data
+ #if $reffa!=None:
+ -T '$reffa'
+ -t '$reffai'
+ #else:
+ --output-fmt-option no_ref
+ #end if
+
+ infile
+
+ ## region filter need to be at the end
+ #if $cond_filter.select_filter == 'yes' and $cond_filter.cond_region.select_region == 'text':
+ '$cond_filter.cond_region.regions'
+ #end if
+
+ ## if data is converted from an unsorted file (SAM, CRAM, or unsorted BAM) to BAM
+ ## then sort the output by coordinate,
+ #if not $input.is_of_type('bam') and $outtype == 'bam':
+ && samtools sort
+ -@ \$addthreads -m \${GALAXY_MEMORY_MB:-768}M -T sorttemp
+ -O bam
+ -o 'tmpsam'
+ outfile
+ && mv tmpsam outfile
+ #if $adv_output.outputpassing == 'yes':
+ && samtools sort
+ -@ \$addthreads -m \${GALAXY_MEMORY_MB:-768}M -T sorttemp
+ -O bam
+ -o 'tmpsam'
+ inv_outfile
+ && mv tmpsam inv_outfile
+ #end if
+ #end if
+ ]]>
+
+
+
+
+ Select output type. In case of counts only the total number of alignments is returned. All filters are taken into account
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+ Reference data as fasta(.gz). Required for SAM input without @SQ headers and useful/required for writing CRAM output (see help).
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+ outtype != 'count'
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+ adv_output['outputpassing'] == 'yes' and outtype != 'count'
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+ outtype == 'count'
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+**What it does**
+
+Samtools view can:
+
+1. filter alignments according to various criteria
+2. convert between alignment formats (SAM, BAM, CRAM)
+
+With no options or regions specified, prints all alignments in the specified input alignment file (in SAM, BAM, or CRAM format) to standard output in SAM format (with no header).
+
+**Alignment format conversion**
+
+Inputs of type SAM, BAM, and CRAM are accepted and can be converted to each of these formats (alternatively alignment counts can be computed) by selecting the appropriate "Output type".
+
+.. class:: infomark
+
+samtools view allows to specify a reference sequence. This is required for SAM input with missing @SQ headers (which include sequence names, length, md5, etc) and useful (and sometimes necessary) for CRAM input and output. In the following the use of reference sequence in the CRAM format is detailed.
+CRAM is (primarily) a reference-based compressed format, i.e. only differences between the stored sequences and the reference are stored. As a consequence the reference that was used to generate the alignemnts is always needed in order to interpret the alignments (a checksum stored in the CRAM file is used to verify that the only the correct sequence can be used), i.e. the CRAM file on its own is not useful per default. This allows for a more space efficient storage compared to BAM. But it is also possible to use CRAM without a reference with the disadvantage that the reference is stored explicitely (as in SAM and BAM).
+
+The Galaxy tool allows both possibilities using the "reference data" option:
+
+- the default ("no reference")
+- reference data can be chosen from history or built in genomes can be used
+
+The reference data required for reading/writing reference based CRAM.
+
+**Filtering alignments**
+
+samtools view allows to filter alignements based on various criteria, i.e. the output will contain only alignemnts matching all criteria (an additional output containing the remaining alignments can be created additionally, see "Output alignments not passing the filter" in "output options"): e.g. by regions (see below), alignment quality (see below), and tags or flags set in the alignments.
+
+
+
+**Filtering by regions**
+
+You may specify one or more space-separated region specifications after the input filename to restrict output to only those alignments which overlap the specified region(s). Use of region specifications requires a coordinate-sorted and indexed input file (in BAM or CRAM format).
+
+Regions can be specified as: RNAME[:STARTPOS[-ENDPOS]] and all position coordinates are 1-based.
+
+Important note: when multiple regions are given, some alignments may be output multiple times if they overlap more than one of the specified regions.
+
+Examples of region specifications:
+
+- chr1 Output all alignments mapped to the reference sequence named 'chr1' (i.e. @SQ SN:chr1).
+- chr2:1000000 The region on chr2 beginning at base position 1,000,000 and ending at the end of the chromosome.
+- chr3:1000-2000 The 1001bp region on chr3 beginning at base position 1,000 and ending at base position 2,000 (including both end positions).
+- '*' Output the unmapped reads at the end of the file. (This does not include any unmapped reads placed on a reference sequence alongside their mapped mates.)
+- . Output all alignments. (Mostly unnecessary as not specifying a region at all has the same effect.)
+
+**Filtering by quality**
+
+This filters based on the MAPQ column of the SAM format which gives an estimate about the correct placement of the alignemnt. Note that aligners do not follow a consistent definition.
+
+The -x, -B, and -s options modify the data which is contained in each alignment.
