# HG changeset patch
# User yhoogstrate
# Date 1446727742 18000
# Node ID 460f0749aac5781df6aed9df528eb0da458e368a
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
diff -r 000000000000 -r 460f0749aac5 README.rst
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/README.rst Thu Nov 05 07:49:02 2015 -0500
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+samtools-parallel-mpileup package for Galaxy
+============================================
+
+https://github.com/yhoogstrate/parallel-mpileup
+
+This wrapper is optimized for faster mpileup generation.
+
+Development
+-----------
+
+* Repository-Maintainer: Youri Hoogstrate
+
+The tool wrapper has been written by Youri Hoogstrate from the Erasmus
+Medical Center (Rotterdam, Netherlands) on behalf of the Translational
+Research IT (TraIT) project:
+
+http://www.ctmm.nl/en/programmas/infrastructuren/traitprojecttranslationeleresearch
+
+More tools by the Translational Research IT (TraIT) project can be found in the following repository:
+
+License
+-------
+
+**samtools-parallel-mpileup**:
+
+MIT License: https://raw.githubusercontent.com/mydatascience/parallel-mpileup/master/samtools-0.1.19/COPYING
+
+ MIT License:
+
+ Copyright (c) 2008-2009 Genome Research Ltd.
+
+ Permission is hereby granted, free of charge, to any person obtaining a copy
+ of this software and associated documentation files (the "Software"), to deal
+ in the Software without restriction, including without limitation the rights
+ to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ copies of the Software, and to permit persons to whom the Software is
+ furnished to do so, subject to the following conditions:
+
+ The above copyright notice and this permission notice shall be included in
+ all copies or substantial portions of the Software.
+
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+ THE SOFTWARE.
+
diff -r 000000000000 -r 460f0749aac5 samtools-parallel-mpileup.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/samtools-parallel-mpileup.xml Thu Nov 05 07:49:02 2015 -0500
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+
+
+ Samtools mpileup (supporting parallelization)
+
+
+ samtools_parallel_mpileup
+ samtools
+
+
+ samtools-parallel-mpileup 2>&1 | grep Version
+
+
+ #if $reference_genome_source.source_select == "attribute" and len({ alignment.metadata.dbkey:True for alignment in $alignments }.keys()) != 1
+ echo "Invalid number of dbkeys are found: ${ len({ alignment.metadata.dbkey:True for alignment in $alignments }.keys()) }, while only one should be used. Make sure that the alignments are done on the same reference genome and that 'tool-data/all_fasta.loc' is configured properly!" >&2
+ #else
+ #if $mpileup_parallelization.mpileup_parallelization_select == "true"
+ samtools-parallel-mpileup mpileup
+ -t $mpileup_parallelization.samtools_threads
+ #else
+ samtools mpileup
+ #end if
+ -f
+ #if $reference_genome_source.source_select == "indexed_filtered"
+ "$reference_genome_source.reference_genome"
+ #else if $reference_genome_source.source_select == "indexed_all"
+ "$reference_genome_source.reference_genome"
+ #else if $reference_genome_source.source_select == "history"
+ "$reference_genome_source.reference_genome"
+ #else
+
+ "${ filter( lambda x: str( x[0] ) == str( { alignment.metadata.dbkey:True for alignment in $alignments }.keys()[0] ), $__app__.tool_data_tables[ 'all_fasta' ].get_fields() )[0][-1] }"
+ #end if
+
+ #if $extended_parameters_regions.samtools_regions == "region"
+ -r $extended_parameters_regions.$samtools_r
+ #elif $extended_parameters_regions.samtools_regions == "regions_file_pos" or $extended_parameters_regions.samtools_regions == "regions_file_bed"
+ -l $extended_parameters_regions.$samtools_l
+ #end if
+
+ #if $extended_parameters.parameters == "extended"
+ $extended_parameters.samtools_6
+ $extended_parameters.samtools_A
+ $extended_parameters.samtools_B
+ -C $extended_parameters.samtools_C
+ -d $extended_parameters.samtools_d
+ $extended_parameters.samtools_E
+ -M $extended_parameters.samtools_M
+ $extended_parameters.samtools_R
+ -q $extended_parameters.samtools_q
+ -Q $extended_parameters.samtools_Q
+
+ -e $extended_parameters.samtools_e
+ -F $extended_parameters.samtools_F
+ -h $extended_parameters.samtools_h
+ $extended_parameters.samtools_I
+ -L $extended_parameters.samtools_L
+ -m $extended_parameters.samtools_m
+ -o $extended_parameters.samtools_o
+ $extended_parameters.samtools_p
+ -P $extended_parameters.samtools_P
+ #end if
+
+ #for $alignment in $alignments
+ ${alignment}
+ #end for
+
+ 2> stderr_1.txt
+
+ #if $sort_mpileup
+ | sort -k1,1V -k2,2g
+ #end if
+
+ > $output ;
+ cat stderr_1.txt
+ #end if
+
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+**Samtools mpileup (supporting parallelization)**
+
+SAM (Sequence Alignment/Map) format is a generic format for storing large nucleotide sequence alignments. SAM aims to be a format that:
+
+Is flexible enough to store all the alignment information generated by various alignment programs;
+Is simple enough to be easily generated by alignment programs or converted from existing alignment formats;
+Is compact in file size;
+Allows most of operations on the alignment to work on a stream without loading the whole alignment into memory;
+Allows the file to be indexed by genomic position to efficiently retrieve all reads aligning to a locus.
+SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.
+
+SAMtools is hosted by SourceForge.net. The project page is http://samtools.sourceforge.net/. The source code releases are available from the download page. You can check out the most recent source code from the github project page with:
+git clone git://github.com/samtools/samtools.git
+https://github.com/mydatascience/parallel-mpileup/
+
+Because samtools does not support parallization of the mpileup command, the project was forked to include paralellization support:
+
+
+However, since the project seems to lack support and contains fatal bugs this project was forked at:
+https://github.com/yhoogstrate/parallel-mpileup/
+
+
+**Input formats**
+
+Satmools accepts sequencing alignments in the same, either SAM or BAM format (http://samtools.sourceforge.net/). The alignment files have to be linked to a reference genome by galaxy. This is indicated under every history item with e.g.: *"database: hg19"* for a link to hg19, or *"database: ?"* if the link is missing.
+
+**Installation**
+
+The installation is fully automatic.
+
+**License**
+
+* parallel-mpileup: MIT License (https://github.com/yhoogstrate/parallel-mpileup/blob/master/samtools-0.1.19/COPYING)
+* samtool: MIT License
+
+
+Contact
+-------
+
+The tool wrapper has been written by Youri Hoogstrate from the Erasmus
+Medical Center (Rotterdam, Netherlands) on behalf of the Translational
+Research IT (TraIT) project:
+
+http://www.ctmm.nl/en/programmas/infrastructuren/traitprojecttranslationeleresearch
+
+More tools by the Translational Research IT (TraIT) project can be found
+in the following toolsheds:
+
+http://toolshed.g2.bx.psu.edu/
+
+http://testtoolshed.g2.bx.psu.edu/
+
+
+
+ @unpublished{samtools_parallel_mpileup,
+ author = {Youri Hoogstrate},
+ title = { Samtools parallel-mpileup, fork of classical samtools },
+ year = 2014,
+ url = { https://github.com/yhoogstrate/parallel-mpileup }
+ }
+
+
+ @misc{SAM_def,
+ title={Definition of SAM/BAM format},
+ url = {https://samtools.github.io/hts-specs/SAMv1.pdf},}
+
+
+ @misc{SamTools_github,
+ title={SAMTools GitHub page},
+ url = {https://github.com/samtools/samtools},}
+
+
+
\ No newline at end of file
diff -r 000000000000 -r 460f0749aac5 test-data/example.bam
Binary file test-data/example.bam has changed
diff -r 000000000000 -r 460f0749aac5 test-data/example.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/example.fa Thu Nov 05 07:49:02 2015 -0500
@@ -0,0 +1,11 @@
+>chr1
+aaataggtcccaaacgttacgcactctatgcctgacaaagttgcgaccacttcctctgcc
+ttgtgtgacacgccggagatagggcatcagcaagtacgttaagtacactgaacgaactgg
+aggtttctacatcgtgcgtgatggctctaggagaagtgggtgtatctgcacagcataagt
+tataagacggaagtaaagcgtcttcaccgttcagcaccccacgctcatagtcaatgctgg
+ttcagcatagtcaagcgccggtggcctccaaaaagacgcactgagtagcttagctacttt
+gctccgcttgcggaagcactaagaggagattgaatttccaaatcccccccgatacctgtg
+cggtcgctacgtaagtgcgaagttctgttagatacgctccccttagtatatgggcgttaa
+tcggaccgtcggtactcactgcattccaggtctcatatagttcgccctagaagcctggga
+tgaacgttgaactatagctgatgtaaaccccgcgtgccaattccaggcgtcatgggggca
+acccctcgcagcctccctcttgctgttggtgcctagtatttcatgatttcgagccgacat
diff -r 000000000000 -r 460f0749aac5 test-data/example.fa.fai
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/example.fa.fai Thu Nov 05 07:49:02 2015 -0500
@@ -0,0 +1,1 @@
+chr1 600 6 60 61
diff -r 000000000000 -r 460f0749aac5 test-data/example.mpileup
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/example.mpileup Thu Nov 05 07:49:02 2015 -0500
@@ -0,0 +1,540 @@
+chr1 1 a 5 ^],^].^],^].^], ~~~~~
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+chr1 208 c 89 .$..,.,..,,..,,..,.....,....,.,,,,,..,..,,...,.,....,,.....,,.,..,.,...,,,.,..,,,,.,,,,,^].^]. ~~~~~~~~~~~~~~~~~~~~~~~ddeeeeexxxx~~~~~~~~~{{{{{{{{{{{{zzzzxxxttteeeeddddO44999>0000==~~~
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+chr1 210 t 91 .$,$.$,..,,..,,..,.....,....,.,,,,,..,..,,...,.,....,,.....,,.,..,.,...,,,.,..,,,,.,,,,,..,,.^]. ~~~~~~~~~~~~~~~~~~~~~ddeeeeexxxx~~~~~~~~~{{{{{{{{{{{{zzzzxxxttteeeedddd```aaaa____^^~~~~~~~
