# HG changeset patch
# User gbcs-embl-heidelberg
# Date 1448473048 18000
# Node ID 424f44e2124ef09e603857523b2e6ab251cc1225
Initial upload
diff -r 000000000000 -r 424f44e2124e je
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/je Wed Nov 25 12:37:28 2015 -0500
@@ -0,0 +1,15 @@
+#!/bin/sh
+# Wrapper around je_1.0_bundle.jar
+
+# where are we stored ?
+DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
+# echo $DIR
+# path to jar file to execute, this jar is supposed to be in the same dir as this script
+JAR_FILE=$DIR"/je_1.0_bundle.jar"
+
+OPTS="-Xmx2g"
+# uncomment to change logging level using your own log4j.xml found in $DIR file
+# OPTS=$OPTS" -Dlog4j.configuration=file:$DIR/log4j.xml"
+
+java $OPTS -jar $JAR_FILE "$@"
+exit $?
diff -r 000000000000 -r 424f44e2124e je-demultiplex.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/je-demultiplex.xml Wed Nov 25 12:37:28 2015 -0500
@@ -0,0 +1,439 @@
+
+ demultiplexes fastq files
+
+ macros.xml
+
+
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+
+ echo '1.0'
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+ AGAGTG:TTGATA) and 'Je demultiplex' needs both barcodes to find
+ the relevant sample. Note that this is the only situation in which all barcode matching
+ options (MM, MMD, Q) accept different values for both barcodes in the form X:Z where X
+ and Z are 2 integers.
+
+ Default value: BOTH. This option can be set to 'null' to clear the default value.
+ Possible values: {READ_1, READ_2, BOTH, NONE}
+
+
+ REDUNDANT_BARCODES=Boolean
+ BRED=Boolean
+
+ This option only applies for paired-end data with BARCODE_READ_POS set to 'BOTH'
+ Indicates if both read's barcodes encode redundant information or if barcodes are
+ supposed to be identical at both ends (or to resolve to the same sample when a pool of
+ barcodes is used per sample).
+ When REDUNDANT_BARCODES=false, the 2 barcodes potentially encode
+ different information. For example, only one of the barcodes encodes the sample identity
+ while
+ the second barcode might be a random barcode (UMI) to tell apart PCR artefacts from real
+ duplicates.
+ Another example is when both barcodes should be used in a combined fashion to resolve the
+ sample.
+ In the first example, you should use BPOS=BOTH BRED=false BM=READ_1.
+ In the second example, you should have BPOS=BOTH BRED=false BM=BOTH.
+ Note that with BPOS=BOTH BRED=true BM=BOTH, the behavior would be different as
+ 'demultiplex' would then check the STRICT option to perform sample resolution.
+ Importantly, when BARCODE_READ_POS (BPOS) == BOTH AND REDUNDANT_BARCODES=false, BLEN,
+ barcode matching options (MM, MMD, Q) and read trimming/clipping options (XT, ZT) accept
+ different values for both barcodes in the form X:Z where X and Z are 2 integers.
+
+ Default value: true. This option can be set to 'null' to clear the default value.
+ Possible values: {true, false}
+
+ STRICT=Boolean
+ S=Boolean
+
+ For paired-end data and when two distinct barcodes/indices are used to encode samples,
+ this option tells if both barcodes should resolve to the same sample.
+ When true and if only one of the two reads has a barcode match, the read pair is
+ 'unassigned'.
+ When false and if only one of the two reads has a barcode match, the read pair is
+ assigned to the
+ corresponding sample
+ When reads resolve to different samples, the read pair is always 'unassigned'.
+
+ Default value: false. This option can be set to 'null' to clear the default value.
+ Possible values: {true, false}
+
+ MAX_MISMATCHES=String
+ MM=String
+
+ Maximum mismatches for a barcode to be considered a match. In situations where both
+ barcodes are used for sample matching i.e. BPOS=BOTH BM=BOTH (or 2 INDEX_FILE given), two
+ distinct
+ values can be given here using the syntax MM=X:Z where X and Z are 2 integers to use for
+ read_1 and read_2 respectively.
+ MM=null is like MM=0
+
+ Default value: 1. This option can be set to 'null' to clear the default value.
+
+ MIN_MISMATCH_DELTA=String
+ MMD=String
+
+ Minimum difference between the number of mismatches against the best and the second best
+ barcode. When MMD is not respected, the read remains unassigned.
+ When two distinct barcodes are used for sample matching (dual encoding), two distinct
+ values can be given using the syntax MMD=X:Z where X and Z are 2 integers to use for
+ first (e.g. from read_1 or index_1)
+ MMD=null is like MMD=0
+
+ Default value: 1. This option can be set to 'null' to clear the default value.