+
+
+
diff -r 000000000000 -r 00d1f08bdcdc test-data/1.bam
Binary file test-data/1.bam has changed
diff -r 000000000000 -r 00d1f08bdcdc test-data/1_sort.bam
Binary file test-data/1_sort.bam has changed
diff -r 000000000000 -r 00d1f08bdcdc test-data/1_sort_read_names.bam
Binary file test-data/1_sort_read_names.bam has changed
diff -r 000000000000 -r 00d1f08bdcdc test-data/bam_to_sam_in1.bam
Binary file test-data/bam_to_sam_in1.bam has changed
diff -r 000000000000 -r 00d1f08bdcdc test-data/bam_to_sam_in1.sam
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bam_to_sam_in1.sam Wed Sep 19 08:21:51 2018 -0400
@@ -0,0 +1,14 @@
+@HD VN:1.0 SO:coordinate
+@SQ SN:chr1 LN:101
+@SQ SN:chr7 LN:404
+@SQ SN:chr8 LN:202
+@RG ID:0 SM:Hi,Mom!
+@PG ID:1 PN:Hey! VN:2.0
+both_reads_align_clip_marked 83 chr7 1 255 101M = 302 201 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0
+both_reads_present_only_first_aligns 89 chr7 1 255 101M * 0 0 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0
+read_2_too_many_gaps 83 chr7 1 255 101M = 302 201 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0
+both_reads_align_clip_adapter 147 chr7 16 255 101M = 21 -96 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0
+both_reads_align_clip_adapter 99 chr7 21 255 101M = 16 96 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0
+both_reads_align_clip_marked 163 chr7 302 255 101M = 1 -201 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA &/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1 RG:Z:0
+read_2_too_many_gaps 163 chr7 302 255 10M1D10M5I76M = 1 -201 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA &/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1 RG:Z:0
+both_reads_present_only_first_aligns 165 * 0 0 * chr7 1 0 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA &/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1 RG:Z:0
diff -r 000000000000 -r 00d1f08bdcdc test-data/bam_to_sam_in2.bam
Binary file test-data/bam_to_sam_in2.bam has changed
diff -r 000000000000 -r 00d1f08bdcdc test-data/bam_to_sam_in2.sam
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bam_to_sam_in2.sam Wed Sep 19 08:21:51 2018 -0400
@@ -0,0 +1,25 @@
+@HD VN:1.0 SO:coordinate
+@SQ SN:chr1 LN:10001
+@SQ SN:chr2 LN:100001
+@SQ SN:chr3 LN:10001
+@SQ SN:chr4 LN:1001
+@RG ID:rg1 SM:s1
+@RG ID:rg2 SM:s3
+bar:record:4 77 chr1 1 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg1
+bar:record:6 77 chr1 1 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg2
+bar:record:1 77 chr1 10 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg1
+bar:record:3 77 chr1 10 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg2
+bar:record:1 141 chr1 20 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1
+bar:record:7 77 chr1 20 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg2
+bar:record:8 77 chr1 30 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg2
+bar:record:4 141 chr1 40 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1
+bar:record:5 77 chr1 40 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg2
+bar:record:6 141 chr1 50 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg2
+bar:record:2 77 chr2 10 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg1
+bar:record:2 141 chr2 30 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg2
+bar:record:3 141 chr3 20 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1
+bar:record:8 141 chr3 20 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1
+bar:record:5 141 chr3 40 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1
+bar:record:9 77 chr4 10 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg1
+bar:record:7 141 chr4 20 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1
+bar:record:9 141 chr4 60 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1
diff -r 000000000000 -r 00d1f08bdcdc test-data/bam_to_sam_out1.sam
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bam_to_sam_out1.sam Wed Sep 19 08:21:51 2018 -0400
@@ -0,0 +1,14 @@
+@HD VN:1.0 SO:coordinate
+@SQ SN:chr1 LN:101
+@SQ SN:chr7 LN:404
+@SQ SN:chr8 LN:202
+@RG ID:0 SM:Hi,Mom!
+@PG ID:1 PN:Hey! VN:2.0
+both_reads_align_clip_marked 83 chr7 1 255 101M = 302 201 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0
+both_reads_present_only_first_aligns 89 chr7 1 255 101M * 0 0 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0
+read_2_too_many_gaps 83 chr7 1 255 101M = 302 201 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0
+both_reads_align_clip_adapter 147 chr7 16 255 101M = 21 -96 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0
+both_reads_align_clip_adapter 99 chr7 21 255 101M = 16 96 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0
+both_reads_align_clip_marked 163 chr7 302 255 101M = 1 -201 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA &/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1 RG:Z:0
+read_2_too_many_gaps 163 chr7 302 255 10M1D10M5I76M = 1 -201 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA &/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1 RG:Z:0
+both_reads_present_only_first_aligns 165 * 0 0 * chr7 1 0 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA &/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1 RG:Z:0
diff -r 000000000000 -r 00d1f08bdcdc test-data/bam_to_sam_out2.sam
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bam_to_sam_out2.sam Wed Sep 19 08:21:51 2018 -0400
@@ -0,0 +1,6 @@
+@HD VN:1.0 SO:coordinate
+@SQ SN:chr1 LN:101
+@SQ SN:chr7 LN:404
+@SQ SN:chr8 LN:202
+@RG ID:0 SM:Hi,Mom!