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+chr1 221 a 83 .$.$,,...,.,....,,.....,,.,..,.,...,,,.,..,,,,.,,,,,..,,..,.,.,,...,...,,...,.,,,.,.^], EERRerzzzzz{{{{{{{{{{{{{{{{{{{{{~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1 222 c 82 ,$,$...,.,....,,.....,,.,..,.,...,,,.,..,,,,.,,,,,..,,..,.,.,,...,...,,...,.,,,.,.,^]. DDUUrrrrrsssz{{{{{{{{{{{{{{{{{~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1 223 g 82 .$..,.,....,,.....,,.,..,.,...,,,.,..,,,,.,,,,,..,,..,.,.,,...,...,,...,.,,,.,.,.^],^], EReeeeerrrz{{{{{{{{{{{{{{{{{~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1 224 c 84 .$.,.,....,,.....,,.,..,.,...,,,.,..,,,,.,,,,,..,,..,.,.,,...,...,,...,.,,,.,.,.,,^].^],^], DUUUUUUUUrvzz{{{{{{{{{{{{{{~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1 225 t 86 .$,$.$,$.$...,,.....,,.,..,.,...,,,.,..,,,,.,,,,,..,,..,.,.,,...,...,,...,.,,,.,.,.,,.,,^].^].^], EEEEERRReezz{{{{{{{{{{{{{{~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1 226 c 84 .$.$.$,,.....,,.,..,.,...,,,.,..,,,,.,,,,,..,,..,.,.,,...,...,,...,.,,,.,.,.,,.,,..,^],^].^]. EEEUbttzzzz{{{{{{{{{{~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1 227 a 84 ,$,.....,,.,..,.,...,,,.,..,,,,.,,,,,..,,..,.,.,,...,...,,...,.,,,.,.,.,,.,,..,,..^],^],^]. DUUUsssswww{{{{{{{~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1 228 t 84 ,$.....,,.,..,.,...,,,.,..,,,,.,,,,,..,,..,.,.,,...,...,,...,.,,,.,.,.,,.,,..,,..,,.^], ERReeeeeeezzz{{{{~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1 229 a 87 .$.$...,,.,..,.,...,,,.,..,,,,.,,,,,..,,..,.,.,,...,...,,...,.,,,.,.,.,,.,,..,,..,,.,^].^].^].^], EEUUUUbbbttttttt~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1 230 g 86 .$.$.$,$,.,..,.,...,,,.,..,,,,.,,,,,..,,..,.,.,,...,...,,...,.,,,.,.,.,,.,,..,,..,,.,...,^]. EEEEUUUeeerrrr~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1 231 t 85 ,$.$,$..,.,...,,,.,..,,,,.,,,,,..,,..,.,.,,...,...,,...,.,,,.,.,.,,.,,..,,..,,.,...,.^],^].^], EEEUUUeeeeuuuuu~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1 232 c 84 .$.$,$.,...,,,.,..,,,,.,,,,,..,,..,.,.,,...,...,,...,.,,,.,.,.,,.,,..,,..,,.,...,.,.,^],^], EEEUUUUeeeer~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1 233 a 82 .$,$.$.$.,,,.,..,,,,.,,,,,..,,..,.,.,,...,...,,...,.,,,.,.,.,,.,,..,,..,,.,...,.,.,,,^]. >>>>EEEE_aaeeeeeeee~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1 234 a 82 .$,$,$,$.,..,,,,.,,,,,..,,..,.,.,,...,...,,...,.,,,.,.,.,,.,,..,,..,,.,...,.,.,,,.^],^].^].^], BBBBU__eeeeeeee~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1 235 t 81 .$,..,,,,.,,,,,..,,..,.,.,,...,...,,...,.,,,.,.,.,,.,,..,,..,,.,...,.,.,,,.,..,^],^],^], EQQeeeeeeee~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1 236 g 82 ,$.$.,,,,.,,,,,..,,..,.,.,,...,...,,...,.,,,.,.,.,,.,,..,,..,,.,...,.,.,,,.,..,,,,^].^]. EEUUUbbbbbuu~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1 237 c 83 .$,$,$,,.,,,,,..,,..,.,.,,...,...,,...,.,,,.,.,.,,.,,..,,..,,.,...,.,.,,,.,..,,,,..^].^],^]. EEEUaaaarr~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1 238 t 81 ,$,.,,,,,..,,..,.,.,,...,...,,...,.,,,.,.,.,,.,,..,,..,,.,...,.,.,,,.,..,,,,...,.^]. EUUUUee~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1 239 g 85 ,$.$,$,$,,,..,,..,.,.,,...,...,,...,.,,,.,.,.,,.,,..,,..,,.,...,.,.,,,.,..,,,,...,..^].^].^].^].^], >>>>EE~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1 240 g 83 ,$,$,..,,..,.,.,,...,...,,...,.,,,.,.,.,,.,,..,,..,,.,...,.,.,,,.,..,,,,...,......,^],^]. BB~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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+chr1 481 t 82 ,$..,,..,.,.,,...,...,,...,.,,,.,.,.,,.,,..,,..,,.,...,.,.,,,.,..,,,,...,......,,.^], ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~E
+chr1 482 g 83 .$.$,,..,.,.,,...,...,,...,.,,,.,.,.,,.,,..,,..,,.,...,.,.,,,.,..,,,,...,......,,.,^],^], ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~UEE
+chr1 483 a 84 ,$,$.$.,.,.,,...,...,,...,.,,,.,.,.,,.,,..,,..,,.,...,.,.,,,.,..,,,,...,......,,.,,,^],^].^]. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~`QQBBB
+chr1 484 a 82 .$,.,.,,...,...,,...,.,,,.,.,.,,.,,..,,..,,.,...,.,.,,,.,..,,,,...,......,,.,,,,..^]. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a``EEEE
+chr1 485 c 83 ,$.$,$.,,...,...,,...,.,,,.,.,.,,.,,..,,..,,.,...,.,.,,,.,..,,,,...,......,,.,,,,...^],^], ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~rreeeUEE
+chr1 486 g 81 .$,$,...,...,,...,.,,,.,.,.,,.,,..,,..,,.,...,.,.,,,.,..,,,,...,......,,.,,,,...,,^]. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~uuuuueUUE
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diff -r 000000000000 -r 460f0749aac5 test-data/example.mpileup.parallel
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/example.mpileup.parallel Thu Nov 05 07:49:02 2015 -0500
@@ -0,0 +1,540 @@
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+chr1 192 a 87 .$,$.,,,,,,,,,.,,.,,......,........,,....,.,..,,..,,..,.....,....,.,,,,,..,..,,...,.,.^].^].^]. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ubbaaaaa`EEEEEEEE
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+chr1 205 c 81 .$.$..,,....,.,..,,..,,..,.....,....,.,,,,,..,..,,...,.,....,,.....,,.,..,.,...,,,. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ddeeeeexxxx~~~~~~~~~{{{{{{{{{{{{zzzzxxxttteeeeddddO
+chr1 206 a 79 G$G$ggGGGGgGgGGggGGggGGgGGGGGgGGGGgGgggggGGgGGggGGGgGgGGGGggGGGGGggGgGGgGgGGGgggG ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ddeeeeexxxx~~~~~~~~~{{{{{{{{{{{{zzzzxxxttteeeeddddO
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+chr1 208 c 89 .$..,.,..,,..,,..,.....,....,.,,,,,..,..,,...,.,....,,.....,,.,..,.,...,,,.,..,,,,.,,,,,^].^]. ~~~~~~~~~~~~~~~~~~~~~~~ddeeeeexxxx~~~~~~~~~{{{{{{{{{{{{zzzzxxxttteeeeddddO44999>0000==~~~
+chr1 209 g 91 .$.,.,..,,..,,..,.....,....,.,,,,,..,..,,...,.,....,,.....,,.,..,.,...,,,.,..,,,,.,,,,,..^],^],^]. ~~~~~~~~~~~~~~~~~~~~~~ddeeeeexxxx~~~~~~~~~{{{{{{{{{{{{zzzzxxxttteeeeddddO;;@@@E4444AA~~~~~~
+chr1 210 t 91 .$,$.$,..,,..,,..,.....,....,.,,,,,..,..,,...,.,....,,.....,,.,..,.,...,,,.,..,,,,.,,,,,..,,.^]. ~~~~~~~~~~~~~~~~~~~~~ddeeeeexxxx~~~~~~~~~{{{{{{{{{{{{zzzzxxxttteeeedddd```aaaa____^^~~~~~~~
+chr1 211 t 91 ,$.$.$,$,$.$.,,..,.....,....,.,,,,,..,..,,...,.,....,,.....,,.,..,.,...,,,.,..,,,,.,,,,,..,,..^],^].^], ~~~~~~~~~~~~~~~~~~ddeeeeexxxx~~~~~~~~~{{{{{{{{{{{{zzzzxxxttteeeedddd```aaaa____aa~~~~~~~~~~
+chr1 212 c 87 .$,$,$.$.,.....,....,.,,,,,..,..,,...,.,....,,.....,,.,..,.,...,,,.,..,,,,.,,,,,..,,..,.,^].^], ~~~~~~~~~~~~ddeeeeexxxx~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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+chr1 214 g 81 .$.$,$....,.,,,,,..,..,,...,.,....,,.....,,.,..,.,...,,,.,..,,,,.,,,,,..,,..,.,.,,^].^]. ~~~UUaaaaassxx~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1 215 c 80 .$.$..,.,,,,,..,..,,...,.,....,,.....,,.,..,.,...,,,.,..,,,,.,,,,,..,,..,.,.,,..^].^], CCUUUUUUUeelsszzzz{{{{{{{{{{{{{{{{{{{{{{{{{{{{~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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+chr1 219 c 78 .$.,..,,...,.,....,,.....,,.,..,.,...,,,.,..,,,,.,,,,,..,,..,.,.,,...,...,,..^].^], :AAYYYYerzzzzz{{{{{{{{{{{{{{{{{{{{{~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1 220 c 84 .$,$..,,...,.,....,,.....,,.,..,.,...,,,.,..,,,,.,,,,,..,,..,.,.,,...,...,,...,^].^],^],^],^].^],^]. ??TTTTerzzzzz{{{{{{{{{{{{{{{{{{{{{~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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+chr1 237 c 83 .$,$,$,,.,,,,,..,,..,.,.,,...,...,,...,.,,,.,.,.,,.,,..,,..,,.,...,.,.,,,.,..,,,,..^].^],^]. EEEUaaaarr~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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+chr1 240 g 83 ,$,$,..,,..,.,.,,...,...,,...,.,,,.,.,.,,.,,..,,..,,.,...,.,.,,,.,..,,,,...,......,^],^]. BB~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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+chr1 484 a 82 .$,.,.,,...,...,,...,.,,,.,.,.,,.,,..,,..,,.,...,.,.,,,.,..,,,,...,......,,.,,,,..^]. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~``EEEE
+chr1 485 c 83 ,$.$,$.,,...,...,,...,.,,,.,.,.,,.,,..,,..,,.,...,.,.,,,.,..,,,,...,......,,.,,,,...^],^], ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~rreeeUEE
+chr1 486 g 81 .$,$,...,...,,...,.,,,.,.,.,,.,,..,,..,,.,...,.,.,,,.,..,,,,...,......,,.,,,,...,,^]. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~uuuuueUUE
+chr1 487 t 83 ,$...,...,,...,.,,,.,.,.,,.,,..,,..,,.,...,.,.,,,.,..,,,,...,......,,.,,,,...,,.^],^],^],^], ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~uuuuue``UBBBB
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+chr1 491 a 80 .$.$,,...,.,,,.,.,.,,.,,..,,..,,.,...,.,.,,,.,..,,,,...,......,,.,,,,...,,.,,,,.., ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~eeeee_QQ
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+chr1 494 a 72 .$,$,$,$.$,$.$,.,,.,,..,,..,,.,...,.,.,,,.,..,,,,...,......,,.,,,,...,,.,,,,.., ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~eeeee_QQ
+chr1 495 t 65 g$GggGggGGggGGggGgGGGgGgGgggGgGGggggGGGgGGGGGGggGggggGGGggGggggGGg ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~eeeee_QQ
+chr1 496 a 64 C$ccCccCCccCCccCcCCCcCcCcccCcCCccccCCCcCCCCCCccCccccCCCccCccccCCc ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~eeeee_QQ
+chr1 497 g 63 c$c$CccCCccCCccCcCCCcCcCcccCcCCccccCCCcCCCCCCccCccccCCCccCccccCCc ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~eeeee_QQ
+chr1 498 c 62 .$,$,$..,,..,,.,...,.,.,,,.,..,,,,...,......,,.,,,,...,,.,,,,..,^], ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~eeeee_QQE