+
+ MIN_BASE_QUALITY=String
+ Q=String
+
+ Minimum base quality during barcode matching: bases which quality is less than this
+ cutoff are always considered as a mismatch.When two distinct barcodes are used for sample
+ matching (dual encoding), two distinct values can be given using the syntax Q=X:Z where X
+ and Z are 2 integers to use for first (e.g. from read_1 or index_1) and second barcode
+ (e.g. from read_2 or index_2) respectively.
+ Q=null is like Q=0.
+
+ Default value: 10. This option can be set to 'null' to clear the default value.
+
+ XTRIMLEN=String
+ XT=String
+
+ Optional extra number of base to be trimmed right after the barcode (only used if
+ CLIP_BARCODE=true).
+ When running paired-end, two distinct values can be given using the syntax XT=X:Z where X
+ and Z are 2 integers to use for read_1 and read_2 respectively. Note that even when
+ BPOS=READ_1 or BPOS=READ_2, a X:Y synthax can be given to trim the read w/o barcode as to
+ end up with reads of the same length (note that this can also be operated using ZT). If a
+ unique value is given, e.g. XT=1, while running paired-end the following rule applies:
+ (1) BPOS=READ_1 or BPOS=READ_2, no trim is applied at the read w/o barcode
+ (2) BPOS=BOTH, the value is used for both reads.
+
+ Note that XT=null is like XT=0.
+ Default value: 0. This option can be set to 'null' to clear the default value.
+
+ ZTRIMLEN=String
+ ZT=String
+
+ Optional extra number of bases to be trimmed from the read end i.e. 3' end.
+ When running paired-end, two distinct values can be given here using the syntax ZT=X:Z
+ where X and Z are 2 integers to use for read_1 and read_2 respectively. Note that even
+ when BPOS=READ_1 or BPOS=READ_2, a X:Y synthax can be given to trim the read w/o barcode
+ as to end up with reads of the same length (note that this can also be operated using
+ XT). Note that if a single value is passed, the value always applies to both reads in
+ paired-end mode without further consideration.
+ ZT=null is like ZT=0.
+
+ Default value: 0. This option can be set to 'null' to clear the default value.
+
+ CLIP_BARCODE=Boolean
+ C=Boolean
+
+ Clip barcode sequence from read sequence, as well as XTRIMLEN (and ZTRIMLEN) bases if
+ applicable, before writing to output file.
+ If false, reads are written without modification to output file.
+ Apply to both barcodes when BPOS=BOTH.
+
+ Default value: true. This option can be set to 'null' to clear the default value.
+ Possible values: {true, false}
+
+ ADD_BARCODE_TO_HEADER=Boolean
+ ADD=Boolean
+
+ Add barcode at the end of the read header. Apply to both barcodes when BPOS=BOTH.
+ If true, the string ':barcode' is added at the end of the read header with a ':' added
+ only if current read header does not end with ':'.
+ If both reads of the pair have a barcode (i.e. BARCODE_READ_POS == BOTH), thenthe second
+ read also has its own matched barcode written. Else, the read without a barcode receives
+ the barcode from the barcoded read.
+ For example:
+ @D3FCO8P1:178:C1WLBACXX:7:1101:1836:1965 2:N:0:
+ becomes:
+ @D3FCO8P1:178:C1WLBACXX:7:1101:1836:1965 2:N:0:BARCODE
+
+ When barcodes containing random positions, i.e. 'N', (for example like in the iCLIP
+ protocol) or are UMIs, the added sequence is the sequence clipped from the read and NOT
+ the matched barcode.
+
+ Default value: true. This option can be set to 'null' to clear the default value.
+ Possible values: {true, false}
+
+
+ ENSURE_IDENTICAL_HEADER_NAMES=Boolean
+ SAME_HEADERS=Boolean
+
+ Makes sure that headers of both reads of a pair are identical, using the following read
+ header pattern (for both reads of a pair):
+ @D3FCO8P1:178:C1WLBACXX:7:1101:1836:1965 SAMPLEBARCODE_READ1:SAMPLEBARCODE_READ2(:CLIPPED_SEQ_FROMREAD1:CLIPPED_SEQ_FROMREAD2)
+ This option only makes sense in
+ paired end mode and ADD=true. Some (if not all) mappers will indeed complain when the
+ read headers are not identical. When molecular barcodes are present in reads (either as
+ additional barcodes or as degenerate barcodes ie with 'N') and the RCHAR is used, you
+ will end with (problematic) read headers like this:
+ HISEQ:44:C6KC0ANXX:5:1101:1491:1994:1:N:0:TAGAACAC:TGGAGTAG
+ HISEQ:44:C6KC0ANXX:5:1101:1491:1994:3:N:0:TAGAACAC:CGTTGTAT
+ SAME_HEADERS=true will instead generates the following identical header for both reads:
+ HISEQ:44:C6KC0ANXX:5:1101:1491:1994:TAGAACAC:TGGAGTAG:CGTTGTAT
+ Note that we also clipped the useless '1:N:0' and '3:N:0' has they will also result in
+ generating different headers.