+@PG ID:1 PN:Hey! VN:2.0
diff -r 000000000000 -r 00d1f08bdcdc test-data/bam_to_sam_out3.sam
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bam_to_sam_out3.sam Wed Sep 19 08:21:51 2018 -0400
@@ -0,0 +1,8 @@
+both_reads_align_clip_marked 83 chr7 1 255 101M = 302 201 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0
+both_reads_present_only_first_aligns 89 chr7 1 255 101M * 0 0 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0
+read_2_too_many_gaps 83 chr7 1 255 101M = 302 201 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0
+both_reads_align_clip_adapter 147 chr7 16 255 101M = 21 -96 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0
+both_reads_align_clip_adapter 99 chr7 21 255 101M = 16 96 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0
+both_reads_align_clip_marked 163 chr7 302 255 101M = 1 -201 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA &/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1 RG:Z:0
+read_2_too_many_gaps 163 chr7 302 255 10M1D10M5I76M = 1 -201 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA &/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1 RG:Z:0
+both_reads_present_only_first_aligns 165 * 0 0 * chr7 1 0 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA &/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1 RG:Z:0
diff -r 000000000000 -r 00d1f08bdcdc test-data/cached_locally/chr_m.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cached_locally/chr_m.fasta Wed Sep 19 08:21:51 2018 -0400
@@ -0,0 +1,335 @@
+>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 000000000000 -r 00d1f08bdcdc test-data/cached_locally/chr_m.fasta.fai
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cached_locally/chr_m.fasta.fai Wed Sep 19 08:21:51 2018 -0400
@@ -0,0 +1,1 @@
+chrM 16660 6 50 51
diff -r 000000000000 -r 00d1f08bdcdc test-data/cached_locally/fasta_indexes.loc
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cached_locally/fasta_indexes.loc Wed Sep 19 08:21:51 2018 -0400
@@ -0,0 +1,1 @@
+equCab2chrM equCab2 Horse (Equus caballus): equCab2 chrM ${__HERE__}/chr_m.fasta
diff -r 000000000000 -r 00d1f08bdcdc test-data/chr_m.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/chr_m.fasta Wed Sep 19 08:21:51 2018 -0400
@@ -0,0 +1,335 @@
+>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 000000000000 -r 00d1f08bdcdc test-data/sam_to_bam_in1.sam
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sam_to_bam_in1.sam Wed Sep 19 08:21:51 2018 -0400
@@ -0,0 +1,13 @@
+@HD VN:1.0 SO:coordinate
+@SQ SN:chrM LN:100001
+@RG ID:rg1 SM:s1
+HWI-EAS91_1_30788AAXX:1:1:1513:715 16 chrM 9563 25 36M * 0 0 CTGACTACCACAACTAAACATCTATGCNNAAAAAAC I+-II?IDIIIIIIIIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 RG:Z:rg1
+HWI-EAS91_1_30788AAXX:1:1:1698:516 16 chrM 2735 25 36M * 0 0 TTTACACTCAGAGGTTCAACTCCTCTCNNTAACAAC I9IIIII5IIIIIIIIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 RG:Z:rg1
+HWI-EAS91_1_30788AAXX:1:1:1491:637 16 chrM 10864 25 36M * 0 0 TGTAGAAGCCCCAATTGCCGGATCCATNNTGCTAGC DBAIIIIIIIIIIIFIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 RG:Z:rg1
+HWI-EAS91_1_30788AAXX:1:1:1711:249 16 chrM 10617 25 36M * 0 0 ACCAAACAGAACGCCTGAACGCAGGCCNNTACTTCC IIIIIIIIIIIIIIIIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 RG:Z:rg1
+HWI-EAS91_1_30788AAXX:1:1:1634:211 0 chrM 9350 25 36M * 0 0 GAAGCAGNNGCTTGATACTGACACTTCGTCGACGTA IIIIIII""IIIIIIIIIIIIIIIIIIIIII9IIDF NM:i:1 X1:i:1 MD:Z:7N0N27 RG:Z:rg1
+HWI-EAS91_1_30788AAXX:1:1:1218:141 16 chrM 14062 25 36M * 0 0 ACAAAACTAACAACAAAAATAACACTCNNAATAAAC I+IIII1IIIIIIIIIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 RG:Z:rg1