+chr1 499 t 74 .$.$,$,..,,.,...,.,.,,,.,..,,,,...,......,,.,,,,...,,.,,,,..,,...,,..,.,..,,^], ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~eeeee_]]___~~}}}TTDDDDUE
+chr1 500 g 72 ,$.$.$,,.,...,.,.,,,.,..,,,,...,......,,.,,,,...,,.,,,,..,,...,,..,.,..,,,^], ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~qqqqqqqqtts~~~~~~~TTTTeUE
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+chr1 502 t 72 ,$...,.,.,,,.,..,,,,...,......,,.,,,,...,,.,,,,..,,...,,..,.,..,,,,.,^],^],^].^], ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~{{{{{{{{{{{{{{{{{{{{{{{{~~~~ttzbbUUEEEE
+chr1 503 g 73 .$.$.$,$.,.,,,.,..,,,,...,......,,.,,,,...,,.,,,,..,,...,,..,.,..,,,,.,,,.,^].^], ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~{{{{{{{{{{{{{{{{{{{{{{{{~~~~vv{eeeePPPPEE
+chr1 504 t 71 .$,.,,,.,..,,,,...,......,,.,,,,...,,.,,,,..,,...,,..,.,..,,,,.,,,.,.,^].^], ~~~~~~~~~~~~~~~~~~~~~~~~~~~~{{{{{{{{{{{{{{{{{{{{{{{{~~~~{{{wwqqUUUUUUEE
+chr1 505 a 71 ,$.$,$,,.,..,,,,...,......,,.,,,,...,,.,,,,..,,...,,..,.,..,,,,.,,,.,.,.,^]. ~~~~~~~~~~~~~~~~~~~~~~~~~~~sssssvzz{{{{{{{{{{{{{{{{~~~~{{{wwqq^^^^]]UUA
+chr1 506 a 72 ,$,$.,..,,,,...,......,,.,,,,...,,.,,,,..,,...,,..,.,..,,,,.,,,.,.,.,.^].^],^],^]. ~~~~~~~~~~~~~~~~~~~~~~~~sssssvzz{{{{{{{{{{{{{{{{~~~~{{{wwqq^^^^]]]]B>>>>
+chr1 507 a 70 .$,..,,,,...,......,,.,,,,...,,.,,,,..,,...,,..,.,..,,,,.,,,.,.,.,..,,. ~~~~~~~~~~~~~~~~~~~~~~sssssvzz{{{{{{{{{{{{{{{{~~~~{{{wwqq^^^^^^__E>>>>
+chr1 508 c 69 ,$.$.$,$,,,...,......,,.,,,,...,,.,,,,..,,...,,..,.,..,,,,.,,,.,.,.,..,,. ~~~~~~~~~~~~~~~~~~~~~sssssvzz{{{{{{{{{{{{{{{{~~~~{{{wwqq^^^^^^__\[[[[
+chr1 509 c 65 ,$,$,$...,......,,.,,,,...,,.,,,,..,,...,,..,.,..,,,,.,,,.,.,.,..,,. ~~~~~~~~~~~~~~~~~sssssvzz{{{{{{{{{{{{{{{{~~~~{{{wwqq^^^^^^__\[[[[
+chr1 510 c 62 .$.$.,......,,.,,,,...,,.,,,,..,,...,,..,.,..,,,,.,,,.,.,.,..,,. ~~~~~~~~~~~~~~sssssvzz{{{{{{{{{{{{{{{{~~~~{{{wwqq^^^^^^__\[[[[
+chr1 511 c 60 .$,$.$.....,,.,,,,...,,.,,,,..,,...,,..,.,..,,,,.,,,.,.,.,..,,. ~~~~~~~~~~~~sssssvzz{{{{{{{{{{{{{{{{~~~~{{{wwqq^^^^^^__\\\\\
+chr1 512 g 57 .$....,,.,,,,...,,.,,,,..,,...,,..,.,..,,,,.,,,.,.,.,..,,. ~~~~~~~~~sssssvzz{{{{{{{{{{{{{{{{~~~~{{{wwvvvvvvvvvvvvvvv
+chr1 513 c 56 .$.$.$.$,$,.,,,,...,,.,,,,..,,...,,..,.,..,,,,.,,,.,.,.,..,,. ~~~~~~~~qqqqqvzz{{{{{{{{{{{{{{{{~~~~{{{wwvvvvvvvvvvvvvvv
+chr1 514 g 51 ,$.$,,,,...,,.,,,,..,,...,,..,.,..,,,,.,,,.,.,.,..,,. ~~~UUooovzz{{{{{{{{{{{{{{{{~~~~{{{wwvvvvvvvvvvvvvvv
+chr1 515 t 49 ,$,,,...,,.,,,,..,,...,,..,.,..,,,,.,,,.,.,.,..,,. ~RReeetzz{{{{{{{{{{{{{{{{~~~~{{{{{{{{{{{{{{{{{{{{
+chr1 516 g 48 ,$,$,...,,.,,,,..,,...,,..,.,..,,,,.,,,.,.,.,..,,. EEUUUett{{{{{{{{{{{{{{{{~~~~{{{{{{{{{{{{{{{{{{{{
+chr1 517 c 46 ,$.$.$.,,.,,,,..,,...,,..,.,..,,,,.,,,.,.,.,..,,. >>>E__aaaaaaaaaaaeerrr~~~~{{{{{{{{{{{{{{{{{{{{
+chr1 518 c 43 .$,,.,,,,..,,...,,..,.,..,,,,.,,,.,.,.,..,,. BUU_aaaaaaaaaaeerrr~~~~{{{{{{{{{{{{{{{{{{{{
+chr1 519 a 42 ,$,$.,,,,..,,...,,..,.,..,,,,.,,,.,.,.,..,,. >>E____aaaaaaeerrr~~~~{{{{{{{{{{{{{{{{{{{{
+chr1 520 a 40 .$,,,,..,,...,,..,.,..,,,,.,,,.,.,.,..,,. BUUUU_aaaaaeerrr~~~~{{{{{{{{{{{{{{{{{{{{
+chr1 521 t 39 ,$,$,$,$..,,...,,..,.,..,,,,.,,,.,.,.,..,,. >>>>E__aaaeerrr~~~~{{{{{{{{{{{{{{{{{{{{
+chr1 522 t 35 .$.,,...,,..,.,..,,,,.,,,.,.,.,..,,. BUUaaaeerrr~~~~{{{{{{{{{{{{{{{{{{{{
+chr1 523 c 34 .$,$,...,,..,.,..,,,,.,,,.,.,.,..,,. >>__aeerrr~~~~{{{{{{{{{{{{{{{{{{{{
+chr1 524 c 32 ,...,,..,.,..,,,,.,,,.,.,.,..,,. UU_eerrr~~~~{{{{{{{{{{{{{{{{{{{{
+chr1 525 a 32 ,$.$..,,..,.,..,,,,.,,,.,.,.,..,,. EEUeerrr~~~~~~~~~~~~~~~~~~~~~~~~
+chr1 526 g 30 .$.,,..,.,..,,,,.,,,.,.,.,..,,. >EE_____eeeez{~~~~~~~~~~~~~~~~
+chr1 527 g 29 .$,$,..,.,..,,,,.,,,.,.,.,..,,. AAUUUUUeeeez{~~~~~~~~~~~~~~~~
+chr1 528 c 27 ,$.$.$,.,..,,,,.,,,.,.,.,..,,. EEERReeeez{~~~~~~~~~~~~~~~~
+chr1 529 g 24 ,$.$,..,,,,.,,,.,.,.,..,,. EEUUbbtz~~~~~~~~~~~~~~~~
+chr1 530 t 22 ,$.$.,,,,.,,,.,.,.,..,,. EEUUee~~~~~~~~~~~~~~~~
+chr1 531 c 20 .$,$,,,.,,,.,.,.,..,,. EEUbu~~~~~~~~~~~~~~~
+chr1 532 a 18 ,$,,.,,,.,.,.,..,,. EUeuu~~~~~~~~~~~~~
+chr1 533 t 17 ,$,.,,,.,.,.,..,,. EUeeuuuu~~~~~~~~~
+chr1 534 g 16 ,$.,,,.,.,.,..,,. >>>>>>>>>EE[[[[[
+chr1 535 g 15 .$,$,,.,.,.,..,,. ;;;;;;;;BBXZZZZ
+chr1 536 g 13 ,$,$.$,$.,.,..,,. 9999::AAXZZZZ
+chr1 537 g 9 .$,$.,..,,. 88??XZZZZ
+chr1 538 g 7 .$,$..,,. >>TZZZZ
+chr1 539 c 5 .$.,,. EUUUU
+chr1 540 a 4 .$,$,$.$ >>>>
diff -r 000000000000 -r 460f0749aac5 test-data/example.sam
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/example.sam Thu Nov 05 07:49:02 2015 -0500
@@ -0,0 +1,610 @@
+@HD VN:1.0 SO:coordinate
+@SQ SN:chr1 LN:600
+read_0.0.0 16 chr1 1 60 35M * 0 0 AAATAGGTCCCAAACGTTACGCAGTCTATGCCTGA *
+read_0.0.1 0 chr1 1 60 35M * 0 0 AAATAGGTCCCAAACGTTACGCAGTCTATGCCTGA *
+read_0.0.2 16 chr1 1 60 35M * 0 0 AAATAGGTCCCAAACGTTACGCAGTCTATGCCTGA *
+read_0.0.3 0 chr1 1 60 35M * 0 0 AAATAGGTCCCAAACGTTACGCAGTCTATGCCTGA *
+read_0.0.4 16 chr1 1 60 35M * 0 0 AAATAGGTCCCAAACGTTACGCAGTCTATGCCTGA *
+read_0.1.0 16 chr1 2 60 35M * 0 0 AATAGGTCCCAAACGTTACGCAGTCTATGCCTGAC *
+read_0.2.0 0 chr1 3 60 35M * 0 0 ATAGGTCCCAAACGTTACGCAGTCTATGCCTGACA *
+read_0.3.0 0 chr1 4 60 35M * 0 0 TAGGTCCCAAACGTTACGCAGTCTATGCCTGACAA *
+read_0.4.0 16 chr1 5 60 35M * 0 0 AGGTCCCAAACGTTACGCAGTCTATGCCTGACAAA *
+read_0.4.1 16 chr1 5 60 35M * 0 0 AGGTCCCAAACGTTACGCAGTCTATGCCTGACAAA *
+read_0.4.2 0 chr1 5 60 35M * 0 0 AGGTCCCAAACGTTACGCAGTCTATGCCTGACAAA *
+read_0.4.3 0 chr1 5 60 35M * 0 0 AGGTCCCAAACGTTACGCAGTCTATGCCTGACAAA *
+read_0.5.0 0 chr1 6 60 35M * 0 0 GGTCCCAAACGTTACGCAGTCTATGCCTGACAAAG *
+read_0.6.0 0 chr1 7 60 35M * 0 0 GTCCCAAACGTTACGCAGTCTATGCCTGACAAAGT *
+read_0.6.1 0 chr1 7 60 35M * 0 0 GTCCCAAACGTTACGCAGTCTATGCCTGACAAAGT *
+read_0.6.2 16 chr1 7 60 35M * 0 0 GTCCCAAACGTTACGCAGTCTATGCCTGACAAAGT *
+read_0.6.3 16 chr1 7 60 35M * 0 0 GTCCCAAACGTTACGCAGTCTATGCCTGACAAAGT *
+read_0.7.0 0 chr1 8 60 35M * 0 0 TCCCAAACGTTACGCAGTCTATGCCTGACAAAGTT *
+read_0.7.1 16 chr1 8 60 35M * 0 0 TCCCAAACGTTACGCAGTCTATGCCTGACAAAGTT *
+read_0.7.2 16 chr1 8 60 35M * 0 0 TCCCAAACGTTACGCAGTCTATGCCTGACAAAGTT *
+read_0.7.3 0 chr1 8 60 35M * 0 0 TCCCAAACGTTACGCAGTCTATGCCTGACAAAGTT *
+read_0.8.0 16 chr1 9 60 35M * 0 0 CCCAAACGTTACGCAGTCTATGCCTGACAAAGTTG *
+read_0.8.1 16 chr1 9 60 35M * 0 0 CCCAAACGTTACGCAGTCTATGCCTGACAAAGTTG *
+read_0.9.0 0 chr1 10 60 35M * 0 0 CCAAACGTTACGCAGTCTATGCCTGACAAAGTTGC *
+read_0.9.1 0 chr1 10 60 35M * 0 0 CCAAACGTTACGCAGTCTATGCCTGACAAAGTTGC *
+read_0.9.2 16 chr1 10 60 35M * 0 0 CCAAACGTTACGCAGTCTATGCCTGACAAAGTTGC *
+read_0.10.0 16 chr1 11 60 35M * 0 0 CAAACGTTACGCAGTCTATGCCTGACAAAGTTGCG *
+read_0.11.0 16 chr1 12 60 35M * 0 0 AAACGTTACGCAGTCTATGCCTGACAAAGTTGCGA *
+read_0.12.0 16 chr1 13 60 35M * 0 0 AACGTTACGCAGTCTATGCCTGACAAAGTTGCGAC *
+read_0.12.1 0 chr1 13 60 35M * 0 0 AACGTTACGCAGTCTATGCCTGACAAAGTTGCGAC *
+read_0.12.2 0 chr1 13 60 35M * 0 0 AACGTTACGCAGTCTATGCCTGACAAAGTTGCGAC *
+read_0.12.3 16 chr1 13 60 35M * 0 0 AACGTTACGCAGTCTATGCCTGACAAAGTTGCGAC *
+read_0.13.0 0 chr1 14 60 35M * 0 0 ACGTTACGCAGTCTATGCCTGACAAAGTTGCGACC *
+read_0.13.1 0 chr1 14 60 35M * 0 0 ACGTTACGCAGTCTATGCCTGACAAAGTTGCGACC *
+read_0.14.0 0 chr1 15 60 35M * 0 0 CGTTACGCAGTCTATGCCTGACAAAGTTGCGACCA *
+read_0.14.1 16 chr1 15 60 35M * 0 0 CGTTACGCAGTCTATGCCTGACAAAGTTGCGACCA *
+read_0.15.0 0 chr1 16 60 35M * 0 0 GTTACGCAGTCTATGCCTGACAAAGTTGCGACCAC *
+read_0.15.1 16 chr1 16 60 35M * 0 0 GTTACGCAGTCTATGCCTGACAAAGTTGCGACCAC *
+read_0.16.0 0 chr1 17 60 35M * 0 0 TTACGCAGTCTATGCCTGACAAAGTTGCGACCACT *
+read_0.16.1 0 chr1 17 60 35M * 0 0 TTACGCAGTCTATGCCTGACAAAGTTGCGACCACT *
+read_0.17.0 0 chr1 18 60 35M * 0 0 TACGCAGTCTATGCCTGACAAAGTTGCGACCACTT *
+read_0.18.0 0 chr1 19 60 35M * 0 0 ACGCAGTCTATGCCTGACAAAGTTGCGACCACTTC *
+read_0.19.0 0 chr1 20 60 35M * 0 0 CGCAGTCTATGCCTGACAAAGTTGCGACCACTTCC *
+read_0.19.1 0 chr1 20 60 35M * 0 0 CGCAGTCTATGCCTGACAAAGTTGCGACCACTTCC *
+read_0.20.0 16 chr1 21 60 35M * 0 0 GCAGTCTATGCCTGACAAAGTTGCGACCACTTCCT *
+read_0.20.1 0 chr1 21 60 35M * 0 0 GCAGTCTATGCCTGACAAAGTTGCGACCACTTCCT *
+read_0.21.0 16 chr1 22 60 35M * 0 0 CAGTCTATGCCTGACAAAGTTGCGACCACTTCCTC *
+read_0.21.1 16 chr1 22 60 35M * 0 0 CAGTCTATGCCTGACAAAGTTGCGACCACTTCCTC *
+read_0.22.0 16 chr1 23 60 35M * 0 0 AGTCTATGCCTGACAAAGTTGCGACCACTTCCTCT *
+read_0.23.0 0 chr1 24 60 35M * 0 0 GTCTATGCCTGACAAAGTTGCGACCACTTCCTCTG *
+read_0.24.0 0 chr1 25 60 35M * 0 0 TCTATGCCTGACAAAGTTGCGACCACTTCCTCTGC *
+read_0.24.1 0 chr1 25 60 35M * 0 0 TCTATGCCTGACAAAGTTGCGACCACTTCCTCTGC *
+read_0.25.0 0 chr1 26 60 35M * 0 0 CTATGCCTGACAAAGTTGCGACCACTTCCTCTGCC *
+read_0.25.1 0 chr1 26 60 35M * 0 0 CTATGCCTGACAAAGTTGCGACCACTTCCTCTGCC *
+read_0.25.2 16 chr1 26 60 35M * 0 0 CTATGCCTGACAAAGTTGCGACCACTTCCTCTGCC *
+read_0.25.3 16 chr1 26 60 35M * 0 0 CTATGCCTGACAAAGTTGCGACCACTTCCTCTGCC *
+read_0.25.4 16 chr1 26 60 35M * 0 0 CTATGCCTGACAAAGTTGCGACCACTTCCTCTGCC *
+read_0.26.0 0 chr1 27 60 34M0N1M * 0 0 TATGCCTGACAAAGTTGCGACCACTTCCTCTGCCT *
+read_0.27.0 0 chr1 28 60 33M0N2M * 0 0 ATGCCTGACAAAGTTGCGACCACTTCCTCTGCCTT *
+read_0.27.1 16 chr1 28 60 33M0N2M * 0 0 ATGCCTGACAAAGTTGCGACCACTTCCTCTGCCTT *
+read_0.27.2 0 chr1 28 60 33M0N2M * 0 0 ATGCCTGACAAAGTTGCGACCACTTCCTCTGCCTT *
+read_0.28.0 16 chr1 29 60 32M0N3M * 0 0 TGCCTGACAAAGTTGCGACCACTTCCTCTGCCTTG *
+read_0.28.1 16 chr1 29 60 32M0N3M * 0 0 TGCCTGACAAAGTTGCGACCACTTCCTCTGCCTTG *
+read_0.29.0 16 chr1 30 60 31M0N4M * 0 0 GCCTGACAAAGTTGCGACCACTTCCTCTGCCTTGT *
+read_0.29.1 0 chr1 30 60 31M0N4M * 0 0 GCCTGACAAAGTTGCGACCACTTCCTCTGCCTTGT *
+read_0.29.2 0 chr1 30 60 31M0N4M * 0 0 GCCTGACAAAGTTGCGACCACTTCCTCTGCCTTGT *
+read_0.30.0 0 chr1 31 60 30M0N5M * 0 0 CCTGACAAAGTTGCGACCACTTCCTCTGCCTTGTG *