+ Important: this option will force RCHAR=: UNLESS you specify RCHAR=null ; in which
+ case a space will be preserved ie:
+ HISEQ:44:C6KC0ANXX:5:1101:1491:1994 TAGAACAC:TGGAGTAG:CGTTGTAT
+
+ Default value: true. This option can be set to 'null' to clear the default value.
+ Possible values: {true, false}
+
+
+ READ_NAME_REPLACE_CHAR=String
+ RCHAR=String
+
+ Replace spaces in read name/header using provided character. This is particularly handy
+ when you need to retain ADDed barcode in read name/header during mapping (everything
+ after space in read name is usually clipped in BAM files). For example, with RCHAR=':':
+ @D3FCO8P1:178:C1WLBACXX:7:1101:1836:1965 2:N:0:
+ becomes
+ @D3FCO8P1:178:C1WLBACXX:7:1101:1836:1965:2:N:0:BARCODE
+ Default value: null.
+
+ QUALITY_FORMAT=FastqQualityFormat
+ V=FastqQualityFormat
+
+ A value describing how the quality values are encoded in the fastq. Either 'Solexa' for
+ pre-pipeline 1.3 style scores (solexa scaling + 66), 'Illumina' for pipeline 1.3 and
+ above (phred scaling + 64) or 'Standard' for phred scaled scores with a character shift
+ of 33. If this value is not specified (or 'null' is given), the quality format will be
+ detected.
+
+ Default value: Standard. This option can be set to 'null' to clear the default value.
+ Possible values: {Solexa, Illumina, Standard}
+
+ KEEP_UNASSIGNED_READ=Boolean
+ UN=Boolean
+
+ Should un-assigned reads be saved in files or simply ignored. File names are
+ automatically created or can be given using UF1 & UF2 options.
+
+ Default value: true. This option can be set to 'null' to clear the default value.
+ Possible values: {true, false}
+
+ BARCODE_DIAG_FILE=String
+ DIAG=String
+
+ Name for a barcode match reporting file (not generated by default).Either a name (in
+ which case the file will be created in the output dir) or full path. This file will
+ contain a line per read pair with the barcode best matching the read subsequence or
+ 'null' when no match is found according to matching parameters ; and the final selected
+ sample. This file is useful for debugging or further processing in case both ends are
+ barcoded.
+ N.B: this file will have a size of about one of the fastq input files.
+
+ Default value: null.
+]]>
+
+
+
diff -r 000000000000 -r 424f44e2124e je_1.0_bundle.jar
Binary file je_1.0_bundle.jar has changed
diff -r 000000000000 -r 424f44e2124e macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Wed Nov 25 12:37:28 2015 -0500
@@ -0,0 +1,336 @@
+
+
+
+ #if str( $library.type ) == "single":
+ F1=${library.input_1}
+ #elif str( $library.type ) == "paired":
+ F1=${library.input_1}
+ F2=${library.input_2}
+ SAME_HEADERS=${library.SAME_HEADERS}
+ #else
+ ## prepare paired-end collection
+ F1=${library.input_1.forward}
+ F2=${library.input_1.reverse}