+HWI-EAS91_1_30788AAXX:1:1:1398:854 16 chrM 3921 25 36M * 0 0 CACCCTTCCCGTACTAATAAATCCCCTNNTCTTCAC IIIII=AIIIIIIIIIIIIIIBIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 RG:Z:rg1
+HWI-EAS91_1_30788AAXX:1:1:1310:991 16 chrM 10002 25 36M * 0 0 CTCCTATGCCTAGAAGGAATAATACTANNACTATTC I:2IEI:IIDIIIIII4IIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 RG:Z:rg1
+HWI-EAS91_1_30788AAXX:1:1:1716:413 0 chrM 6040 25 36M * 0 0 GATCCAANNCTTTATCAACACCTATTCTGATTCTTC IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 RG:Z:rg1
+HWI-EAS91_1_30788AAXX:1:1:1630:59 16 chrM 12387 25 36M * 0 0 TCATACTCGACCCCAACCTTACCAACCNNCCGCTCC FIIHII;IIIIIIIIIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 RG:Z:rg1
diff -r 000000000000 -r 00d1f08bdcdc test-data/sam_to_bam_noheader_in2.sam
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sam_to_bam_noheader_in2.sam Wed Sep 19 08:21:51 2018 -0400
@@ -0,0 +1,10 @@
+HWI-EAS91_1_30788AAXX:1:1:1513:715 16 chrM 9563 25 36M * 0 0 CTGACTACCACAACTAAACATCTATGCNNAAAAAAC I+-II?IDIIIIIIIIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 RG:Z:rg1
+HWI-EAS91_1_30788AAXX:1:1:1698:516 16 chrM 2735 25 36M * 0 0 TTTACACTCAGAGGTTCAACTCCTCTCNNTAACAAC I9IIIII5IIIIIIIIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 RG:Z:rg1
+HWI-EAS91_1_30788AAXX:1:1:1491:637 16 chrM 10864 25 36M * 0 0 TGTAGAAGCCCCAATTGCCGGATCCATNNTGCTAGC DBAIIIIIIIIIIIFIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 RG:Z:rg1
+HWI-EAS91_1_30788AAXX:1:1:1711:249 16 chrM 10617 25 36M * 0 0 ACCAAACAGAACGCCTGAACGCAGGCCNNTACTTCC IIIIIIIIIIIIIIIIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 RG:Z:rg1
+HWI-EAS91_1_30788AAXX:1:1:1634:211 0 chrM 9350 25 36M * 0 0 GAAGCAGNNGCTTGATACTGACACTTCGTCGACGTA IIIIIII""IIIIIIIIIIIIIIIIIIIIII9IIDF NM:i:1 X1:i:1 MD:Z:7N0N27 RG:Z:rg1
+HWI-EAS91_1_30788AAXX:1:1:1218:141 16 chrM 14062 25 36M * 0 0 ACAAAACTAACAACAAAAATAACACTCNNAATAAAC I+IIII1IIIIIIIIIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 RG:Z:rg1
+HWI-EAS91_1_30788AAXX:1:1:1398:854 16 chrM 3921 25 36M * 0 0 CACCCTTCCCGTACTAATAAATCCCCTNNTCTTCAC IIIII=AIIIIIIIIIIIIIIBIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 RG:Z:rg1
+HWI-EAS91_1_30788AAXX:1:1:1310:991 16 chrM 10002 25 36M * 0 0 CTCCTATGCCTAGAAGGAATAATACTANNACTATTC I:2IEI:IIDIIIIII4IIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 RG:Z:rg1
+HWI-EAS91_1_30788AAXX:1:1:1716:413 0 chrM 6040 25 36M * 0 0 GATCCAANNCTTTATCAACACCTATTCTGATTCTTC IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 RG:Z:rg1
+HWI-EAS91_1_30788AAXX:1:1:1630:59 16 chrM 12387 25 36M * 0 0 TCATACTCGACCCCAACCTTACCAACCNNCCGCTCC FIIHII;IIIIIIIIIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 RG:Z:rg1
diff -r 000000000000 -r 00d1f08bdcdc test-data/sam_to_bam_out1.bam
Binary file test-data/sam_to_bam_out1.bam has changed
diff -r 000000000000 -r 00d1f08bdcdc test-data/sam_to_bam_out2.bam
Binary file test-data/sam_to_bam_out2.bam has changed
diff -r 000000000000 -r 00d1f08bdcdc test-data/sam_to_bam_out3.bam
Binary file test-data/sam_to_bam_out3.bam has changed
diff -r 000000000000 -r 00d1f08bdcdc test-data/tag.as.sort.expected.sam
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tag.as.sort.expected.sam Wed Sep 19 08:21:51 2018 -0400
@@ -0,0 +1,24 @@
+@HD VN:1.4 SO:unknown
+@SQ SN:insert LN:599
+@SQ SN:ref1 LN:45
+@SQ SN:ref2 LN:40
+@SQ SN:ref3 LN:4
+@PG ID:llama
+@RG ID:fish PG:llama
+@RG ID:cow PU:13_&^&&*(:332 PG:donkey
+@RG PU:*9u8jkjjkjd: ID:colt
+@PG ID:bull PP:donkey
+@PG ID:donkey
+@CO Do you know?