+read_0.31.0 16 chr1 32 60 29M0N6M * 0 0 CTGACAAAGTTGCGACCACTTCCTCTGCCTTGTGT *
+read_0.32.0 0 chr1 33 60 28M0N7M * 0 0 TGACAAAGTTGCGACCACTTCCTCTGCCTTGTGTG *
+read_0.33.0 0 chr1 34 60 27M0N8M * 0 0 GACAAAGTTGCGACCACTTCCTCTGCCTTGTGTGA *
+read_0.33.1 0 chr1 34 60 27M0N8M * 0 0 GACAAAGTTGCGACCACTTCCTCTGCCTTGTGTGA *
+read_0.34.0 0 chr1 35 60 26M0N9M * 0 0 ACAAAGTTGCGACCACTTCCTCTGCCTTGTGTGAC *
+read_0.34.1 0 chr1 35 60 26M0N9M * 0 0 ACAAAGTTGCGACCACTTCCTCTGCCTTGTGTGAC *
+read_0.35.0 16 chr1 36 60 25M0N10M * 0 0 CAAAGTTGCGACCACTTCCTCTGCCTTGTGTGACA *
+read_0.35.1 0 chr1 36 60 25M0N10M * 0 0 CAAAGTTGCGACCACTTCCTCTGCCTTGTGTGACA *
+read_0.35.2 16 chr1 36 60 25M0N10M * 0 0 CAAAGTTGCGACCACTTCCTCTGCCTTGTGTGACA *
+read_0.36.0 0 chr1 37 60 24M0N11M * 0 0 AAAGTTGCGACCACTTCCTCTGCCTTGTGTGACAC *
+read_0.36.1 0 chr1 37 60 24M0N11M * 0 0 AAAGTTGCGACCACTTCCTCTGCCTTGTGTGACAC *
+read_0.37.0 16 chr1 38 60 23M0N12M * 0 0 AAGTTGCGACCACTTCCTCTGCCTTGTGTGACACG *
+read_0.37.1 0 chr1 38 60 23M0N12M * 0 0 AAGTTGCGACCACTTCCTCTGCCTTGTGTGACACG *
+read_0.37.2 0 chr1 38 60 23M0N12M * 0 0 AAGTTGCGACCACTTCCTCTGCCTTGTGTGACACG *
+read_0.37.3 16 chr1 38 60 23M0N12M * 0 0 AAGTTGCGACCACTTCCTCTGCCTTGTGTGACACG *
+read_0.37.4 16 chr1 38 60 23M0N12M * 0 0 AAGTTGCGACCACTTCCTCTGCCTTGTGTGACACG *
+read_0.38.0 0 chr1 39 60 22M0N13M * 0 0 AGTTGCGACCACTTCCTCTGCCTTGTGTGACACGC *
+read_0.38.1 16 chr1 39 60 22M0N13M * 0 0 AGTTGCGACCACTTCCTCTGCCTTGTGTGACACGC *
+read_0.38.2 16 chr1 39 60 22M0N13M * 0 0 AGTTGCGACCACTTCCTCTGCCTTGTGTGACACGC *
+read_0.38.3 0 chr1 39 60 22M0N13M * 0 0 AGTTGCGACCACTTCCTCTGCCTTGTGTGACACGC *
+read_0.38.4 16 chr1 39 60 22M0N13M * 0 0 AGTTGCGACCACTTCCTCTGCCTTGTGTGACACGC *
+read_0.39.0 0 chr1 40 60 21M0N14M * 0 0 GTTGCGACCACTTCCTCTGCCTTGTGTGACACGCC *
+read_0.40.0 0 chr1 41 60 20M0N15M * 0 0 TTGCGACCACTTCCTCTGCCTTGTGTGACACGCCG *
+read_0.40.1 16 chr1 41 60 20M0N15M * 0 0 TTGCGACCACTTCCTCTGCCTTGTGTGACACGCCG *
+read_0.41.0 16 chr1 42 60 19M0N16M * 0 0 TGCGACCACTTCCTCTGCCTTGTGTGACACGCCGG *
+read_0.42.0 16 chr1 43 60 18M0N17M * 0 0 GCGACCACTTCCTCTGCCTTGTGTGACACGCCGGA *
+read_0.42.1 0 chr1 43 60 18M0N17M * 0 0 GCGACCACTTCCTCTGCCTTGTGTGACACGCCGGA *
+read_0.43.0 16 chr1 44 60 17M0N18M * 0 0 CGACCACTTCCTCTGCCTTGTGTGACACGCCGGAG *
+read_0.43.1 16 chr1 44 60 17M0N18M * 0 0 CGACCACTTCCTCTGCCTTGTGTGACACGCCGGAG *
+read_0.44.0 0 chr1 45 60 16M0N19M * 0 0 GACCACTTCCTCTGCCTTGTGTGACACGCCGGAGA *
+read_0.45.0 0 chr1 46 60 15M0N20M * 0 0 ACCACTTCCTCTGCCTTGTGTGACACGCCGGAGAT *
+read_0.45.1 0 chr1 46 60 15M0N20M * 0 0 ACCACTTCCTCTGCCTTGTGTGACACGCCGGAGAT *
+read_0.46.0 0 chr1 47 60 14M0N21M * 0 0 CCACTTCCTCTGCCTTGTGTGACACGCCGGAGATA *
+read_0.46.1 16 chr1 47 60 14M0N21M * 0 0 CCACTTCCTCTGCCTTGTGTGACACGCCGGAGATA *
+read_0.46.2 0 chr1 47 60 14M0N21M * 0 0 CCACTTCCTCTGCCTTGTGTGACACGCCGGAGATA *
+read_0.47.0 0 chr1 48 60 13M0N22M * 0 0 CACTTCCTCTGCCTTGTGTGACACGCCGGAGATAG *
+read_0.47.1 0 chr1 48 60 13M0N22M * 0 0 CACTTCCTCTGCCTTGTGTGACACGCCGGAGATAG *
+read_0.48.0 16 chr1 49 60 12M0N23M * 0 0 ACTTCCTCTGCCTTGTGTGACACGCCGGAGATAGG *
+read_0.49.0 0 chr1 50 60 11M0N24M * 0 0 CTTCCTCTGCCTTGTGTGACACGCCGGAGATAGGA *
+read_0.49.1 0 chr1 50 60 11M0N24M * 0 0 CTTCCTCTGCCTTGTGTGACACGCCGGAGATAGGA *
+read_0.50.0 16 chr1 51 60 10M0N25M * 0 0 TTCCTCTGCCTTGTGTGACACGCCGGAGATAGGAC *
+read_0.50.1 0 chr1 51 60 10M0N25M * 0 0 TTCCTCTGCCTTGTGTGACACGCCGGAGATAGGAC *
+read_0.50.2 0 chr1 51 60 10M0N25M * 0 0 TTCCTCTGCCTTGTGTGACACGCCGGAGATAGGAC *
+read_0.51.0 0 chr1 52 60 9M0N26M * 0 0 TCCTCTGCCTTGTGTGACACGCCGGAGATAGGACA *
+read_0.51.1 0 chr1 52 60 9M0N26M * 0 0 TCCTCTGCCTTGTGTGACACGCCGGAGATAGGACA *
+read_0.52.0 0 chr1 53 60 8M0N27M * 0 0 CCTCTGCCTTGTGTGACACGCCGGAGATAGGACAT *
+read_0.53.0 0 chr1 54 60 7M0N28M * 0 0 CTCTGCCTTGTGTGACACGCCGGAGATAGGACATC *
+read_0.53.1 0 chr1 54 60 7M0N28M * 0 0 CTCTGCCTTGTGTGACACGCCGGAGATAGGACATC *
+read_0.54.0 16 chr1 55 60 6M0N29M * 0 0 TCTGCCTTGTGTGACACGCCGGAGATAGGACATCA *
+read_0.54.1 16 chr1 55 60 6M0N29M * 0 0 TCTGCCTTGTGTGACACGCCGGAGATAGGACATCA *
+read_0.54.2 16 chr1 55 60 6M0N29M * 0 0 TCTGCCTTGTGTGACACGCCGGAGATAGGACATCA *
+read_0.55.0 16 chr1 56 60 5M0N30M * 0 0 CTGCCTTGTGTGACACGCCGGAGATAGGACATCAG *
+read_0.56.0 0 chr1 57 60 4M0N31M * 0 0 TGCCTTGTGTGACACGCCGGAGATAGGACATCAGC *
+read_0.56.1 0 chr1 57 60 4M0N31M * 0 0 TGCCTTGTGTGACACGCCGGAGATAGGACATCAGC *
+read_0.57.0 16 chr1 58 60 3M0N32M * 0 0 GCCTTGTGTGACACGCCGGAGATAGGACATCAGCA *
+read_0.58.0 0 chr1 59 60 2M0N33M * 0 0 CCTTGTGTGACACGCCGGAGATAGGACATCAGCAA *
+read_0.59.0 0 chr1 60 60 1M0N34M * 0 0 CTTGTGTGACACGCCGGAGATAGGACATCAGCAAG *
+read_0.59.1 16 chr1 60 60 1M0N34M * 0 0 CTTGTGTGACACGCCGGAGATAGGACATCAGCAAG *
+read_0.59.2 16 chr1 60 60 1M0N34M * 0 0 CTTGTGTGACACGCCGGAGATAGGACATCAGCAAG *
+read_1.60.0 16 chr1 61 60 35M * 0 0 TTGTGTGACACGCCGGAGATAGGACATCAGCAAGT *
+read_1.61.0 0 chr1 62 60 35M * 0 0 TGTGTGACACGCCGGAGATAGGACATCAGCAAGTA *
+read_1.61.1 0 chr1 62 60 35M * 0 0 TGTGTGACACGCCGGAGATAGGACATCAGCAAGTA *
+read_1.62.0 16 chr1 63 60 35M * 0 0 GTGTGACACGCCGGAGATAGGACATCAGCAAGTAC *
+read_1.62.1 16 chr1 63 60 35M * 0 0 GTGTGACACGCCGGAGATAGGACATCAGCAAGTAC *
+read_1.63.0 0 chr1 64 60 35M * 0 0 TGTGACACGCCGGAGATAGGACATCAGCAAGTACG *
+read_1.64.0 16 chr1 65 60 35M * 0 0 GTGACACGCCGGAGATAGGACATCAGCAAGTACGT *
+read_1.65.0 0 chr1 66 60 35M * 0 0 TGACACGCCGGAGATAGGACATCAGCAAGTACGTT *
+read_1.65.1 0 chr1 66 60 35M * 0 0 TGACACGCCGGAGATAGGACATCAGCAAGTACGTT *
+read_1.65.2 16 chr1 66 60 35M * 0 0 TGACACGCCGGAGATAGGACATCAGCAAGTACGTT *
+read_1.65.3 0 chr1 66 60 35M * 0 0 TGACACGCCGGAGATAGGACATCAGCAAGTACGTT *
+read_1.66.0 0 chr1 67 60 35M * 0 0 GACACGCCGGAGATAGGACATCAGCAAGTACGTTA *
+read_1.67.0 16 chr1 68 60 35M * 0 0 ACACGCCGGAGATAGGACATCAGCAAGTACGTTAA *
+read_1.67.1 16 chr1 68 60 35M * 0 0 ACACGCCGGAGATAGGACATCAGCAAGTACGTTAA *
+read_1.68.0 0 chr1 69 60 35M * 0 0 CACGCCGGAGATAGGACATCAGCAAGTACGTTAAG *
+read_1.69.0 0 chr1 70 60 35M * 0 0 ACGCCGGAGATAGGACATCAGCAAGTACGTTAAGT *
+read_1.69.1 0 chr1 70 60 35M * 0 0 ACGCCGGAGATAGGACATCAGCAAGTACGTTAAGT *
+read_1.69.2 16 chr1 70 60 35M * 0 0 ACGCCGGAGATAGGACATCAGCAAGTACGTTAAGT *
+read_1.69.3 16 chr1 70 60 35M * 0 0 ACGCCGGAGATAGGACATCAGCAAGTACGTTAAGT *
+read_1.70.0 16 chr1 71 60 35M * 0 0 CGCCGGAGATAGGACATCAGCAAGTACGTTAAGTA *
+read_1.70.1 16 chr1 71 60 35M * 0 0 CGCCGGAGATAGGACATCAGCAAGTACGTTAAGTA *
+read_1.71.0 0 chr1 72 60 35M * 0 0 GCCGGAGATAGGACATCAGCAAGTACGTTAAGTAC *
+read_1.71.1 0 chr1 72 60 35M * 0 0 GCCGGAGATAGGACATCAGCAAGTACGTTAAGTAC *
+read_1.71.2 16 chr1 72 60 35M * 0 0 GCCGGAGATAGGACATCAGCAAGTACGTTAAGTAC *
+read_1.72.0 16 chr1 73 60 35M * 0 0 CCGGAGATAGGACATCAGCAAGTACGTTAAGTACA *
+read_1.72.1 0 chr1 73 60 35M * 0 0 CCGGAGATAGGACATCAGCAAGTACGTTAAGTACA *
+read_1.72.2 16 chr1 73 60 35M * 0 0 CCGGAGATAGGACATCAGCAAGTACGTTAAGTACA *
+read_1.73.0 0 chr1 74 60 35M * 0 0 CGGAGATAGGACATCAGCAAGTACGTTAAGTACAC *
+read_1.73.1 0 chr1 74 60 35M * 0 0 CGGAGATAGGACATCAGCAAGTACGTTAAGTACAC *
+read_1.74.0 16 chr1 75 60 35M * 0 0 GGAGATAGGACATCAGCAAGTACGTTAAGTACACT *
+read_1.75.0 0 chr1 76 60 35M * 0 0 GAGATAGGACATCAGCAAGTACGTTAAGTACACTG *
+read_1.75.1 16 chr1 76 60 35M * 0 0 GAGATAGGACATCAGCAAGTACGTTAAGTACACTG *
+read_1.76.0 16 chr1 77 60 35M * 0 0 AGATAGGACATCAGCAAGTACGTTAAGTACACTGA *
+read_1.77.0 16 chr1 78 60 35M * 0 0 GATAGGACATCAGCAAGTACGTTAAGTACACTGAA *
+read_1.77.1 0 chr1 78 60 35M * 0 0 GATAGGACATCAGCAAGTACGTTAAGTACACTGAA *
+read_1.77.2 0 chr1 78 60 35M * 0 0 GATAGGACATCAGCAAGTACGTTAAGTACACTGAA *
+read_1.78.0 0 chr1 79 60 35M * 0 0 ATAGGACATCAGCAAGTACGTTAAGTACACTGAAC *
+read_1.79.0 0 chr1 80 60 35M * 0 0 TAGGACATCAGCAAGTACGTTAAGTACACTGAACG *
+read_1.80.0 0 chr1 81 60 35M * 0 0 AGGACATCAGCAAGTACGTTAAGTACACTGAACGA *
+read_1.81.0 0 chr1 82 60 35M * 0 0 GGACATCAGCAAGTACGTTAAGTACACTGAACGAA *
+read_1.81.1 0 chr1 82 60 35M * 0 0 GGACATCAGCAAGTACGTTAAGTACACTGAACGAA *
+read_1.81.2 0 chr1 82 60 35M * 0 0 GGACATCAGCAAGTACGTTAAGTACACTGAACGAA *
+read_1.82.0 16 chr1 83 60 35M * 0 0 GACATCAGCAAGTACGTTAAGTACACTGAACGAAC *
+read_1.82.1 16 chr1 83 60 35M * 0 0 GACATCAGCAAGTACGTTAAGTACACTGAACGAAC *
+read_1.82.2 16 chr1 83 60 35M * 0 0 GACATCAGCAAGTACGTTAAGTACACTGAACGAAC *
+read_1.83.0 16 chr1 84 60 35M * 0 0 ACATCAGCAAGTACGTTAAGTACACTGAACGAACT *
+read_1.83.1 0 chr1 84 60 35M * 0 0 ACATCAGCAAGTACGTTAAGTACACTGAACGAACT *
+read_1.83.2 16 chr1 84 60 35M * 0 0 ACATCAGCAAGTACGTTAAGTACACTGAACGAACT *
+read_1.83.3 16 chr1 84 60 35M * 0 0 ACATCAGCAAGTACGTTAAGTACACTGAACGAACT *
+read_1.84.0 0 chr1 85 60 35M * 0 0 CATCAGCAAGTACGTTAAGTACACTGAACGAACTG *
+read_1.84.1 0 chr1 85 60 35M * 0 0 CATCAGCAAGTACGTTAAGTACACTGAACGAACTG *
+read_1.85.0 16 chr1 86 60 35M * 0 0 ATCAGCAAGTACGTTAAGTACACTGAACGAACTGG *
+read_1.85.1 0 chr1 86 60 35M * 0 0 ATCAGCAAGTACGTTAAGTACACTGAACGAACTGG *
+read_1.85.2 16 chr1 86 60 35M * 0 0 ATCAGCAAGTACGTTAAGTACACTGAACGAACTGG *
+read_1.85.3 16 chr1 86 60 35M * 0 0 ATCAGCAAGTACGTTAAGTACACTGAACGAACTGG *
+read_1.86.0 16 chr1 87 60 34M0N1M * 0 0 TCAGCAAGTACGTTAAGTACACTGAACGAACTGGA *
+read_1.87.0 16 chr1 88 60 33M0N2M * 0 0 CAGCAAGTACGTTAAGTACACTGAACGAACTGGAG *
+read_1.87.1 0 chr1 88 60 33M0N2M * 0 0 CAGCAAGTACGTTAAGTACACTGAACGAACTGGAG *
+read_1.88.0 0 chr1 89 60 32M0N3M * 0 0 AGCAAGTACGTTAAGTACACTGAACGAACTGGAGG *
+read_1.88.1 0 chr1 89 60 32M0N3M * 0 0 AGCAAGTACGTTAAGTACACTGAACGAACTGGAGG *
+read_1.88.2 16 chr1 89 60 32M0N3M * 0 0 AGCAAGTACGTTAAGTACACTGAACGAACTGGAGG *
+read_1.88.3 16 chr1 89 60 32M0N3M * 0 0 AGCAAGTACGTTAAGTACACTGAACGAACTGGAGG *
+read_1.88.4 0 chr1 89 60 32M0N3M * 0 0 AGCAAGTACGTTAAGTACACTGAACGAACTGGAGG *
+read_1.89.0 16 chr1 90 60 31M0N4M * 0 0 GCAAGTACGTTAAGTACACTGAACGAACTGGAGGT *
+read_1.89.1 16 chr1 90 60 31M0N4M * 0 0 GCAAGTACGTTAAGTACACTGAACGAACTGGAGGT *