+ SAME_HEADERS=${library.SAME_HEADERS}
+ #end if
+
+
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+ @single_or_paired_cmd@
+ I1=$library.I1
+ #if str( $library.type ) != "single":
+ #if str( $library.I2_CONDITIONAL.I2_AVAILABLE ) == "true":
+ I2=${library.I2_CONDITIONAL.I2}
+ BRED=${library.I2_CONDITIONAL.BRED_CONDITIONAL.BRED}
+ #if str( $library.I2_CONDITIONAL.BRED_CONDITIONAL.BRED ) == "true":
+ STRICT=${library.I2_CONDITIONAL.BRED_CONDITIONAL.STRICT}
+ #end if
+ #end if
+ #end if
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+ BPOS=$library.BPOS_CONDITIONAL.BPOS
+ #if str( $library.BPOS_CONDITIONAL.BPOS ) == "BOTH":
+ BM=${library.BPOS_CONDITIONAL.BM_CONDITIIONAL.BM}
+ #if str( $library.BPOS_CONDITIONAL.BM_CONDITIIONAL.BM ) == "BOTH":
+ BRED=${library.BPOS_CONDITIONAL.BM_CONDITIIONAL.BRED_CONDITIONAL.BRED}
+ #if str( $library.BPOS_CONDITIONAL.BM_CONDITIIONAL.BRED_CONDITIONAL.BRED ) == "true":
+ STRICT=${library.BPOS_CONDITIONAL.BM_CONDITIIONAL.BRED_CONDITIONAL.STRICT}
+ #end if
+ #end if
+ #end if
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+ #if str( $barcodes.barcode_list_type_con ) == "text":
+ BARCODE_FILE=${barcode_file_from_text}
+ #else if str( $barcodes.barcode_list_type_con ) == "file":
+ BARCODE_FILE=${barcodes.BARCODE_FILE}
+ #end if
+
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+ #set from_text_area = ''
+#if str( $barcodes.barcode_list_type_con ) == "text":
+#set from_text_area = $barcodes.barcode_text
+#end if
+${from_text_area}
+
+
+
+ #if str( $LEN ) != "":
+ BCLEN=$LEN
+ #end if
+
+
+
+
+
+
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+
+
+ ADD=${ADD}
+ MM=$MM
+ MMD=$MMD
+ Q=$MIN_BASE_QUALITY
+ QUALITY_FORMAT=$QUALITY_FORMAT
+
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+ KEEP_UNASSIGNED_READ=$KEEP_UNASSIGNED_READ
+ STATS_ONLY=${adv_options.STATS_ONLY}
+ #if str( $adv_options.DIAG ) == "true":
+ BARCODE_DIAG_FILE=$BARCODE_DIAG_FILE
+ #end if
+
+
+
+
+
+
+
+ XT=${XT}
+ ZT=${ZT}
+ #if str( $RCHAR ) != "":
+ RCHAR=${RCHAR}
+ #end if
+ GZ=${GZ}
+ OUTPUT_DIR=results
+
+
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+ METRICS_FILE_NAME=$METRICS_FILE_NAME
+
+
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+
+ (adv_options['DIAG'] == 'true')
+
+
+
+
diff -r 000000000000 -r 424f44e2124e test-data/barcodes_PE.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/barcodes_PE.txt Wed Nov 25 12:37:28 2015 -0500
@@ -0,0 +1,4 @@
+sample1 CACTGT:GTATAG sample1_1_PE.txt sample1_2_PE.txt
+sample2 ATTCCG:TCCGTC sample2_1_PE.txt sample2_2_PE.txt
+sample3 GCTACC:TGGTCA sample3_1_PE.txt sample3_2_PE.txt
+sample4 CGAAAC:CACTGT sample4_1_PE.txt sample4_2_PE.txt
\ No newline at end of file
diff -r 000000000000 -r 424f44e2124e test-data/barcodes_SE.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/barcodes_SE.txt Wed Nov 25 12:37:28 2015 -0500