+r006 16 ref1 29 30 6H5M * 0 0 TAGGC * RG:Z:colt PG:Z:donkey FI:i:3
+x11 0 ref2 12 30 24M * 0 0 AATAATTAAGTCTACAGAGCAACT ???????????????????????? RG:Z:cow PG:Z:bull FI:Z:a
+r007 0 ref1 16 30 6M14N1I5M * 0 0 ATAGCTCTCAGC * RG:Z:colt PG:Z:donkey AS:i:-5 FI:f:3.5
+x10 0 ref2 10 30 25M * 0 0 CAAATAATTAAGTCTACAGAGCAAC ????????????????????????? RG:Z:cow PG:Z:bull AS:i:0 FI:A:b
+r007 0 ref1 9 30 5H6M * 0 0 AGCTAA * RG:Z:colt PG:Z:donkey AS:i:1 FI:i:4
+r005 163 ref1 7 30 8M4I4M1D3M = 37 39 TTAGATAAAGAGGATACTG * XX:B:S,12561,2,20,112 YY:i:100 RG:Z:colt PG:Z:donkey AS:i:10 FI:i:5
+x8 0 ref2 2 30 21M * 0 0 GGTTTTATAAAACAAATAATT ????????????????????? RG:Z:cow PG:Z:bull AS:i:10 FI:f:1.5
+r006 0 ref1 9 30 1S2I6M1P1I1P1I4M2I * 0 0 AAAAGATAAGGGATAAA * XA:Z:abc XB:i:-10 RG:Z:colt PG:Z:donkey AS:i:20 FI:f:4.5
+x9 0 ref2 6 30 9M4I13M * 0 0 TTATAAAACAAATAATTAAGTCTACA ?????????????????????????? RG:Z:cow PG:Z:bull AS:i:20 FI:i:1
+x7 0 ref2 1 30 20M * 0 0 AGGTTTTATAAAACAAATAA * RG:Z:cow PG:Z:bull AS:i:50 FI:i:2
+r005 83 ref1 37 30 9M = 7 -39 CAGCGCCAT * RG:Z:colt PG:Z:donkey AS:i:100 FI:f:2.5
+x12 0 ref2 14 30 23M * 0 0 TAATTAAGTCTACAGAGCAACTA ??????????????????????? RG:Z:cow PG:Z:bull AS:i:65100
diff -r 000000000000 -r 00d1f08bdcdc test-data/tag.fi.sort.expected.sam
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tag.fi.sort.expected.sam Wed Sep 19 08:21:51 2018 -0400
@@ -0,0 +1,24 @@
+@HD VN:1.4 SO:unknown
+@SQ SN:insert LN:599
+@SQ SN:ref1 LN:45
+@SQ SN:ref2 LN:40
+@SQ SN:ref3 LN:4
+@PG ID:llama
+@RG ID:fish PG:llama
+@RG ID:cow PU:13_&^&&*(:332 PG:donkey
+@RG PU:*9u8jkjjkjd: ID:colt
+@PG ID:bull PP:donkey
+@PG ID:donkey
+@CO Do you know?