+read_1.90.0 16 chr1 91 60 30M0N5M * 0 0 CAAGTACGTTAAGTACACTGAACGAACTGGAGGTT *
+read_1.90.1 16 chr1 91 60 30M0N5M * 0 0 CAAGTACGTTAAGTACACTGAACGAACTGGAGGTT *
+read_1.90.2 0 chr1 91 60 30M0N5M * 0 0 CAAGTACGTTAAGTACACTGAACGAACTGGAGGTT *
+read_1.91.0 0 chr1 92 60 29M0N6M * 0 0 AAGTACGTTAAGTACACTGAACGAACTGGAGGTTT *
+read_1.91.1 0 chr1 92 60 29M0N6M * 0 0 AAGTACGTTAAGTACACTGAACGAACTGGAGGTTT *
+read_1.92.0 0 chr1 93 60 28M0N7M * 0 0 AGTACGTTAAGTACACTGAACGAACTGGAGGTTTC *
+read_1.92.1 0 chr1 93 60 28M0N7M * 0 0 AGTACGTTAAGTACACTGAACGAACTGGAGGTTTC *
+read_1.92.2 0 chr1 93 60 28M0N7M * 0 0 AGTACGTTAAGTACACTGAACGAACTGGAGGTTTC *
+read_1.93.0 0 chr1 94 60 27M0N8M * 0 0 GTACGTTAAGTACACTGAACGAACTGGAGGTTTCT *
+read_1.93.1 16 chr1 94 60 27M0N8M * 0 0 GTACGTTAAGTACACTGAACGAACTGGAGGTTTCT *
+read_1.94.0 0 chr1 95 60 26M0N9M * 0 0 TACGTTAAGTACACTGAACGAACTGGAGGTTTCTA *
+read_1.94.1 0 chr1 95 60 26M0N9M * 0 0 TACGTTAAGTACACTGAACGAACTGGAGGTTTCTA *
+read_1.94.2 16 chr1 95 60 26M0N9M * 0 0 TACGTTAAGTACACTGAACGAACTGGAGGTTTCTA *
+read_1.94.3 0 chr1 95 60 26M0N9M * 0 0 TACGTTAAGTACACTGAACGAACTGGAGGTTTCTA *
+read_1.95.0 0 chr1 96 60 25M0N10M * 0 0 ACGTTAAGTACACTGAACGAACTGGAGGTTTCTAC *
+read_1.96.0 0 chr1 97 60 24M0N11M * 0 0 CGTTAAGTACACTGAACGAACTGGAGGTTTCTACA *
+read_1.96.1 16 chr1 97 60 24M0N11M * 0 0 CGTTAAGTACACTGAACGAACTGGAGGTTTCTACA *
+read_1.97.0 16 chr1 98 60 23M0N12M * 0 0 GTTAAGTACACTGAACGAACTGGAGGTTTCTACAT *
+read_1.98.0 0 chr1 99 60 22M0N13M * 0 0 TTAAGTACACTGAACGAACTGGAGGTTTCTACATC *
+read_1.99.0 0 chr1 100 60 21M0N14M * 0 0 TAAGTACACTGAACGAACTGGAGGTTTCTACATCG *
+read_1.100.0 16 chr1 101 60 20M0N15M * 0 0 AAGTACACTGAACGAACTGGAGGTTTCTACATCGT *
+read_1.100.1 16 chr1 101 60 20M0N15M * 0 0 AAGTACACTGAACGAACTGGAGGTTTCTACATCGT *
+read_1.100.2 16 chr1 101 60 20M0N15M * 0 0 AAGTACACTGAACGAACTGGAGGTTTCTACATCGT *
+read_1.100.3 16 chr1 101 60 20M0N15M * 0 0 AAGTACACTGAACGAACTGGAGGTTTCTACATCGT *
+read_1.100.4 0 chr1 101 60 20M0N15M * 0 0 AAGTACACTGAACGAACTGGAGGTTTCTACATCGT *
+read_1.101.0 16 chr1 102 60 19M0N16M * 0 0 AGTACACTGAACGAACTGGAGGTTTCTACATCGTG *
+read_1.102.0 16 chr1 103 60 18M0N17M * 0 0 GTACACTGAACGAACTGGAGGTTTCTACATCGTGC *
+read_1.102.1 16 chr1 103 60 18M0N17M * 0 0 GTACACTGAACGAACTGGAGGTTTCTACATCGTGC *
+read_1.102.2 0 chr1 103 60 18M0N17M * 0 0 GTACACTGAACGAACTGGAGGTTTCTACATCGTGC *
+read_1.103.0 16 chr1 104 60 17M0N18M * 0 0 TACACTGAACGAACTGGAGGTTTCTACATCGTGCG *
+read_1.103.1 0 chr1 104 60 17M0N18M * 0 0 TACACTGAACGAACTGGAGGTTTCTACATCGTGCG *
+read_1.104.0 16 chr1 105 60 16M0N19M * 0 0 ACACTGAACGAACTGGAGGTTTCTACATCGTGCGT *
+read_1.104.1 0 chr1 105 60 16M0N19M * 0 0 ACACTGAACGAACTGGAGGTTTCTACATCGTGCGT *
+read_1.104.2 16 chr1 105 60 16M0N19M * 0 0 ACACTGAACGAACTGGAGGTTTCTACATCGTGCGT *
+read_1.105.0 0 chr1 106 60 15M0N20M * 0 0 CACTGAACGAACTGGAGGTTTCTACATCGTGCGTG *
+read_1.105.1 16 chr1 106 60 15M0N20M * 0 0 CACTGAACGAACTGGAGGTTTCTACATCGTGCGTG *
+read_1.105.2 16 chr1 106 60 15M0N20M * 0 0 CACTGAACGAACTGGAGGTTTCTACATCGTGCGTG *
+read_1.106.0 16 chr1 107 60 14M0N21M * 0 0 ACTGAACGAACTGGAGGTTTCTACATCGTGCGTGA *
+read_1.107.0 16 chr1 108 60 13M0N22M * 0 0 CTGAACGAACTGGAGGTTTCTACATCGTGCGTGAT *
+read_1.108.0 0 chr1 109 60 12M0N23M * 0 0 TGAACGAACTGGAGGTTTCTACATCGTGCGTGATG *
+read_1.108.1 0 chr1 109 60 12M0N23M * 0 0 TGAACGAACTGGAGGTTTCTACATCGTGCGTGATG *
+read_1.109.0 16 chr1 110 60 11M0N24M * 0 0 GAACGAACTGGAGGTTTCTACATCGTGCGTGATGG *
+read_1.109.1 0 chr1 110 60 11M0N24M * 0 0 GAACGAACTGGAGGTTTCTACATCGTGCGTGATGG *
+read_1.109.2 16 chr1 110 60 11M0N24M * 0 0 GAACGAACTGGAGGTTTCTACATCGTGCGTGATGG *
+read_1.110.0 16 chr1 111 60 10M0N25M * 0 0 AACGAACTGGAGGTTTCTACATCGTGCGTGATGGC *
+read_1.110.1 16 chr1 111 60 10M0N25M * 0 0 AACGAACTGGAGGTTTCTACATCGTGCGTGATGGC *
+read_1.111.0 0 chr1 112 60 9M0N26M * 0 0 ACGAACTGGAGGTTTCTACATCGTGCGTGATGGCC *
+read_1.111.1 0 chr1 112 60 9M0N26M * 0 0 ACGAACTGGAGGTTTCTACATCGTGCGTGATGGCC *
+read_1.111.2 16 chr1 112 60 9M0N26M * 0 0 ACGAACTGGAGGTTTCTACATCGTGCGTGATGGCC *
+read_1.111.3 16 chr1 112 60 9M0N26M * 0 0 ACGAACTGGAGGTTTCTACATCGTGCGTGATGGCC *
+read_1.111.4 16 chr1 112 60 9M0N26M * 0 0 ACGAACTGGAGGTTTCTACATCGTGCGTGATGGCC *
+read_1.111.5 0 chr1 112 60 9M0N26M * 0 0 ACGAACTGGAGGTTTCTACATCGTGCGTGATGGCC *
+read_1.111.6 0 chr1 112 60 9M0N26M * 0 0 ACGAACTGGAGGTTTCTACATCGTGCGTGATGGCC *
+read_1.112.0 16 chr1 113 60 8M0N27M * 0 0 CGAACTGGAGGTTTCTACATCGTGCGTGATGGCCC *
+read_1.113.0 16 chr1 114 60 7M0N28M * 0 0 GAACTGGAGGTTTCTACATCGTGCGTGATGGCCCT *
+read_1.113.1 16 chr1 114 60 7M0N28M * 0 0 GAACTGGAGGTTTCTACATCGTGCGTGATGGCCCT *
+read_1.114.0 0 chr1 115 60 6M0N29M * 0 0 AACTGGAGGTTTCTACATCGTGCGTGATGGCCCTA *
+read_1.114.1 0 chr1 115 60 6M0N29M * 0 0 AACTGGAGGTTTCTACATCGTGCGTGATGGCCCTA *
+read_1.114.2 16 chr1 115 60 6M0N29M * 0 0 AACTGGAGGTTTCTACATCGTGCGTGATGGCCCTA *
+read_1.114.3 0 chr1 115 60 6M0N29M * 0 0 AACTGGAGGTTTCTACATCGTGCGTGATGGCCCTA *
+read_1.114.4 16 chr1 115 60 6M0N29M * 0 0 AACTGGAGGTTTCTACATCGTGCGTGATGGCCCTA *
+read_1.115.0 16 chr1 116 60 5M0N30M * 0 0 ACTGGAGGTTTCTACATCGTGCGTGATGGCCCTAG *
+read_1.116.0 0 chr1 117 60 4M0N31M * 0 0 CTGGAGGTTTCTACATCGTGCGTGATGGCCCTAGG *
+read_1.117.0 0 chr1 118 60 3M0N32M * 0 0 TGGAGGTTTCTACATCGTGCGTGATGGCCCTAGGA *
+read_1.117.1 0 chr1 118 60 3M0N32M * 0 0 TGGAGGTTTCTACATCGTGCGTGATGGCCCTAGGA *
+read_1.118.0 0 chr1 119 60 2M0N33M * 0 0 GGAGGTTTCTACATCGTGCGTGATGGCCCTAGGAG *
+read_1.118.1 16 chr1 119 60 2M0N33M * 0 0 GGAGGTTTCTACATCGTGCGTGATGGCCCTAGGAG *
+read_1.119.0 0 chr1 120 60 1M0N34M * 0 0 GAGGTTTCTACATCGTGCGTGATGGCCCTAGGAGA *
+read_1.119.1 0 chr1 120 60 1M0N34M * 0 0 GAGGTTTCTACATCGTGCGTGATGGCCCTAGGAGA *
+read_1.119.2 16 chr1 120 60 1M0N34M * 0 0 GAGGTTTCTACATCGTGCGTGATGGCCCTAGGAGA *
+read_2.120.0 16 chr1 121 60 35M * 0 0 AGGTTTCTACATCGTGCGTGATGGCCCTAGGAGAA *
+read_2.121.0 16 chr1 122 60 35M * 0 0 GGTTTCTACATCGTGCGTGATGGCCCTAGGAGAAG *
+read_2.121.1 16 chr1 122 60 35M * 0 0 GGTTTCTACATCGTGCGTGATGGCCCTAGGAGAAG *
+read_2.121.2 0 chr1 122 60 35M * 0 0 GGTTTCTACATCGTGCGTGATGGCCCTAGGAGAAG *
+read_2.121.3 0 chr1 122 60 35M * 0 0 GGTTTCTACATCGTGCGTGATGGCCCTAGGAGAAG *
+read_2.121.4 0 chr1 122 60 35M * 0 0 GGTTTCTACATCGTGCGTGATGGCCCTAGGAGAAG *
+read_2.121.5 0 chr1 122 60 35M * 0 0 GGTTTCTACATCGTGCGTGATGGCCCTAGGAGAAG *
+read_2.122.0 0 chr1 123 60 35M * 0 0 GTTTCTACATCGTGCGTGATGGCCCTAGGAGAAGT *
+read_2.122.1 0 chr1 123 60 35M * 0 0 GTTTCTACATCGTGCGTGATGGCCCTAGGAGAAGT *
+read_2.122.2 0 chr1 123 60 35M * 0 0 GTTTCTACATCGTGCGTGATGGCCCTAGGAGAAGT *
+read_2.123.0 0 chr1 124 60 35M * 0 0 TTTCTACATCGTGCGTGATGGCCCTAGGAGAAGTG *
+read_2.123.1 0 chr1 124 60 35M * 0 0 TTTCTACATCGTGCGTGATGGCCCTAGGAGAAGTG *
+read_2.124.0 16 chr1 125 60 35M * 0 0 TTCTACATCGTGCGTGATGGCCCTAGGAGAAGTGG *
+read_2.124.1 0 chr1 125 60 35M * 0 0 TTCTACATCGTGCGTGATGGCCCTAGGAGAAGTGG *
+read_2.124.2 16 chr1 125 60 35M * 0 0 TTCTACATCGTGCGTGATGGCCCTAGGAGAAGTGG *
+read_2.125.0 0 chr1 126 60 35M * 0 0 TCTACATCGTGCGTGATGGCCCTAGGAGAAGTGGG *
+read_2.126.0 0 chr1 127 60 35M * 0 0 CTACATCGTGCGTGATGGCCCTAGGAGAAGTGGGT *
+read_2.126.1 0 chr1 127 60 35M * 0 0 CTACATCGTGCGTGATGGCCCTAGGAGAAGTGGGT *
+read_2.126.2 0 chr1 127 60 35M * 0 0 CTACATCGTGCGTGATGGCCCTAGGAGAAGTGGGT *
+read_2.127.0 0 chr1 128 60 35M * 0 0 TACATCGTGCGTGATGGCCCTAGGAGAAGTGGGTG *
+read_2.127.1 16 chr1 128 60 35M * 0 0 TACATCGTGCGTGATGGCCCTAGGAGAAGTGGGTG *
+read_2.128.0 16 chr1 129 60 35M * 0 0 ACATCGTGCGTGATGGCCCTAGGAGAAGTGGGTGT *
+read_2.128.1 0 chr1 129 60 35M * 0 0 ACATCGTGCGTGATGGCCCTAGGAGAAGTGGGTGT *
+read_2.128.2 0 chr1 129 60 35M * 0 0 ACATCGTGCGTGATGGCCCTAGGAGAAGTGGGTGT *
+read_2.129.0 0 chr1 130 60 35M * 0 0 CATCGTGCGTGATGGCCCTAGGAGAAGTGGGTGTA *
+read_2.129.1 0 chr1 130 60 35M * 0 0 CATCGTGCGTGATGGCCCTAGGAGAAGTGGGTGTA *
+read_2.129.2 0 chr1 130 60 35M * 0 0 CATCGTGCGTGATGGCCCTAGGAGAAGTGGGTGTA *
+read_2.130.0 0 chr1 131 60 35M * 0 0 ATCGTGCGTGATGGCCCTAGGAGAAGTGGGTGTAT *
+read_2.130.1 0 chr1 131 60 35M * 0 0 ATCGTGCGTGATGGCCCTAGGAGAAGTGGGTGTAT *
+read_2.130.2 0 chr1 131 60 35M * 0 0 ATCGTGCGTGATGGCCCTAGGAGAAGTGGGTGTAT *
+read_2.131.0 16 chr1 132 60 35M * 0 0 TCGTGCGTGATGGCCCTAGGAGAAGTGGGTGTATC *
+read_2.132.0 0 chr1 133 60 35M * 0 0 CGTGCGTGATGGCCCTAGGAGAAGTGGGTGTATCT *
+read_2.132.1 0 chr1 133 60 35M * 0 0 CGTGCGTGATGGCCCTAGGAGAAGTGGGTGTATCT *
+read_2.132.2 0 chr1 133 60 35M * 0 0 CGTGCGTGATGGCCCTAGGAGAAGTGGGTGTATCT *
+read_2.133.0 0 chr1 134 60 35M * 0 0 GTGCGTGATGGCCCTAGGAGAAGTGGGTGTATCTG *
+read_2.133.1 16 chr1 134 60 35M * 0 0 GTGCGTGATGGCCCTAGGAGAAGTGGGTGTATCTG *
+read_2.134.0 16 chr1 135 60 35M * 0 0 TGCGTGATGGCCCTAGGAGAAGTGGGTGTATCTGC *
+read_2.134.1 16 chr1 135 60 35M * 0 0 TGCGTGATGGCCCTAGGAGAAGTGGGTGTATCTGC *
+read_2.134.2 0 chr1 135 60 35M * 0 0 TGCGTGATGGCCCTAGGAGAAGTGGGTGTATCTGC *
+read_2.135.0 0 chr1 136 60 35M * 0 0 GCGTGATGGCCCTAGGAGAAGTGGGTGTATCTGCA *
+read_2.135.1 16 chr1 136 60 35M * 0 0 GCGTGATGGCCCTAGGAGAAGTGGGTGTATCTGCA *
+read_2.135.2 0 chr1 136 60 35M * 0 0 GCGTGATGGCCCTAGGAGAAGTGGGTGTATCTGCA *
+read_2.136.0 16 chr1 137 60 35M * 0 0 CGTGATGGCCCTAGGAGAAGTGGGTGTATCTGCAC *
+read_2.136.1 0 chr1 137 60 35M * 0 0 CGTGATGGCCCTAGGAGAAGTGGGTGTATCTGCAC *
+read_2.137.0 0 chr1 138 60 35M * 0 0 GTGATGGCCCTAGGAGAAGTGGGTGTATCTGCACA *
+read_2.137.1 16 chr1 138 60 35M * 0 0 GTGATGGCCCTAGGAGAAGTGGGTGTATCTGCACA *
+read_2.137.2 0 chr1 138 60 35M * 0 0 GTGATGGCCCTAGGAGAAGTGGGTGTATCTGCACA *
+read_2.138.0 16 chr1 139 60 35M * 0 0 TGATGGCCCTAGGAGAAGTGGGTGTATCTGCACAG *
+read_2.139.0 0 chr1 140 60 35M * 0 0 GATGGCCCTAGGAGAAGTGGGTGTATCTGCACAGC *
+read_2.139.1 16 chr1 140 60 35M * 0 0 GATGGCCCTAGGAGAAGTGGGTGTATCTGCACAGC *
+read_2.139.2 16 chr1 140 60 35M * 0 0 GATGGCCCTAGGAGAAGTGGGTGTATCTGCACAGC *