@@ -0,0 +1,4 @@
+sample1 CACTGT sample1_SE.txt
+sample2 ATTCCG sample2_SE.txt
+sample3 GCTACC sample3_SE.txt
+sample4 CGAAAC sample4_SE.txt
\ No newline at end of file
diff -r 000000000000 -r 424f44e2124e test-data/clip_barcode_result_file.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/clip_barcode_result_file.txt Wed Nov 25 12:37:28 2015 -0500
@@ -0,0 +1,26 @@
+READ_HEADER BC_SEQ_READ1 BC_QUAL_READ1
+1:N:0: CACTGT CCCFFF
+1:N:0: CACTGT BBCFFF
+1:N:0: CACTGT CCCFFF
+1:N:0: CACTGT =?@D;D
+1:N:0: CACTGT BB=DDD
+1:N:0: CACTGT CCCFFF
+1:N:0: ATTCCG @BCFFF
+1:N:0: ATTCCG @BCFFF
+1:N:0: ATTCCG @@CFFF
+1:N:0: ATTCCG CCCFFF
+1:N:0: ATTCCG 1?8ADD
+1:N:0: ATTCCG CCCFFF
+1:N:0: ATTCCG @@CFFF
+1:N:0: GCTACC CCCFFF
+1:N:0: GCTACC CC@FFF
+1:N:0: GCTACC CCCFFF
+1:N:0: GCTACC CCCFFF
+1:N:0: GCTACC CCCFFF
+1:N:0: GCTACC CCCFFF
+1:N:0: CGAAAC CCCFFF
+1:N:0: CGAAAC CCCFFF
+1:N:0: CGAAAC ?@@FFD
+1:N:0: CGAAAC @@@DAD
+1:N:0: CGAAAC ;@@BDD
+1:N:0: CGAAAC CCCFFF
diff -r 000000000000 -r 424f44e2124e test-data/clip_dataset1_PE.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/clip_dataset1_PE.fastq Wed Nov 25 12:37:28 2015 -0500
@@ -0,0 +1,100 @@
+@D3FCO8P1:229:C49NHACXX:8:1101:1347:2097:1:N:0:CACTGT
+TCAATGCCAATAGCAATGAAACCACCCATANAANNNNNACGGCTGAACANNNNNNNACNNGATATAGCATAAATGNANNNTNNNNANTNNNNNN
++
+FFHHHHHJJJJJJJJJJJIJJJIJJJJJJI#1?#####00?FHIJJJJI#######--##,,=A=CDDDDDDDEE###################
+@D3FCO8P1:229:C49NHACXX:8:1101:1406:2140:1:N:0:CACTGT
+AATTTATCTCTTTTCATATAACTCTCTGGTAATNNNNAACATAAAACCGANCGCACATGATAATTCTTCCAAATTTATATATNAATTTTATANN
++
+DFHHHGHHIJJJJJJIJIJIGHHHIJJJJGGIJ####11?DHHIIIIGHI#-?CAAC??9?B@9??C:(:@A::@CC:4+:>@C@AAC(>9?CCCC@
+@D3FCO8P1:229:C49NHACXX:8:1101:1452:2184:1:N:0:CACTGT
+GTGGGAAAGGGAAGGGCAAGGGGGAGGGGAAGAATTTAACCGGGCGGGAGGAGAATCGGGCAGGGAAGAATGGTTGGTTGGTGGAACAACTGAA
++
+EDHHHDHJJGIGIJCBDHEHGJJJBGEHIBGGHFGFFGGHFFDD>?BDBBDDDDDD@ADD;>@D98AB?CCDD:CBBEEFFFFFFFACCEACEDCDCCCCCDCDEEDDDE(:ACCD:@D@
+@D3FCO8P1:229:C49NHACXX:8:1101:1339:2211:1:N:0:ATTCCG
+AGTAAATTAAATGCGAAAATAAAAGGCAGCATGAGNTANTTACTNAAANGGGGTCATNAACAGTACTTGTGCTCCNCCANGTCGNCGNTNCNCT
++
+FFFHHHHJJJIJJJJJJJIJIJJJJJJJJJJJJJJ#0?#0?DHI#-;F#-;DH?EFH#,;BCDEEEEEDDCCCDD#,8?#,5?B##########
+@D3FCO8P1:229:C49NHACXX:8:1101:1402:2222:1:N:0:ATTCCG
+ATAGTAATAATATTACCTAATACAAATAATGAAATATCATATTGATGAAATCATTTTACTATACCTGATACAGTTGTTATAGCTCCGATAGCTC
++
+FDFHHHHJJIIJJJGJIIJJIIJHIJIJIJIIJJJJJJJIIJJIGGHIJJJIJGJJIIIHIIHJ>GHIIIIIIGGGIIJJJJIH)=ABDDDDEE
+@D3FCO8P1:229:C49NHACXX:8:1101:1388:2233:1:N:0:ATTCCG
+AATTTAATGCAATTACCAATCTTACAAGTTATTATACCAATAATTGCATCTATGTTTTGCTTTCTTGACAAGAAACACAAGGTAACTTGGGTTA
++
+DDACAA:@?C
+@D3FCO8P1:229:C49NHACXX:8:1101:1664:2088:1:N:0:GCTACC
+AAGTTTATAAATGGCAACCTTAAGTGTAANNNANNNNNTATGCACAGNANNNNNNNNANNNATGCAAAACGACTCNNNNNNNNNNNNCNNNNNN