+x12 0 ref2 14 30 23M * 0 0 TAATTAAGTCTACAGAGCAACTA ??????????????????????? RG:Z:cow PG:Z:bull AS:i:65100
+x10 0 ref2 10 30 25M * 0 0 CAAATAATTAAGTCTACAGAGCAAC ????????????????????????? RG:Z:cow PG:Z:bull AS:i:0 FI:A:b
+x11 0 ref2 12 30 24M * 0 0 AATAATTAAGTCTACAGAGCAACT ???????????????????????? RG:Z:cow PG:Z:bull FI:Z:a
+x9 0 ref2 6 30 9M4I13M * 0 0 TTATAAAACAAATAATTAAGTCTACA ?????????????????????????? RG:Z:cow PG:Z:bull AS:i:20 FI:i:1
+x8 0 ref2 2 30 21M * 0 0 GGTTTTATAAAACAAATAATT ????????????????????? RG:Z:cow PG:Z:bull AS:i:10 FI:f:1.5
+x7 0 ref2 1 30 20M * 0 0 AGGTTTTATAAAACAAATAA * RG:Z:cow PG:Z:bull AS:i:50 FI:i:2
+r005 83 ref1 37 30 9M = 7 -39 CAGCGCCAT * RG:Z:colt PG:Z:donkey AS:i:100 FI:f:2.5
+r006 16 ref1 29 30 6H5M * 0 0 TAGGC * RG:Z:colt PG:Z:donkey FI:i:3
+r007 0 ref1 16 30 6M14N1I5M * 0 0 ATAGCTCTCAGC * RG:Z:colt PG:Z:donkey AS:i:-5 FI:f:3.5
+r007 0 ref1 9 30 5H6M * 0 0 AGCTAA * RG:Z:colt PG:Z:donkey AS:i:1 FI:i:4
+r006 0 ref1 9 30 1S2I6M1P1I1P1I4M2I * 0 0 AAAAGATAAGGGATAAA * XA:Z:abc XB:i:-10 RG:Z:colt PG:Z:donkey AS:i:20 FI:f:4.5
+r005 163 ref1 7 30 8M4I4M1D3M = 37 39 TTAGATAAAGAGGATACTG * XX:B:S,12561,2,20,112 YY:i:100 RG:Z:colt PG:Z:donkey AS:i:10 FI:i:5
diff -r 000000000000 -r 00d1f08bdcdc test-data/tag.rg.n.sort.expected.sam
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tag.rg.n.sort.expected.sam Wed Sep 19 08:21:51 2018 -0400
@@ -0,0 +1,28 @@
+@HD VN:1.4 SO:unknown
+@SQ SN:insert LN:599
+@SQ SN:ref1 LN:45
+@SQ SN:ref2 LN:40
+@SQ SN:ref3 LN:4
+@RG ID:fish PG:donkey
+@RG ID:cow PU:13_&^&&*(:332
+@RG PU:*9u8jkjjkjd: ID:colt
+@PG ID:bull PP:donkey
+@PG ID:donkey
+@PG ID:moose
+@PG PP:moose ID:cow
+@CO
+r002 0 ref1 9 30 1S2I6M1P1I1P1I4M2I * 0 0 AAAAGATAAGGGATAAA * XA:Z:abc XB:i:-10 PG:Z:colt
+u1 4 * 0 30 23M * 0 0 TAATTAAGTCTACAGAAAAAAAA ???????????????????????
+r004 0 ref1 16 30 6M14N1I5M * 0 0 ATAGCTCTCAGC * RG:Z:colt PG:Z:colt
+x1 0 ref2 1 30 20M * 0 0 AGGTTTTATAAAACAAATAA * RG:Z:colt PG:Z:bull
+x2 0 ref2 2 30 21M * 0 0 GGTTTTATAAAACAAATAATT ????????????????????? RG:Z:colt PG:Z:bull
+r000 99 insert 50 30 10M = 80 30 ATTTAGCTAC AAAAAAAAAA RG:Z:cow PG:Z:bull
+r000 211 insert 80 30 10M = 50 -30 CCCAATCATT AAAAAAAAAA RG:Z:cow PG:Z:bull
+r003 0 ref1 9 30 5H6M * 0 0 AGCTAA * RG:Z:cow
+r003 16 ref1 29 30 6H5M * 0 0 TAGGC * RG:Z:cow PG:Z:colt
+x6 0 ref2 14 30 23M * 0 0 TAATTAAGTCTACAGAGCAACTA ??????????????????????? RG:Z:cow
+r001 83 ref1 37 30 9M = 7 -39 CAGCGCCAT * RG:Z:fish PG:Z:colt
+r001 163 ref1 7 30 8M4I4M1D3M = 37 39 TTAGATAAAGAGGATACTG * XX:B:S,12561,2,20,112 YY:i:100 RG:Z:fish PG:Z:colt
+x3 0 ref2 6 30 9M4I13M * 0 0 TTATAAAACAAATAATTAAGTCTACA ?????????????????????????? RG:Z:fish PG:Z:bull
+x4 0 ref2 10 30 25M * 0 0 CAAATAATTAAGTCTACAGAGCAAC ????????????????????????? RG:Z:fish PG:Z:bull
+x5 0 ref2 12 30 24M * 0 0 AATAATTAAGTCTACAGAGCAACT ???????????????????????? RG:Z:fish PG:Z:bull
diff -r 000000000000 -r 00d1f08bdcdc test-data/tag.rg.sort.expected.sam
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tag.rg.sort.expected.sam Wed Sep 19 08:21:51 2018 -0400
@@ -0,0 +1,28 @@
+@HD VN:1.4 SO:unknown
+@SQ SN:insert LN:599
+@SQ SN:ref1 LN:45
+@SQ SN:ref2 LN:40
+@SQ SN:ref3 LN:4
+@RG ID:fish PG:donkey
+@RG ID:cow PU:13_&^&&*(:332
+@RG PU:*9u8jkjjkjd: ID:colt
+@PG ID:bull PP:donkey
+@PG ID:donkey
+@PG ID:moose
+@PG PP:moose ID:cow
+@CO
+r002 0 ref1 9 30 1S2I6M1P1I1P1I4M2I * 0 0 AAAAGATAAGGGATAAA * XA:Z:abc XB:i:-10 PG:Z:colt
+u1 4 * 0 30 23M * 0 0 TAATTAAGTCTACAGAAAAAAAA ???????????????????????