+read_2.140.0 16 chr1 141 60 35M * 0 0 ATGGCCCTAGGAGAAGTGGGTGTATCTGCACAGCA *
+read_2.141.0 16 chr1 142 60 35M * 0 0 TGGCCCTAGGAGAAGTGGGTGTATCTGCACAGCAT *
+read_2.141.1 0 chr1 142 60 35M * 0 0 TGGCCCTAGGAGAAGTGGGTGTATCTGCACAGCAT *
+read_2.142.0 16 chr1 143 60 35M * 0 0 GGCCCTAGGAGAAGTGGGTGTATCTGCACAGCATA *
+read_2.142.1 0 chr1 143 60 35M * 0 0 GGCCCTAGGAGAAGTGGGTGTATCTGCACAGCATA *
+read_2.142.2 16 chr1 143 60 35M * 0 0 GGCCCTAGGAGAAGTGGGTGTATCTGCACAGCATA *
+read_2.143.0 0 chr1 144 60 35M * 0 0 GCCCTAGGAGAAGTGGGTGTATCTGCACAGCATAA *
+read_2.144.0 0 chr1 145 60 35M * 0 0 CCCTAGGAGAAGTGGGTGTATCTGCACAGCATAAG *
+read_2.144.1 0 chr1 145 60 35M * 0 0 CCCTAGGAGAAGTGGGTGTATCTGCACAGCATAAG *
+read_2.145.0 16 chr1 146 60 35M * 0 0 CCTAGGAGAAGTGGGTGTATCTGCACAGCATAAGT *
+read_2.146.0 16 chr1 147 60 34M0N1M * 0 0 CTAGGAGAAGTGGGTGTATCTGCACAGCATAAGTT *
+read_2.146.1 16 chr1 147 60 34M0N1M * 0 0 CTAGGAGAAGTGGGTGTATCTGCACAGCATAAGTT *
+read_2.146.2 16 chr1 147 60 34M0N1M * 0 0 CTAGGAGAAGTGGGTGTATCTGCACAGCATAAGTT *
+read_2.146.3 0 chr1 147 60 34M0N1M * 0 0 CTAGGAGAAGTGGGTGTATCTGCACAGCATAAGTT *
+read_2.147.0 0 chr1 148 60 33M0N2M * 0 0 TAGGAGAAGTGGGTGTATCTGCACAGCATAAGTTA *
+read_2.147.1 0 chr1 148 60 33M0N2M * 0 0 TAGGAGAAGTGGGTGTATCTGCACAGCATAAGTTA *
+read_2.147.2 16 chr1 148 60 33M0N2M * 0 0 TAGGAGAAGTGGGTGTATCTGCACAGCATAAGTTA *
+read_2.147.3 0 chr1 148 60 33M0N2M * 0 0 TAGGAGAAGTGGGTGTATCTGCACAGCATAAGTTA *
+read_2.148.0 0 chr1 149 60 32M0N3M * 0 0 AGGAGAAGTGGGTGTATCTGCACAGCATAAGTTAT *
+read_2.148.1 0 chr1 149 60 32M0N3M * 0 0 AGGAGAAGTGGGTGTATCTGCACAGCATAAGTTAT *
+read_2.148.2 0 chr1 149 60 32M0N3M * 0 0 AGGAGAAGTGGGTGTATCTGCACAGCATAAGTTAT *
+read_2.149.0 16 chr1 150 60 31M0N4M * 0 0 GGAGAAGTGGGTGTATCTGCACAGCATAAGTTATA *
+read_2.149.1 16 chr1 150 60 31M0N4M * 0 0 GGAGAAGTGGGTGTATCTGCACAGCATAAGTTATA *
+read_2.149.2 16 chr1 150 60 31M0N4M * 0 0 GGAGAAGTGGGTGTATCTGCACAGCATAAGTTATA *
+read_2.149.3 0 chr1 150 60 31M0N4M * 0 0 GGAGAAGTGGGTGTATCTGCACAGCATAAGTTATA *
+read_2.149.4 16 chr1 150 60 31M0N4M * 0 0 GGAGAAGTGGGTGTATCTGCACAGCATAAGTTATA *
+read_2.149.5 16 chr1 150 60 31M0N4M * 0 0 GGAGAAGTGGGTGTATCTGCACAGCATAAGTTATA *
+read_2.149.6 0 chr1 150 60 31M0N4M * 0 0 GGAGAAGTGGGTGTATCTGCACAGCATAAGTTATA *
+read_2.149.7 16 chr1 150 60 31M0N4M * 0 0 GGAGAAGTGGGTGTATCTGCACAGCATAAGTTATA *
+read_2.149.8 16 chr1 150 60 31M0N4M * 0 0 GGAGAAGTGGGTGTATCTGCACAGCATAAGTTATA *
+read_2.149.9 0 chr1 150 60 31M0N4M * 0 0 GGAGAAGTGGGTGTATCTGCACAGCATAAGTTATA *
+read_2.150.0 0 chr1 151 60 30M0N5M * 0 0 GAGAAGTGGGTGTATCTGCACAGCATAAGTTATAA *
+read_2.150.1 0 chr1 151 60 30M0N5M * 0 0 GAGAAGTGGGTGTATCTGCACAGCATAAGTTATAA *
+read_2.150.2 0 chr1 151 60 30M0N5M * 0 0 GAGAAGTGGGTGTATCTGCACAGCATAAGTTATAA *
+read_2.151.0 16 chr1 152 60 29M0N6M * 0 0 AGAAGTGGGTGTATCTGCACAGCATAAGTTATAAG *
+read_2.151.1 0 chr1 152 60 29M0N6M * 0 0 AGAAGTGGGTGTATCTGCACAGCATAAGTTATAAG *
+read_2.151.2 0 chr1 152 60 29M0N6M * 0 0 AGAAGTGGGTGTATCTGCACAGCATAAGTTATAAG *
+read_2.152.0 16 chr1 153 60 28M0N7M * 0 0 GAAGTGGGTGTATCTGCACAGCATAAGTTATAAGA *
+read_2.152.1 16 chr1 153 60 28M0N7M * 0 0 GAAGTGGGTGTATCTGCACAGCATAAGTTATAAGA *
+read_2.153.0 16 chr1 154 60 27M0N8M * 0 0 AAGTGGGTGTATCTGCACAGCATAAGTTATAAGAC *
+read_2.154.0 0 chr1 155 60 26M0N9M * 0 0 AGTGGGTGTATCTGCACAGCATAAGTTATAAGACG *
+read_2.154.1 0 chr1 155 60 26M0N9M * 0 0 AGTGGGTGTATCTGCACAGCATAAGTTATAAGACG *
+read_2.155.0 16 chr1 156 60 25M0N10M * 0 0 GTGGGTGTATCTGCACAGCATAAGTTATAAGACGG *
+read_2.156.0 0 chr1 157 60 24M0N11M * 0 0 TGGGTGTATCTGCACAGCATAAGTTATAAGACGGA *
+read_2.157.0 0 chr1 158 60 23M0N12M * 0 0 GGGTGTATCTGCACAGCATAAGTTATAAGACGGAA *
+read_2.157.1 16 chr1 158 60 23M0N12M * 0 0 GGGTGTATCTGCACAGCATAAGTTATAAGACGGAA *
+read_2.158.0 0 chr1 159 60 22M0N13M * 0 0 GGTGTATCTGCACAGCATAAGTTATAAGACGGAAG *
+read_2.158.1 16 chr1 159 60 22M0N13M * 0 0 GGTGTATCTGCACAGCATAAGTTATAAGACGGAAG *
+read_2.159.0 16 chr1 160 60 21M0N14M * 0 0 GTGTATCTGCACAGCATAAGTTATAAGACGGAAGT *
+read_2.159.1 16 chr1 160 60 21M0N14M * 0 0 GTGTATCTGCACAGCATAAGTTATAAGACGGAAGT *
+read_2.160.0 16 chr1 161 60 20M0N15M * 0 0 TGTATCTGCACAGCATAAGTTATAAGACGGAAGTA *
+read_2.161.0 16 chr1 162 60 19M0N16M * 0 0 GTATCTGCACAGCATAAGTTATAAGACGGAAGTAA *
+read_2.161.1 16 chr1 162 60 19M0N16M * 0 0 GTATCTGCACAGCATAAGTTATAAGACGGAAGTAA *
+read_2.162.0 16 chr1 163 60 18M0N17M * 0 0 TATCTGCACAGCATAAGTTATAAGACGGAAGTAAA *
+read_2.162.1 16 chr1 163 60 18M0N17M * 0 0 TATCTGCACAGCATAAGTTATAAGACGGAAGTAAA *
+read_2.162.2 16 chr1 163 60 18M0N17M * 0 0 TATCTGCACAGCATAAGTTATAAGACGGAAGTAAA *
+read_2.163.0 0 chr1 164 60 17M0N18M * 0 0 ATCTGCACAGCATAAGTTATAAGACGGAAGTAAAG *
+read_2.164.0 16 chr1 165 60 16M0N19M * 0 0 TCTGCACAGCATAAGTTATAAGACGGAAGTAAAGC *
+read_2.165.0 16 chr1 166 60 15M0N20M * 0 0 CTGCACAGCATAAGTTATAAGACGGAAGTAAAGCG *
+read_2.165.1 0 chr1 166 60 15M0N20M * 0 0 CTGCACAGCATAAGTTATAAGACGGAAGTAAAGCG *
+read_2.165.2 16 chr1 166 60 15M0N20M * 0 0 CTGCACAGCATAAGTTATAAGACGGAAGTAAAGCG *
+read_2.165.3 16 chr1 166 60 15M0N20M * 0 0 CTGCACAGCATAAGTTATAAGACGGAAGTAAAGCG *
+read_2.165.4 0 chr1 166 60 15M0N20M * 0 0 CTGCACAGCATAAGTTATAAGACGGAAGTAAAGCG *
+read_2.165.5 0 chr1 166 60 15M0N20M * 0 0 CTGCACAGCATAAGTTATAAGACGGAAGTAAAGCG *
+read_2.165.6 0 chr1 166 60 15M0N20M * 0 0 CTGCACAGCATAAGTTATAAGACGGAAGTAAAGCG *
+read_2.166.0 0 chr1 167 60 14M0N21M * 0 0 TGCACAGCATAAGTTATAAGACGGAAGTAAAGCGT *
+read_2.166.1 0 chr1 167 60 14M0N21M * 0 0 TGCACAGCATAAGTTATAAGACGGAAGTAAAGCGT *
+read_2.167.0 0 chr1 168 60 13M0N22M * 0 0 GCACAGCATAAGTTATAAGACGGAAGTAAAGCGTC *
+read_2.168.0 16 chr1 169 60 12M0N23M * 0 0 CACAGCATAAGTTATAAGACGGAAGTAAAGCGTCT *
+read_2.168.1 0 chr1 169 60 12M0N23M * 0 0 CACAGCATAAGTTATAAGACGGAAGTAAAGCGTCT *
+read_2.169.0 0 chr1 170 60 11M0N24M * 0 0 ACAGCATAAGTTATAAGACGGAAGTAAAGCGTCTT *
+read_2.169.1 0 chr1 170 60 11M0N24M * 0 0 ACAGCATAAGTTATAAGACGGAAGTAAAGCGTCTT *
+read_2.169.2 0 chr1 170 60 11M0N24M * 0 0 ACAGCATAAGTTATAAGACGGAAGTAAAGCGTCTT *
+read_2.170.0 0 chr1 171 60 10M0N25M * 0 0 CAGCATAAGTTATAAGACGGAAGTAAAGCGTCTTC *
+read_2.170.1 0 chr1 171 60 10M0N25M * 0 0 CAGCATAAGTTATAAGACGGAAGTAAAGCGTCTTC *
+read_2.171.0 0 chr1 172 60 9M0N26M * 0 0 AGCATAAGTTATAAGACGGAAGTAAAGCGTCTTCG *
+read_2.171.1 0 chr1 172 60 9M0N26M * 0 0 AGCATAAGTTATAAGACGGAAGTAAAGCGTCTTCG *
+read_2.172.0 16 chr1 173 60 8M0N27M * 0 0 GCATAAGTTATAAGACGGAAGTAAAGCGTCTTCGC *
+read_2.172.1 16 chr1 173 60 8M0N27M * 0 0 GCATAAGTTATAAGACGGAAGTAAAGCGTCTTCGC *
+read_2.172.2 0 chr1 173 60 8M0N27M * 0 0 GCATAAGTTATAAGACGGAAGTAAAGCGTCTTCGC *
+read_2.173.0 0 chr1 174 60 7M0N28M * 0 0 CATAAGTTATAAGACGGAAGTAAAGCGTCTTCGCC *
+read_2.174.0 0 chr1 175 60 6M0N29M * 0 0 ATAAGTTATAAGACGGAAGTAAAGCGTCTTCGCCG *
+read_2.175.0 0 chr1 176 60 5M0N30M * 0 0 TAAGTTATAAGACGGAAGTAAAGCGTCTTCGCCGT *
+read_2.175.1 16 chr1 176 60 5M0N30M * 0 0 TAAGTTATAAGACGGAAGTAAAGCGTCTTCGCCGT *
+read_2.175.2 0 chr1 176 60 5M0N30M * 0 0 TAAGTTATAAGACGGAAGTAAAGCGTCTTCGCCGT *
+read_2.176.0 16 chr1 177 60 4M0N31M * 0 0 AAGTTATAAGACGGAAGTAAAGCGTCTTCGCCGTT *
+read_2.176.1 0 chr1 177 60 4M0N31M * 0 0 AAGTTATAAGACGGAAGTAAAGCGTCTTCGCCGTT *
+read_2.176.2 0 chr1 177 60 4M0N31M * 0 0 AAGTTATAAGACGGAAGTAAAGCGTCTTCGCCGTT *
+read_2.176.3 16 chr1 177 60 4M0N31M * 0 0 AAGTTATAAGACGGAAGTAAAGCGTCTTCGCCGTT *
+read_2.176.4 16 chr1 177 60 4M0N31M * 0 0 AAGTTATAAGACGGAAGTAAAGCGTCTTCGCCGTT *
+read_2.176.5 0 chr1 177 60 4M0N31M * 0 0 AAGTTATAAGACGGAAGTAAAGCGTCTTCGCCGTT *
+read_2.177.0 0 chr1 178 60 3M0N32M * 0 0 AGTTATAAGACGGAAGTAAAGCGTCTTCGCCGTTC *
+read_2.177.1 16 chr1 178 60 3M0N32M * 0 0 AGTTATAAGACGGAAGTAAAGCGTCTTCGCCGTTC *
+read_2.177.2 16 chr1 178 60 3M0N32M * 0 0 AGTTATAAGACGGAAGTAAAGCGTCTTCGCCGTTC *
+read_2.177.3 0 chr1 178 60 3M0N32M * 0 0 AGTTATAAGACGGAAGTAAAGCGTCTTCGCCGTTC *
+read_2.178.0 0 chr1 179 60 2M0N33M * 0 0 GTTATAAGACGGAAGTAAAGCGTCTTCGCCGTTCA *
+read_2.178.1 16 chr1 179 60 2M0N33M * 0 0 GTTATAAGACGGAAGTAAAGCGTCTTCGCCGTTCA *
+read_2.178.2 0 chr1 179 60 2M0N33M * 0 0 GTTATAAGACGGAAGTAAAGCGTCTTCGCCGTTCA *
+read_2.178.3 0 chr1 179 60 2M0N33M * 0 0 GTTATAAGACGGAAGTAAAGCGTCTTCGCCGTTCA *
+read_2.178.4 0 chr1 179 60 2M0N33M * 0 0 GTTATAAGACGGAAGTAAAGCGTCTTCGCCGTTCA *
+read_2.179.0 0 chr1 180 60 1M0N34M * 0 0 TTATAAGACGGAAGTAAAGCGTCTTCGCCGTTCAG *
+read_2.179.1 0 chr1 180 60 1M0N34M * 0 0 TTATAAGACGGAAGTAAAGCGTCTTCGCCGTTCAG *
+read_2.179.2 16 chr1 180 60 1M0N34M * 0 0 TTATAAGACGGAAGTAAAGCGTCTTCGCCGTTCAG *
+read_3.180.0 0 chr1 181 60 35M * 0 0 TATAAGACGGAAGTAAAGCGTCTTCGCCGTTCAGC *
+read_3.180.1 0 chr1 181 60 35M * 0 0 TATAAGACGGAAGTAAAGCGTCTTCGCCGTTCAGC *
+read_3.181.0 0 chr1 182 60 35M * 0 0 ATAAGACGGAAGTAAAGCGTCTTCGCCGTTCAGCA *
+read_3.181.1 0 chr1 182 60 35M * 0 0 ATAAGACGGAAGTAAAGCGTCTTCGCCGTTCAGCA *
+read_3.181.2 16 chr1 182 60 35M * 0 0 ATAAGACGGAAGTAAAGCGTCTTCGCCGTTCAGCA *
+read_3.181.3 0 chr1 182 60 35M * 0 0 ATAAGACGGAAGTAAAGCGTCTTCGCCGTTCAGCA *
+read_3.181.4 16 chr1 182 60 35M * 0 0 ATAAGACGGAAGTAAAGCGTCTTCGCCGTTCAGCA *
+read_3.182.0 16 chr1 183 60 35M * 0 0 TAAGACGGAAGTAAAGCGTCTTCGCCGTTCAGCAC *
+read_3.182.1 16 chr1 183 60 35M * 0 0 TAAGACGGAAGTAAAGCGTCTTCGCCGTTCAGCAC *
+read_3.183.0 16 chr1 184 60 35M * 0 0 AAGACGGAAGTAAAGCGTCTTCGCCGTTCAGCACC *
+read_3.183.1 16 chr1 184 60 35M * 0 0 AAGACGGAAGTAAAGCGTCTTCGCCGTTCAGCACC *
+read_3.184.0 0 chr1 185 60 35M * 0 0 AGACGGAAGTAAAGCGTCTTCGCCGTTCAGCACCC *
+read_3.185.0 0 chr1 186 60 35M * 0 0 GACGGAAGTAAAGCGTCTTCGCCGTTCAGCACCCC *
+read_3.185.1 16 chr1 186 60 35M * 0 0 GACGGAAGTAAAGCGTCTTCGCCGTTCAGCACCCC *
+read_3.186.0 0 chr1 187 60 35M * 0 0 ACGGAAGTAAAGCGTCTTCGCCGTTCAGCACCCCA *
+read_3.186.1 0 chr1 187 60 35M * 0 0 ACGGAAGTAAAGCGTCTTCGCCGTTCAGCACCCCA *