++
+FFHHHHHJJJJJJJJJJJJJJJJJIIHIJ###1#####20?FHJJJJ#.########-###--;BDFEEECDDDD###################
+@D3FCO8P1:229:C49NHACXX:8:1101:1512:2095:1:N:0:GCTACC
+ACGTTCATAAGATACATTAGCTAAACAAAANAANNNNNAAGAACATAAANNNNNNNCANNTATTAATGTATAAGANCNNNANNNNCNTNNNNNN
++
+FFHHHHHJJJJJJIJJJJIJJJJIJJJJJJ#1C#####00?FIJJJJJJ#######--##,5?DDEEEFCFFEDD###################
+@D3FCO8P1:229:C49NHACXX:8:1101:1630:2114:1:N:0:GCTACC
+CGTTGGAGGAGGAGCCGCCATGAATGCCCTGCGNNNNTTCTACCTGGAGANNNCGGTGGTCACACGAGCCTACACCACGGTCNNCGTGCTNNNN
++
+FFHHHHGJJGHJGHIJJJJJJJJJJJJJJJJJJ####.-;DHIJJHHHHH###,,=?BDBDDDDDDDDDDDDDDDDDDDDDD##+28@DD####
+@D3FCO8P1:229:C49NHACXX:8:1101:1540:2119:1:N:0:GCTACC
+TGGACTCAAGACCTAATTGCATTAACCGTCTGTNNNNTACGTAGCGTATGNNATTGCGCACTTCTTCTGCGGATAGTCCTTCNNCATCTCNNNN
++
+FFHHHHHJJJJJJJJJJJJJJJJJJJJJJJJIJ####20?GHIJJJIJIJ##-5CEFHFFDDEEDDDDDDDDDDDDDEDDDD##+2?BDD####
+@D3FCO8P1:229:C49NHACXX:8:1101:1503:2124:1:N:0:GCTACC
+TACATATACTTATAGGCATACTTATACGACTTCNNNNCCCGGTTAATATGNNGTGGCCCGTATAAGTTAATGGGCACAACCGNNTGGGACNNNN
++
+FFHHHHHIJJJJJJJJJJJIJJJJJJJJJJJJJ####00BFHGIIJJJJJ##--BEHJJHDFFEDEEFEEEDDDDDDDDDDD##+2AC@@CB@BBA@?BBBBA@CCDCCCCC<493?CCCCCC>:>A<8???AC####
+@D3FCO8P1:229:C49NHACXX:8:1101:1563:2176:1:N:0:CGAAAC
+GGAAGAGAAAAAAATATAAAGTGTCAAGGGGCGTGTGCAGCGACACTTCGCCGACCCCTCCCCACATTATTTTTTTGCCGCCCGCTGGTAGCAG
++
+DA:DBFDF;A?CAAC??9?B@9??C:(:@A::@CC:4+:>@C@AAC(>9?CCCC@
+@D3FCO8P1:229:C49NHACXX:8:1101:1452:2184 1:N:0:
+GTGGGAAAGGGAAGGGCAAGGGGGAGGGGAAGAATTTAACCGGGCGGGAGGAGAATCGGGCAGGGAAGAATGGTTGGTTGGTGGAACAACTGAA
++
+EDHHHDHJJGIGIJCBDHEHGJJJBGEHIBGGHFGFFGGHFFDD>?BDBBDDDDDD@ADD;>@D98AB?CCDD:CBBEEFFFFFFFACCEACEDCDCCCCCDCDEEDDDE(:ACCD:@D@
+@D3FCO8P1:229:C49NHACXX:8:1101:1339:2211 1:N:0:
+AGTAAATTAAATGCGAAAATAAAAGGCAGCATGAGNTANTTACTNAAANGGGGTCATNAACAGTACTTGTGCTCCNCCANGTCGNCGNTNCNCT
++
+FFFHHHHJJJIJJJJJJJIJIJJJJJJJJJJJJJJ#0?#0?DHI#-;F#-;DH?EFH#,;BCDEEEEEDDCCCDD#,8?#,5?B##########
+@D3FCO8P1:229:C49NHACXX:8:1101:1402:2222 1:N:0:
+ATAGTAATAATATTACCTAATACAAATAATGAAATATCATATTGATGAAATCATTTTACTATACCTGATACAGTTGTTATAGCTCCGATAGCTC
++
+FDFHHHHJJIIJJJGJIIJJIIJHIJIJIJIIJJJJJJJIIJJIGGHIJJJIJGJJIIIHIIHJ>GHIIIIIIGGGIIJJJJIH)=ABDDDDEE
+@D3FCO8P1:229:C49NHACXX:8:1101:1388:2233 1:N:0:
+AATTTAATGCAATTACCAATCTTACAAGTTATTATACCAATAATTGCATCTATGTTTTGCTTTCTTGACAAGAAACACAAGGTAACTTGGGTTA
++
+DDACAA:@?C
+@D3FCO8P1:229:C49NHACXX:8:1101:1664:2088 1:N:0:
+AAGTTTATAAATGGCAACCTTAAGTGTAANNNANNNNNTATGCACAGNANNNNNNNNANNNATGCAAAACGACTCNNNNNNNNNNNNCNNNNNN
++
+FFHHHHHJJJJJJJJJJJJJJJJJIIHIJ###1#####20?FHJJJJ#.########-###--;BDFEEECDDDD###################
+@D3FCO8P1:229:C49NHACXX:8:1101:1512:2095 1:N:0:
+ACGTTCATAAGATACATTAGCTAAACAAAANAANNNNNAAGAACATAAANNNNNNNCANNTATTAATGTATAAGANCNNNANNNNCNTNNNNNN
++
+FFHHHHHJJJJJJIJJJJIJJJJIJJJJJJ#1C#####00?FIJJJJJJ#######--##,5?DDEEEFCFFEDD###################