+r004 0 ref1 16 30 6M14N1I5M * 0 0 ATAGCTCTCAGC * RG:Z:colt PG:Z:colt
+x1 0 ref2 1 30 20M * 0 0 AGGTTTTATAAAACAAATAA * RG:Z:colt PG:Z:bull
+x2 0 ref2 2 30 21M * 0 0 GGTTTTATAAAACAAATAATT ????????????????????? RG:Z:colt PG:Z:bull
+r000 99 insert 50 30 10M = 80 30 ATTTAGCTAC AAAAAAAAAA RG:Z:cow PG:Z:bull
+r000 211 insert 80 30 10M = 50 -30 CCCAATCATT AAAAAAAAAA RG:Z:cow PG:Z:bull
+r003 0 ref1 9 30 5H6M * 0 0 AGCTAA * RG:Z:cow
+r003 16 ref1 29 30 6H5M * 0 0 TAGGC * RG:Z:cow PG:Z:colt
+x6 0 ref2 14 30 23M * 0 0 TAATTAAGTCTACAGAGCAACTA ??????????????????????? RG:Z:cow
+r001 163 ref1 7 30 8M4I4M1D3M = 37 39 TTAGATAAAGAGGATACTG * XX:B:S,12561,2,20,112 YY:i:100 RG:Z:fish PG:Z:colt
+r001 83 ref1 37 30 9M = 7 -39 CAGCGCCAT * RG:Z:fish PG:Z:colt
+x3 0 ref2 6 30 9M4I13M * 0 0 TTATAAAACAAATAATTAAGTCTACA ?????????????????????????? RG:Z:fish PG:Z:bull
+x4 0 ref2 10 30 25M * 0 0 CAAATAATTAAGTCTACAGAGCAAC ????????????????????????? RG:Z:fish PG:Z:bull
+x5 0 ref2 12 30 24M * 0 0 AATAATTAAGTCTACAGAGCAACT ???????????????????????? RG:Z:fish PG:Z:bull
diff -r 000000000000 -r 00d1f08bdcdc test-data/test.bam
Binary file test-data/test.bam has changed
diff -r 000000000000 -r 00d1f08bdcdc test-data/test.cram
Binary file test-data/test.cram has changed
diff -r 000000000000 -r 00d1f08bdcdc test-data/test.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test.fa Wed Sep 19 08:21:51 2018 -0400
@@ -0,0 +1,3 @@
+>CHROMOSOME_I
+gcctaagcctaagcctaagcctaagcctaagcctaagcctaagcctaagc
+ctaagcctaagcctaagcctaagcctaagcctaagcctaagcctaagcct
diff -r 000000000000 -r 00d1f08bdcdc test-data/test.fa.fai
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test.fa.fai Wed Sep 19 08:21:51 2018 -0400
@@ -0,0 +1,1 @@
+CHROMOSOME_I 100 14 50 51
diff -r 000000000000 -r 00d1f08bdcdc test-data/test.sam
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test.sam Wed Sep 19 08:21:51 2018 -0400
@@ -0,0 +1,15 @@
+@HD VN:1.4 SO:unsorted
+@SQ SN:CHROMOSOME_I LN:100
+@RG ID:UNKNOWN SM:UNKNOWN
+@PG ID:bowtie2 PN:bowtie2 VN:2.0.0-beta5
+@PG ID:0 CL:aaaaa/aaa/aaaaa/aaaaaa/aaaaaaaaa/aaa/iuc/package_aaaaaaaaa_x_y/aaaaaaaaaaaa/bin/aaaaaaaaaaaaaaaaa aaaaaaaaaa /aaaa/aaaaa/aaa/aaaaaaaaaaaaaaaaaaa/tools/aaaaaaaaa/test-data/test.cram aa /aaaa/aaaaa/aaa/aaaaaaaaaaaaaaaaaaa/tools/aaaaaaaaa/test-data/test.fa -O test PN:samtools VN:1.2
+SRR065390.14978392 16 CHROMOSOME_I 2 1 27M1D73M * 0 0 CCTAGCCCTAACCCTAACCCTAACCCTAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA #############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC RG:Z:UNKNOWN XG:i:1 XM:i:5 XN:i:0 XO:i:1 AS:i:-18 XS:i:-18 YT:Z:UU
+SRR065390.921023 16 CHROMOSOME_I 3 12 100M * 0 0 CTAAGCCTAAATCTAAGCCTAACCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA ###############################################???88:;98768700000<>:BBA?BBAB?BBBBBBBB>B>BB::;?:00000 RG:Z:UNKNOWN XG:i:0 XM:i:3 XN:i:0 XO:i:0 AS:i:-6 XS:i:-13 YT:Z:UU
+SRR065390.1871511 16 CHROMOSOME_I 3 1 100M * 0 0 CTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA 0:BB@>B<=B@???@=8@B>BB@CA@DACDCBBCCCA@CCCCACCBCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC RG:Z:UNKNOWN XG:i:0 XM:i:0 XN:i:0 XO:i:0 AS:i:0 XS:i:0 YT:Z:UU