+read_3.187.0 16 chr1 188 60 35M * 0 0 CGGAAGTAAAGCGTCTTCGCCGTTCAGCACCCCAC *
+read_3.187.1 16 chr1 188 60 35M * 0 0 CGGAAGTAAAGCGTCTTCGCCGTTCAGCACCCCAC *
+read_3.188.0 0 chr1 189 60 35M * 0 0 GGAAGTAAAGCGTCTTCGCCGTTCAGCACCCCACG *
+read_3.189.0 0 chr1 190 60 35M * 0 0 GAAGTAAAGCGTCTTCGCCGTTCAGCACCCCACGC *
+read_3.190.0 0 chr1 191 60 35M * 0 0 AAGTAAAGCGTCTTCGCCGTTCAGCACCCCACGCT *
+read_3.190.1 16 chr1 191 60 35M * 0 0 AAGTAAAGCGTCTTCGCCGTTCAGCACCCCACGCT *
+read_3.190.2 0 chr1 191 60 35M * 0 0 AAGTAAAGCGTCTTCGCCGTTCAGCACCCCACGCT *
+read_3.190.3 16 chr1 191 60 35M * 0 0 AAGTAAAGCGTCTTCGCCGTTCAGCACCCCACGCT *
+read_3.190.4 0 chr1 191 60 35M * 0 0 AAGTAAAGCGTCTTCGCCGTTCAGCACCCCACGCT *
+read_3.191.0 0 chr1 192 60 35M * 0 0 AGTAAAGCGTCTTCGCCGTTCAGCACCCCACGCTC *
+read_3.191.1 0 chr1 192 60 35M * 0 0 AGTAAAGCGTCTTCGCCGTTCAGCACCCCACGCTC *
+read_3.191.2 0 chr1 192 60 35M * 0 0 AGTAAAGCGTCTTCGCCGTTCAGCACCCCACGCTC *
+read_3.192.0 16 chr1 193 60 35M * 0 0 GTAAAGCGTCTTCGCCGTTCAGCACCCCACGCTCA *
+read_3.193.0 16 chr1 194 60 35M * 0 0 TAAAGCGTCTTCGCCGTTCAGCACCCCACGCTCAT *
+read_3.194.0 0 chr1 195 60 35M * 0 0 AAAGCGTCTTCGCCGTTCAGCACCCCACGCTCATA *
+read_3.194.1 0 chr1 195 60 35M * 0 0 AAAGCGTCTTCGCCGTTCAGCACCCCACGCTCATA *
+read_3.195.0 0 chr1 196 60 35M * 0 0 AAGCGTCTTCGCCGTTCAGCACCCCACGCTCATAG *
+read_3.195.1 0 chr1 196 60 35M * 0 0 AAGCGTCTTCGCCGTTCAGCACCCCACGCTCATAG *
+read_3.195.2 0 chr1 196 60 35M * 0 0 AAGCGTCTTCGCCGTTCAGCACCCCACGCTCATAG *
+read_3.195.3 16 chr1 196 60 35M * 0 0 AAGCGTCTTCGCCGTTCAGCACCCCACGCTCATAG *
+read_3.196.0 16 chr1 197 60 35M * 0 0 AGCGTCTTCGCCGTTCAGCACCCCACGCTCATAGT *
+read_3.196.1 0 chr1 197 60 35M * 0 0 AGCGTCTTCGCCGTTCAGCACCCCACGCTCATAGT *
+read_3.196.2 16 chr1 197 60 35M * 0 0 AGCGTCTTCGCCGTTCAGCACCCCACGCTCATAGT *
+read_3.197.0 0 chr1 198 60 35M * 0 0 GCGTCTTCGCCGTTCAGCACCCCACGCTCATAGTC *
+read_3.197.1 0 chr1 198 60 35M * 0 0 GCGTCTTCGCCGTTCAGCACCCCACGCTCATAGTC *
+read_3.197.2 16 chr1 198 60 35M * 0 0 GCGTCTTCGCCGTTCAGCACCCCACGCTCATAGTC *
+read_3.198.0 0 chr1 199 60 35M * 0 0 CGTCTTCGCCGTTCAGCACCCCACGCTCATAGTCA *
+read_3.198.1 16 chr1 199 60 35M * 0 0 CGTCTTCGCCGTTCAGCACCCCACGCTCATAGTCA *
+read_3.198.2 0 chr1 199 60 35M * 0 0 CGTCTTCGCCGTTCAGCACCCCACGCTCATAGTCA *
+read_3.198.3 0 chr1 199 60 35M * 0 0 CGTCTTCGCCGTTCAGCACCCCACGCTCATAGTCA *
+read_3.199.0 0 chr1 200 60 35M * 0 0 GTCTTCGCCGTTCAGCACCCCACGCTCATAGTCAA *
+read_3.199.1 16 chr1 200 60 35M * 0 0 GTCTTCGCCGTTCAGCACCCCACGCTCATAGTCAA *
+read_3.199.2 16 chr1 200 60 35M * 0 0 GTCTTCGCCGTTCAGCACCCCACGCTCATAGTCAA *
+read_3.199.3 16 chr1 200 60 35M * 0 0 GTCTTCGCCGTTCAGCACCCCACGCTCATAGTCAA *
+read_3.200.0 0 chr1 201 60 35M * 0 0 TCTTCGCCGTTCAGCACCCCACGCTCATAGTCAAT *
+read_3.201.0 16 chr1 202 60 35M * 0 0 CTTCGCCGTTCAGCACCCCACGCTCATAGTCAATG *
+read_3.201.1 0 chr1 202 60 35M * 0 0 CTTCGCCGTTCAGCACCCCACGCTCATAGTCAATG *
+read_3.202.0 0 chr1 203 60 35M * 0 0 TTCGCCGTTCAGCACCCCACGCTCATAGTCAATGC *
+read_3.202.1 16 chr1 203 60 35M * 0 0 TTCGCCGTTCAGCACCCCACGCTCATAGTCAATGC *
+read_3.202.2 16 chr1 203 60 35M * 0 0 TTCGCCGTTCAGCACCCCACGCTCATAGTCAATGC *
+read_3.203.0 16 chr1 204 60 35M * 0 0 TCGCCGTTCAGCACCCCACGCTCATAGTCAATGCT *
+read_3.204.0 16 chr1 205 60 35M * 0 0 CGCCGTTCAGCACCCCACGCTCATAGTCAATGCTG *
+read_3.204.1 0 chr1 205 60 35M * 0 0 CGCCGTTCAGCACCCCACGCTCATAGTCAATGCTG *
+read_3.204.2 16 chr1 205 60 35M * 0 0 CGCCGTTCAGCACCCCACGCTCATAGTCAATGCTG *
+read_3.204.3 16 chr1 205 60 35M * 0 0 CGCCGTTCAGCACCCCACGCTCATAGTCAATGCTG *
+read_3.205.0 16 chr1 206 60 35M * 0 0 GCCGTTCAGCACCCCACGCTCATAGTCAATGCTGG *
+read_3.205.1 16 chr1 206 60 35M * 0 0 GCCGTTCAGCACCCCACGCTCATAGTCAATGCTGG *
+read_3.206.0 16 chr1 207 60 34M240N1M * 0 0 CCGTTCAGCACCCCACGCTCATAGTCAATGCTGGT *
+read_3.207.0 0 chr1 208 60 33M240N2M * 0 0 CGTTCAGCACCCCACGCTCATAGTCAATGCTGGTG *
+read_3.207.1 0 chr1 208 60 33M240N2M * 0 0 CGTTCAGCACCCCACGCTCATAGTCAATGCTGGTG *
+read_3.208.0 16 chr1 209 60 32M240N3M * 0 0 GTTCAGCACCCCACGCTCATAGTCAATGCTGGTGA *
+read_3.208.1 16 chr1 209 60 32M240N3M * 0 0 GTTCAGCACCCCACGCTCATAGTCAATGCTGGTGA *
+read_3.208.2 0 chr1 209 60 32M240N3M * 0 0 GTTCAGCACCCCACGCTCATAGTCAATGCTGGTGA *
+read_3.209.0 0 chr1 210 60 31M240N4M * 0 0 TTCAGCACCCCACGCTCATAGTCAATGCTGGTGAA *
+read_3.210.0 16 chr1 211 60 30M240N5M * 0 0 TCAGCACCCCACGCTCATAGTCAATGCTGGTGAAC *
+read_3.210.1 0 chr1 211 60 30M240N5M * 0 0 TCAGCACCCCACGCTCATAGTCAATGCTGGTGAAC *
+read_3.210.2 16 chr1 211 60 30M240N5M * 0 0 TCAGCACCCCACGCTCATAGTCAATGCTGGTGAAC *
+read_3.211.0 0 chr1 212 60 29M240N6M * 0 0 CAGCACCCCACGCTCATAGTCAATGCTGGTGAACG *
+read_3.211.1 16 chr1 212 60 29M240N6M * 0 0 CAGCACCCCACGCTCATAGTCAATGCTGGTGAACG *
+read_3.212.0 16 chr1 213 60 28M240N7M * 0 0 AGCACCCCACGCTCATAGTCAATGCTGGTGAACGT *
+read_3.213.0 0 chr1 214 60 27M240N8M * 0 0 GCACCCCACGCTCATAGTCAATGCTGGTGAACGTT *
+read_3.213.1 0 chr1 214 60 27M240N8M * 0 0 GCACCCCACGCTCATAGTCAATGCTGGTGAACGTT *
+read_3.214.0 0 chr1 215 60 26M240N9M * 0 0 CACCCCACGCTCATAGTCAATGCTGGTGAACGTTG *
+read_3.214.1 16 chr1 215 60 26M240N9M * 0 0 CACCCCACGCTCATAGTCAATGCTGGTGAACGTTG *
+read_3.215.0 0 chr1 216 60 25M240N10M * 0 0 ACCCCACGCTCATAGTCAATGCTGGTGAACGTTGA *
+read_3.216.0 0 chr1 217 60 24M240N11M * 0 0 CCCCACGCTCATAGTCAATGCTGGTGAACGTTGAA *
+read_3.216.1 0 chr1 217 60 24M240N11M * 0 0 CCCCACGCTCATAGTCAATGCTGGTGAACGTTGAA *
+read_3.217.0 16 chr1 218 60 23M240N12M * 0 0 CCCACGCTCATAGTCAATGCTGGTGAACGTTGAAC *
+read_3.217.1 16 chr1 218 60 23M240N12M * 0 0 CCCACGCTCATAGTCAATGCTGGTGAACGTTGAAC *
+read_3.217.2 0 chr1 218 60 23M240N12M * 0 0 CCCACGCTCATAGTCAATGCTGGTGAACGTTGAAC *
+read_3.217.3 0 chr1 218 60 23M240N12M * 0 0 CCCACGCTCATAGTCAATGCTGGTGAACGTTGAAC *
+read_3.218.0 0 chr1 219 60 22M240N13M * 0 0 CCACGCTCATAGTCAATGCTGGTGAACGTTGAACT *
+read_3.218.1 16 chr1 219 60 22M240N13M * 0 0 CCACGCTCATAGTCAATGCTGGTGAACGTTGAACT *
+read_3.219.0 0 chr1 220 60 21M240N14M * 0 0 CACGCTCATAGTCAATGCTGGTGAACGTTGAACTA *
+read_3.219.1 16 chr1 220 60 21M240N14M * 0 0 CACGCTCATAGTCAATGCTGGTGAACGTTGAACTA *
+read_3.219.2 16 chr1 220 60 21M240N14M * 0 0 CACGCTCATAGTCAATGCTGGTGAACGTTGAACTA *
+read_3.219.3 16 chr1 220 60 21M240N14M * 0 0 CACGCTCATAGTCAATGCTGGTGAACGTTGAACTA *
+read_3.219.4 0 chr1 220 60 21M240N14M * 0 0 CACGCTCATAGTCAATGCTGGTGAACGTTGAACTA *
+read_3.219.5 16 chr1 220 60 21M240N14M * 0 0 CACGCTCATAGTCAATGCTGGTGAACGTTGAACTA *
+read_3.219.6 0 chr1 220 60 21M240N14M * 0 0 CACGCTCATAGTCAATGCTGGTGAACGTTGAACTA *
+read_3.220.0 16 chr1 221 60 20M240N15M * 0 0 ACGCTCATAGTCAATGCTGGTGAACGTTGAACTAG *
+read_3.221.0 0 chr1 222 60 19M240N16M * 0 0 CGCTCATAGTCAATGCTGGTGAACGTTGAACTAGC *
+read_3.222.0 16 chr1 223 60 18M240N17M * 0 0 GCTCATAGTCAATGCTGGTGAACGTTGAACTAGCC *
+read_3.222.1 16 chr1 223 60 18M240N17M * 0 0 GCTCATAGTCAATGCTGGTGAACGTTGAACTAGCC *
+read_3.223.0 0 chr1 224 60 17M240N18M * 0 0 CTCATAGTCAATGCTGGTGAACGTTGAACTAGCCC *
+read_3.223.1 16 chr1 224 60 17M240N18M * 0 0 CTCATAGTCAATGCTGGTGAACGTTGAACTAGCCC *
+read_3.223.2 16 chr1 224 60 17M240N18M * 0 0 CTCATAGTCAATGCTGGTGAACGTTGAACTAGCCC *
+read_3.224.0 0 chr1 225 60 16M240N19M * 0 0 TCATAGTCAATGCTGGTGAACGTTGAACTAGCCCT *
+read_3.224.1 0 chr1 225 60 16M240N19M * 0 0 TCATAGTCAATGCTGGTGAACGTTGAACTAGCCCT *
+read_3.224.2 16 chr1 225 60 16M240N19M * 0 0 TCATAGTCAATGCTGGTGAACGTTGAACTAGCCCT *
+read_3.225.0 16 chr1 226 60 15M240N20M * 0 0 CATAGTCAATGCTGGTGAACGTTGAACTAGCCCTG *
+read_3.225.1 0 chr1 226 60 15M240N20M * 0 0 CATAGTCAATGCTGGTGAACGTTGAACTAGCCCTG *
+read_3.225.2 0 chr1 226 60 15M240N20M * 0 0 CATAGTCAATGCTGGTGAACGTTGAACTAGCCCTG *
+read_3.226.0 16 chr1 227 60 14M240N21M * 0 0 ATAGTCAATGCTGGTGAACGTTGAACTAGCCCTGA *
+read_3.226.1 16 chr1 227 60 14M240N21M * 0 0 ATAGTCAATGCTGGTGAACGTTGAACTAGCCCTGA *
+read_3.226.2 0 chr1 227 60 14M240N21M * 0 0 ATAGTCAATGCTGGTGAACGTTGAACTAGCCCTGA *
+read_3.227.0 16 chr1 228 60 13M240N22M * 0 0 TAGTCAATGCTGGTGAACGTTGAACTAGCCCTGAT *
+read_3.228.0 0 chr1 229 60 12M240N23M * 0 0 AGTCAATGCTGGTGAACGTTGAACTAGCCCTGATG *
+read_3.228.1 0 chr1 229 60 12M240N23M * 0 0 AGTCAATGCTGGTGAACGTTGAACTAGCCCTGATG *
+read_3.228.2 0 chr1 229 60 12M240N23M * 0 0 AGTCAATGCTGGTGAACGTTGAACTAGCCCTGATG *
+read_3.228.3 16 chr1 229 60 12M240N23M * 0 0 AGTCAATGCTGGTGAACGTTGAACTAGCCCTGATG *
+read_3.229.0 0 chr1 230 60 11M240N24M * 0 0 GTCAATGCTGGTGAACGTTGAACTAGCCCTGATGT *
+read_3.230.0 16 chr1 231 60 10M240N25M * 0 0 TCAATGCTGGTGAACGTTGAACTAGCCCTGATGTA *
+read_3.230.1 0 chr1 231 60 10M240N25M * 0 0 TCAATGCTGGTGAACGTTGAACTAGCCCTGATGTA *
+read_3.230.2 16 chr1 231 60 10M240N25M * 0 0 TCAATGCTGGTGAACGTTGAACTAGCCCTGATGTA *
+read_3.231.0 16 chr1 232 60 9M240N26M * 0 0 CAATGCTGGTGAACGTTGAACTAGCCCTGATGTAA *
+read_3.231.1 16 chr1 232 60 9M240N26M * 0 0 CAATGCTGGTGAACGTTGAACTAGCCCTGATGTAA *
+read_3.232.0 0 chr1 233 60 8M240N27M * 0 0 AATGCTGGTGAACGTTGAACTAGCCCTGATGTAAA *
+read_3.233.0 16 chr1 234 60 7M240N28M * 0 0 ATGCTGGTGAACGTTGAACTAGCCCTGATGTAAAC *
+read_3.233.1 0 chr1 234 60 7M240N28M * 0 0 ATGCTGGTGAACGTTGAACTAGCCCTGATGTAAAC *
+read_3.233.2 0 chr1 234 60 7M240N28M * 0 0 ATGCTGGTGAACGTTGAACTAGCCCTGATGTAAAC *
+read_3.233.3 16 chr1 234 60 7M240N28M * 0 0 ATGCTGGTGAACGTTGAACTAGCCCTGATGTAAAC *
+read_3.234.0 16 chr1 235 60 6M240N29M * 0 0 TGCTGGTGAACGTTGAACTAGCCCTGATGTAAACC *
+read_3.234.1 16 chr1 235 60 6M240N29M * 0 0 TGCTGGTGAACGTTGAACTAGCCCTGATGTAAACC *
+read_3.234.2 16 chr1 235 60 6M240N29M * 0 0 TGCTGGTGAACGTTGAACTAGCCCTGATGTAAACC *
+read_3.235.0 0 chr1 236 60 5M240N30M * 0 0 GCTGGTGAACGTTGAACTAGCCCTGATGTAAACCC *
+read_3.235.1 0 chr1 236 60 5M240N30M * 0 0 GCTGGTGAACGTTGAACTAGCCCTGATGTAAACCC *
+read_3.236.0 0 chr1 237 60 4M240N31M * 0 0 CTGGTGAACGTTGAACTAGCCCTGATGTAAACCCC *