+@D3FCO8P1:229:C49NHACXX:8:1101:1630:2114 1:N:0:
+CGTTGGAGGAGGAGCCGCCATGAATGCCCTGCGNNNNTTCTACCTGGAGANNNCGGTGGTCACACGAGCCTACACCACGGTCNNCGTGCTNNNN
++
+FFHHHHGJJGHJGHIJJJJJJJJJJJJJJJJJJ####.-;DHIJJHHHHH###,,=?BDBDDDDDDDDDDDDDDDDDDDDDD##+28@DD####
+@D3FCO8P1:229:C49NHACXX:8:1101:1540:2119 1:N:0:
+TGGACTCAAGACCTAATTGCATTAACCGTCTGTNNNNTACGTAGCGTATGNNATTGCGCACTTCTTCTGCGGATAGTCCTTCNNCATCTCNNNN
++
+FFHHHHHJJJJJJJJJJJJJJJJJJJJJJJJIJ####20?GHIJJJIJIJ##-5CEFHFFDDEEDDDDDDDDDDDDDEDDDD##+2?BDD####
+@D3FCO8P1:229:C49NHACXX:8:1101:1503:2124 1:N:0:
+TACATATACTTATAGGCATACTTATACGACTTCNNNNCCCGGTTAATATGNNGTGGCCCGTATAAGTTAATGGGCACAACCGNNTGGGACNNNN
++
+FFHHHHHIJJJJJJJJJJJIJJJJJJJJJJJJJ####00BFHGIIJJJJJ##--BEHJJHDFFEDEEFEEEDDDDDDDDDDD##+2AC@@CB@BBA@?BBBBA@CCDCCCCC<493?CCCCCC>:>A<8???AC####
+@D3FCO8P1:229:C49NHACXX:8:1101:1563:2176 1:N:0:
+GGAAGAGAAAAAAATATAAAGTGTCAAGGGGCGTGTGCAGCGACACTTCGCCGACCCCTCCCCACATTATTTTTTTGCCGCCCGCTGGTAGCAG
++
+DA:DBFDF;A@@@@@@####43@#####11=?????????>?????????????????????@?#####################################
+@D3FCO8P1:229:C49NHACXX:8:1101:1406:2140:4:N:0:GTATAG
+TTATATGAAAGNAATATAAAATTTATATATAAATTTGGAAGAATTATCATGTGCGCTCNNNNNNNNNTTANANATNNNNNNAGAGTTATATGAN
++
+2@@@@@@@?@@#3=>?@@?@@@?@?@>?????>????????????>??????@?????####################################
+@D3FCO8P1:229:C49NHACXX:8:1101:1418:2170:4:N:0:GTATAG
+GCTATTGGATTATTAGGATTTATTGTATGAGCTCATCATATATTTACCGTTGGAATAGATNTAGATACTCGAGCTTATTTTACCTCAGCTACTA
++
+FFHHHHHJEHIHHJIJJHIJJIJJJIJJJIJJJJIJJJJIJIIJIGJJJJJJJJJJJJJJ#-;CFHIJJJHHHFFFFFEEEEEEEDDDDDDDDD
+@D3FCO8P1:229:C49NHACXX:8:1101:1385:2179:4:N:0:GTATAG
+AGAGATCTGCATCTAATCTAGCTGCTCCCATGCTACCCCTGAATACCCTACACGGCCTGAACAGTCGCCCCACAAGTCTGGCGTGGGGCTGTCT
++
+DFHF?HHGBHHIJJIGIIIJGIJBEHIGID<9EHIIJJI@;?BGGHIIIIIIIIIIIAGE@HHH?EDFDDB?B?9?:ACCC(85>>B>>@BBD@
+@D3FCO8P1:229:C49NHACXX:8:1101:1452:2184:4:N:0:GTATAG
+CATTCTGTATGCCCTTCCCTCTCGCACACTCGACCCAATGACCCGCTTTGCTCTGTTTACCTCTCCGCTCTGTTTTTGCACTTGGAAATTGCTA
++
+FFHGDHHGGIJJIJJJGHIIIGFHHIIGIIIJIJJEHGEGGIJJIIIIGGGHGGFHHFEC@BCEDECDDDDDDDDDD?AC>ACCCCACADCCDD
+@D3FCO8P1:229:C49NHACXX:8:1101:1370:2193:4:N:0:GTATAG
+TGAAAGCAAGGAGCGCAAGAAATCGTATGCCCATGTTGACCAGTTTGAATATGAGATAATCGTGCAAACACTCCCAAGGAACTGTCTCTTATAC
++
+FFHHHHHJJJJJJJJJJJJJJJJJJJJJJJJJIJJJJJHJJJJJGHIIIIIJJIJIJEEEEHHFFFEEEEDED3=CDDDDDDDDCDDDDDDDDD
+@D3FCO8P1:229:C49NHACXX:8:1101:1486:2204:4:N:0:TCCGTC
+TTCTTCGACTTCCAAGACGTTCATAAGATACATTAGCTAAACAAAATAACCCAGAAGAACATAAACCATGAGCAATTATTAATGTATAAGAACC
++
+FFHHHFHIJJJJJJJJJJIIGIIIJJIIGHJJJJIJJIIJIJJJIJJIJJJJJJJJIGIJIIJJHHFHHFFFFFEDEEEFFFEDDDEFEDDDDD
+@D3FCO8P1:229:C49NHACXX:8:1101:1460:2207:4:N:0:TCCGTC
+TATATTTATTGGAGTTAATTTAACATTTTTTCCTCAACATTTTTTAGGATTGGCTGGAATACCTCGACGTTATTCAGATTACCCAGATGCTTAC
++
+FDHDHHHIJJJJEHHHIIIIJIJHIHIJJJJIGHEIIIJJIJJJHHGIIIJIJIJIJEHGHGFHFH8?ABC?BC>>AADDCACDDDDD<@CD>>