+SRR065390.3743423 16 CHROMOSOME_I 3 1 100M * 0 0 CTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA ##################?6@:7<=@3=@ABAAB>BDBBABADABDDDBDDBCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC RG:Z:UNKNOWN XG:i:0 XM:i:0 XN:i:0 XO:i:0 AS:i:0 XS:i:0 YT:Z:UU
+SRR065390.4251890 16 CHROMOSOME_I 3 1 100M * 0 0 CTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA ###########@BB=BCBBC?B>B;>B@@ADBBB@DBBBBDCCBBCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC RG:Z:UNKNOWN XG:i:0 XM:i:0 XN:i:0 XO:i:0 AS:i:0 XS:i:0 YT:Z:UU
+SRR065390.5238868 16 CHROMOSOME_I 3 1 100M * 0 0 CTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA @,=@@D8D;?BBB>;?BBB==BB@D;>D>BBB>BBDDBA@@BCCB@=BACBCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC RG:Z:UNKNOWN XG:i:0 XM:i:0 XN:i:0 XO:i:0 AS:i:0 XS:i:0 YT:Z:UU
+SRR065390.8289592 16 CHROMOSOME_I 3 1 100M * 0 0 CTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA ###############################A?@C9@@BC=AABDD@A@DC@CB=@BA?6@CCAAC@+CCCCCCCCCCCCCCC@CCCCCCCCCCCCCCCC RG:Z:UNKNOWN XG:i:0 XM:i:0 XN:i:0 XO:i:0 AS:i:0 XS:i:0 YT:Z:UU
diff -r 000000000000 -r 00d1f08bdcdc test-data/test2.cram
Binary file test-data/test2.cram has changed
diff -r 000000000000 -r 00d1f08bdcdc test-data/test_input_1_a.bam
Binary file test-data/test_input_1_a.bam has changed
diff -r 000000000000 -r 00d1f08bdcdc tool-data/fasta_indexes.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/fasta_indexes.loc.sample Wed Sep 19 08:21:51 2018 -0400
@@ -0,0 +1,29 @@
+#This is a sample file distributed with Galaxy that enables tools
+#to use a directory of Samtools indexed sequences data files. You will need
+#to create these data files and then create a fasta_indexes.loc file
+#similar to this one (store it in this directory) that points to
+#the directories in which those files are stored. The fasta_indexes.loc
+#file has this format (white space characters are TAB characters):
+#
+#
+#
+#So, for example, if you had hg19 Canonical indexed stored in
+#
+# /depot/data2/galaxy/hg19/sam/,
+#
+#then the fasta_indexes.loc entry would look like this:
+#
+#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa
+#
+#and your /depot/data2/galaxy/hg19/sam/ directory
+#would contain hg19canon.fa and hg19canon.fa.fai files.
+#
+#Your fasta_indexes.loc file should include an entry per line for
+#each index set you have stored. The file in the path does actually
+#exist, but it should never be directly used. Instead, the name serves
+#as a prefix for the index file. For example:
+#
+#hg18canon hg18 Human (Homo sapiens): hg18 Canonical /depot/data2/galaxy/hg18/sam/hg18canon.fa
+#hg18full hg18 Human (Homo sapiens): hg18 Full /depot/data2/galaxy/hg18/sam/hg18full.fa
+#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa
+#hg19full hg19 Human (Homo sapiens): hg19 Full /depot/data2/galaxy/hg19/sam/hg19full.fa
diff -r 000000000000 -r 00d1f08bdcdc tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample Wed Sep 19 08:21:51 2018 -0400
@@ -0,0 +1,7 @@
+
+
+
+ value, dbkey, name, path
+
+
+
diff -r 000000000000 -r 00d1f08bdcdc tool_data_table_conf.xml.test
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.test Wed Sep 19 08:21:51 2018 -0400
@@ -0,0 +1,6 @@
+
+
+ value, dbkey, name, path
+
+
+