+read_3.236.1 16 chr1 237 60 4M240N31M * 0 0 CTGGTGAACGTTGAACTAGCCCTGATGTAAACCCC *
+read_3.236.2 0 chr1 237 60 4M240N31M * 0 0 CTGGTGAACGTTGAACTAGCCCTGATGTAAACCCC *
+read_3.237.0 0 chr1 238 60 3M240N32M * 0 0 TGGTGAACGTTGAACTAGCCCTGATGTAAACCCCG *
+read_3.238.0 0 chr1 239 60 2M240N33M * 0 0 GGTGAACGTTGAACTAGCCCTGATGTAAACCCCGC *
+read_3.238.1 0 chr1 239 60 2M240N33M * 0 0 GGTGAACGTTGAACTAGCCCTGATGTAAACCCCGC *
+read_3.238.2 0 chr1 239 60 2M240N33M * 0 0 GGTGAACGTTGAACTAGCCCTGATGTAAACCCCGC *
+read_3.238.3 0 chr1 239 60 2M240N33M * 0 0 GGTGAACGTTGAACTAGCCCTGATGTAAACCCCGC *
+read_3.238.4 16 chr1 239 60 2M240N33M * 0 0 GGTGAACGTTGAACTAGCCCTGATGTAAACCCCGC *
+read_3.239.0 16 chr1 240 60 1M240N34M * 0 0 GTGAACGTTGAACTAGCCCTGATGTAAACCCCGCG *
+read_3.239.1 0 chr1 240 60 1M240N34M * 0 0 GTGAACGTTGAACTAGCCCTGATGTAAACCCCGCG *
+read_4.240.0 16 chr1 481 60 35M * 0 0 TGAACGTTGAACTAGCCCTGATGTAAACCCCGCGT *
+read_4.241.0 16 chr1 482 60 35M * 0 0 GAACGTTGAACTAGCCCTGATGTAAACCCCGCGTG *
+read_4.241.1 16 chr1 482 60 35M * 0 0 GAACGTTGAACTAGCCCTGATGTAAACCCCGCGTG *
+read_4.242.0 16 chr1 483 60 35M * 0 0 AACGTTGAACTAGCCCTGATGTAAACCCCGCGTGC *
+read_4.242.1 0 chr1 483 60 35M * 0 0 AACGTTGAACTAGCCCTGATGTAAACCCCGCGTGC *
+read_4.242.2 0 chr1 483 60 35M * 0 0 AACGTTGAACTAGCCCTGATGTAAACCCCGCGTGC *
+read_4.243.0 0 chr1 484 60 35M * 0 0 ACGTTGAACTAGCCCTGATGTAAACCCCGCGTGCC *
+read_4.244.0 16 chr1 485 60 35M * 0 0 CGTTGAACTAGCCCTGATGTAAACCCCGCGTGCCA *
+read_4.244.1 16 chr1 485 60 35M * 0 0 CGTTGAACTAGCCCTGATGTAAACCCCGCGTGCCA *
+read_4.245.0 0 chr1 486 60 35M * 0 0 GTTGAACTAGCCCTGATGTAAACCCCGCGTGCCAA *
+read_4.246.0 16 chr1 487 60 35M * 0 0 TTGAACTAGCCCTGATGTAAACCCCGCGTGCCAAT *
+read_4.246.1 16 chr1 487 60 35M * 0 0 TTGAACTAGCCCTGATGTAAACCCCGCGTGCCAAT *
+read_4.246.2 16 chr1 487 60 35M * 0 0 TTGAACTAGCCCTGATGTAAACCCCGCGTGCCAAT *
+read_4.246.3 16 chr1 487 60 35M * 0 0 TTGAACTAGCCCTGATGTAAACCCCGCGTGCCAAT *
+read_4.247.0 0 chr1 488 60 35M * 0 0 TGAACTAGCCCTGATGTAAACCCCGCGTGCCAATT *
+read_4.248.0 0 chr1 489 60 35M * 0 0 GAACTAGCCCTGATGTAAACCCCGCGTGCCAATTC *
+read_4.248.1 16 chr1 489 60 35M * 0 0 GAACTAGCCCTGATGTAAACCCCGCGTGCCAATTC *
+read_4.250.0 16 chr1 491 60 35M * 0 0 ACTAGCCCTGATGTAAACCCCGCGTGCCAATTCCA *
+read_4.250.1 0 chr1 491 60 35M * 0 0 ACTAGCCCTGATGTAAACCCCGCGTGCCAATTCCA *
+read_4.251.0 0 chr1 492 60 35M * 0 0 CTAGCCCTGATGTAAACCCCGCGTGCCAATTCCAG *
+read_4.252.0 0 chr1 493 60 35M * 0 0 TAGCCCTGATGTAAACCCCGCGTGCCAATTCCAGG *
+read_4.252.1 16 chr1 493 60 35M * 0 0 TAGCCCTGATGTAAACCCCGCGTGCCAATTCCAGG *
+read_4.253.0 16 chr1 494 60 35M * 0 0 AGCCCTGATGTAAACCCCGCGTGCCAATTCCAGGC *
+read_4.253.1 0 chr1 494 60 35M * 0 0 AGCCCTGATGTAAACCCCGCGTGCCAATTCCAGGC *
+read_4.253.2 0 chr1 494 60 35M * 0 0 AGCCCTGATGTAAACCCCGCGTGCCAATTCCAGGC *
+read_4.254.0 16 chr1 495 60 35M * 0 0 GCCCTGATGTAAACCCCGCGTGCCAATTCCAGGCG *
+read_4.254.1 0 chr1 495 60 35M * 0 0 GCCCTGATGTAAACCCCGCGTGCCAATTCCAGGCG *
+read_4.255.0 16 chr1 496 60 35M * 0 0 CCCTGATGTAAACCCCGCGTGCCAATTCCAGGCGT *
+read_4.255.1 0 chr1 496 60 35M * 0 0 CCCTGATGTAAACCCCGCGTGCCAATTCCAGGCGT *
+read_4.256.0 0 chr1 497 60 35M * 0 0 CCTGATGTAAACCCCGCGTGCCAATTCCAGGCGTC *
+read_4.256.1 16 chr1 497 60 35M * 0 0 CCTGATGTAAACCCCGCGTGCCAATTCCAGGCGTC *
+read_4.257.0 16 chr1 498 60 35M * 0 0 CTGATGTAAACCCCGCGTGCCAATTCCAGGCGTCA *
+read_4.258.0 16 chr1 499 60 35M * 0 0 TGATGTAAACCCCGCGTGCCAATTCCAGGCGTCAT *
+read_4.259.0 16 chr1 500 60 35M * 0 0 GATGTAAACCCCGCGTGCCAATTCCAGGCGTCATG *
+read_4.260.0 0 chr1 501 60 35M * 0 0 ATGTAAACCCCGCGTGCCAATTCCAGGCGTCATGG *
+read_4.260.1 16 chr1 501 60 35M * 0 0 ATGTAAACCCCGCGTGCCAATTCCAGGCGTCATGG *
+read_4.261.0 16 chr1 502 60 35M * 0 0 TGTAAACCCCGCGTGCCAATTCCAGGCGTCATGGG *
+read_4.261.1 16 chr1 502 60 35M * 0 0 TGTAAACCCCGCGTGCCAATTCCAGGCGTCATGGG *
+read_4.261.2 0 chr1 502 60 35M * 0 0 TGTAAACCCCGCGTGCCAATTCCAGGCGTCATGGG *
+read_4.261.3 16 chr1 502 60 35M * 0 0 TGTAAACCCCGCGTGCCAATTCCAGGCGTCATGGG *
+read_4.262.0 0 chr1 503 60 35M * 0 0 GTAAACCCCGCGTGCCAATTCCAGGCGTCATGGGG *
+read_4.262.1 16 chr1 503 60 35M * 0 0 GTAAACCCCGCGTGCCAATTCCAGGCGTCATGGGG *
+read_4.263.0 0 chr1 504 60 35M * 0 0 TAAACCCCGCGTGCCAATTCCAGGCGTCATGGGGG *
+read_4.263.1 16 chr1 504 60 35M * 0 0 TAAACCCCGCGTGCCAATTCCAGGCGTCATGGGGG *
+read_4.264.0 0 chr1 505 60 35M * 0 0 AAACCCCGCGTGCCAATTCCAGGCGTCATGGGGGC *
+read_4.265.0 0 chr1 506 60 35M * 0 0 AACCCCGCGTGCCAATTCCAGGCGTCATGGGGGCA *
+read_4.265.1 16 chr1 506 60 35M * 0 0 AACCCCGCGTGCCAATTCCAGGCGTCATGGGGGCA *
+read_4.265.2 16 chr1 506 60 35M * 0 0 AACCCCGCGTGCCAATTCCAGGCGTCATGGGGGCA *
+read_4.265.3 0 chr1 506 60 35M * 0 0 AACCCCGCGTGCCAATTCCAGGCGTCATGGGGGCA *
diff -r 000000000000 -r 460f0749aac5 test-data/generate_reads.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/generate_reads.py Thu Nov 05 07:49:02 2015 -0500
@@ -0,0 +1,120 @@
+#!/usr/bin/env python
+
+
+import random
+import math
+
+
+__version_info__ = ('1', '0', '0')
+__version__ = '.'.join(__version_info__)
+
+
+class Region:
+ def __init__(self,start,stop,sequence):
+ self.start = start
+ self.stop = stop
+ self.sequence = sequence.strip().replace("\n","").replace(" ","")
+ if(len(self.sequence) != self.getSpanningLength()):
+ print "ERROR: sequence length: "+str(len(self.sequence))+", while spanning region is: "+str(self.getSpanningLength())
+ import sys
+ sys.exit()
+
+ def getSpanningLength(self):
+ return abs(self.stop-self.start+1)
+
+class ReadSynthesizer:
+ def __init__(self,chromosome):
+ self.regions = []
+ self.chromosome = chromosome
+
+ def addRegion(self,region):
+ self.regions.append(region)
+
+ def produceReads(self,readDensity = 1,read_length = 50):
+ """
+ Produces uniform reads by walking iteratively over self.regions
+ """
+
+ mRNA = self.getTotalmRNA()
+ spanning_length = self.getRegionSpanningLength()
+ n = spanning_length['total'] - read_length + 1
+
+ j = 0
+ k = 0
+
+ for i in range(n):
+ # "alpha is playing the role of k and beta is playing the role of theta"
+ dd = max(0,int(round(random.lognormvariate(math.log(readDensity),0.5))))# Notice this is NOT a binomial distribution!!
+
+ for d in range(dd):
+ sequence = mRNA[i:i+read_length]
+
+ if(random.randint(0,1) == 0):
+ strand = 0
+ else:
+ strand = 16
+ flag = strand + 0
+
+ print "read_"+str(j)+"."+str(i)+"."+str(d)+"\t"+str(flag)+"\t"+self.chromosome+"\t"+str(self.regions[j].start + k)+"\t60\t"+self.getMappingString(read_length,j,k)+"\t*\t0\t0\t"+str(sequence.upper())+"\t*"
+
+ spanning_length['iter'][j] -= 1
+ if(k >= self.regions[j].getSpanningLength()-1):
+ j += 1
+ k = 0
+ else:
+ k += 1
+
+ def getMappingString(self,length,j,offset):
+ m = 0
+
+ out = ""
+
+ for i in range(length):
+ k = i + offset
+
+ if(k >= self.regions[j].getSpanningLength()):
+ j += 1
+
+ out += str(m)+"M"
+ out += (str(self.regions[j].start - self.regions[j-1].stop-1))+"N"
+ m = 1
+
+ offset = -k
+ else:
+ m += 1
+
+ out += str(m) + "M"
+
+
+ return out
+
+ def getRegionSpanningLength(self):
+ length = {'total':0,'iter':[]}
+ for r in self.regions:
+ l = r.getSpanningLength()
+ length['iter'].append(l)
+ length['total'] += l
+ return length
+
+ def getTotalmRNA(self):
+ mRNA = ""
+ for r in self.regions:
+ mRNA += r.sequence
+ return mRNA
+
+
+
+if __name__ == "__main__":
+ # Artificial SNP
+ rs = ReadSynthesizer('chr1')
+ rs.addRegion(Region( 0+1, 59+1,'aaataggtcccaaacgttacgca'+'G'+'tctatgcctgacaaagttgcgaccacttcctctgcc'))#c -> G
+ rs.addRegion(Region( 60+1,119+1,'ttgtgtgacacgccggagatagg'+'A'+'catcagcaagtacgttaagtacactgaacgaactgg'))#g -> A
+ rs.addRegion(Region(120+1,179+1,'aggtttctacatcgtgcgtgatggc'+'C'+'ctaggagaagtgggtgtatctgcacagcataagt'))#t -> C
+ rs.addRegion(Region(180+1,239+1,'tataagacggaagtaaagcgtcttc'+'G'+'ccgttcagcaccccacgctcatagtcaatgctgg'))#a -> G
+ #rs.addRegion(Region(240+1,299+1,'ttcagcatagtcaagcgccggtggcctccaaaaagacgcactgagtagcttagctacttt'))
+ #rs.addRegion(Region(300+1,359+1,'gctccgcttgcggaagcactaagaggagattgaatttccaaatcccccccgatacctgtg'))
+ #rs.addRegion(Region(360+1,419+1,'cggtcgctacgtaagtgcgaagttctgttagatacgctccccttagtatatgggcgttaa'))
+ #rs.addRegion(Region(420+1,479+1,'tcggaccgtcggtactcactgcattccaggtctcatatagttcgccctagaagcctggga'))
+ rs.addRegion(Region(480+1,539+1,'tgaacgttgaacta'+'GCC'+'ctgatgtaaaccccgcgtgccaattccaggcgtcatgggggca'))#tag -> gcc
+ #rs.addRegion(Region(540+1,599+1,'acccctcgcagcctccctcttgctgttggtgcctagtatttcatgatttcgagccgacat'))
+ rs.produceReads(2,35)
diff -r 000000000000 -r 460f0749aac5 tool-data/all_fasta.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/all_fasta.loc.sample Thu Nov 05 07:49:02 2015 -0500
@@ -0,0 +1,18 @@
+#This file lists the locations and dbkeys of all the fasta files
+#under the "genome" directory (a directory that contains a directory
+#for each build). The script extract_fasta.py will generate the file
+#all_fasta.loc. This file has the format (white space characters are
+#TAB characters):
+#
+#
+#
+#So, all_fasta.loc could look something like this:
+#
+#apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa
+#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa
+#hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa
+#
+#Your all_fasta.loc file should contain an entry for each individual
+#fasta file. So there will be multiple fasta files for each build,
+#such as with hg19 above.
+#
diff -r 000000000000 -r 460f0749aac5 tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample Thu Nov 05 07:49:02 2015 -0500
@@ -0,0 +1,9 @@
+
+
+
+
+ value, dbkey, name, path
+
+
+
+
diff -r 000000000000 -r 460f0749aac5 tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Thu Nov 05 07:49:02 2015 -0500
@@ -0,0 +1,10 @@
+
+
+
+
+
+
+
+
+
+