+@D3FCO8P1:229:C49NHACXX:8:1101:1339:2211:4:N:0:TCCGTC
+GGCATAGCCATCGAGGTGTGTCCGGTGTCAAATCAAGTGCTGCAACTGGGCGTGGACTATCGGAATCATCCGGCGGCACTGCTGTTGGCCGCCA
++
+FFHHHHGJJJJJJIJJAGHHGIHHIDFGHIJJJGIJJGIJJIIJIJJIJJJJHHFEFEECACDDBB@CCD@?BDDDDDDDDDDDDCDB:@>BBD
+@D3FCO8P1:229:C49NHACXX:8:1101:1402:2222:4:N:0:TCCGTC
+GACCATTAACAGGAGCTATCGGAGCTATAACAACTGTATCAGGTATAGTAAAATGATTTCATCAATATGATATTTCATTATTTGTATTAGGTAA
++
+FFHHFHGJJJJJJIIJJGJIIJGHGHIIIJIJJIGIHIIGIIJBFDIIGHJJIJJGIEIEGHIJCH@EHFHGHHHGFFFFFFFFFDDEEDCAC@
+@D3FCO8P1:229:C49NHACXX:8:1101:1388:2233:4:N:0:TCCGTC
+AACCAAGATACCTTGTGTTTCTTGGCAAGAAAGCAAAACATTGATGCAATTATTGGTATAATAACTTGTAAGATTGGTAATTGCATTAAATTGT
++
+D4DB?:3E3+2AEAHHFIIIIIIIE9?9?3DGFF>;;F;D9BD9?@DCFFICFGF@FCF@@F@C@DF<7C@E3?ECC>7@DDBAADA;;;>A:A
+@D3FCO8P1:229:C49NHACXX:8:1101:1497:2240:4:N:0:TCCGTC
+CAGCAATCGCAGCAACAACTAAATGGAAACCAACAGCATCTGCCCATCAATCGTCAACCGGCGCCACAGCAATCACACTTCCTGGACAATTCAA
++
+FDHDHHHIGJIJJJJJJJIJJIJJJJJIJJJIIJJJJJJIIJJJHHGGGEGIJEHIJGHFFDDDDD@BBDCDDDDDDDDDDDDDDBDDBDDDDE
+@D3FCO8P1:229:C49NHACXX:8:1101:1399:2245:4:N:0:TCCGTC
+TTTATTAAATAGAATTGTTTCTTGATCTTGAATTTCTATAATTTTATTATCTTTTTTATCTTTTTTTAGAGCTGCTTATACTTTATATTTATAT
++
+EDHFHHGJIIHIEEHIIIIJIJJJ?FFHGHFGHIJHGGIGDFFIG9EHGHEHIJJJJGIFHIGIJJA=;?>CEBBEECCC;>CDCA;BDD>@;C
+@D3FCO8P1:229:C49NHACXX:8:1101:1664:2088:4:N:0:TGGTCA
+TAATTTGTTNNNNNNNNNNNNTTCACAATTTGGTCAATAGCTTGCATAGAAAAATTANNNNNNNNNNNNNNNNNNNNNNNNNNTAATCCAGCNN
++
+2@>@@@@@@############11=???????????????????????>????@@@@@#####################################
+@D3FCO8P1:229:C49NHACXX:8:1101:1512:2095:4:N:0:TGGTCA
+TTCTATCAGNNNNTTTNNNNNTAACTTATTGAGGTTTATGTGGTTCTTATACATTAANNNNNNNNNNNNNNNNNNNNNNNNNTGGGTTATTTNN
++
+2@@@?@@@@####43@#####11=???????8??>??>??????????????@@@@@#####################################
+@D3FCO8P1:229:C49NHACXX:8:1101:1630:2114:4:N:0:TGGTCA
+AAGTTGGCANNNNATATNNNCGAAGATAATACACGTACACGTCATCCGCGATTTAGAANNNNNNNNNNNNNNNNNNNNNNNNCGCCAAGGTGNN
++
+2@@@@@@@?####33@@###14=???????????????????????????????????####################################
+@D3FCO8P1:229:C49NHACXX:8:1101:1540:2119:4:N:0:TGGTCA
+CACACCAATNNNATTATNATGTTATTTAATACATTTATTAAAGAGAATAATGAAATTTNNNNNNNNNANNNNNNNNNNNNNNTATATTCTGCNN
++
+2@@@@@@@?###34@@@#1@????????????????????????????????@@@@@@####################################
+@D3FCO8P1:229:C49NHACXX:8:1101:1503:2124:4:N:0:TGGTCA
+AAGAGAGTANNNATAAGATACTCCAAGCAAAAGCAGAGTATCTGTAAACACTTCGCTCNNNNNNNNNGNNNNNNNNNNNNNCCGTGCAAGTCNN
++
+2@??@?@??###44@@@@?@?@@@????????????>?????????????@@???@####################################
+@D3FCO8P1:229:C49NHACXX:8:1101:1671:2150:4:N:0:TGGTCA
+AAGACAGTGACAATTCAAATTACACATGCGCGTTGCGCACTCACAGATACAAAGATACANNNANNNNCGGGCATACNTNNNAACAGAGCGACTG
++
+<@@@@@??@@@@?@@@@@@@@@@@@@@@???????????????????????????????###################################
+@D3FCO8P1:229:C49NHACXX:8:1101:1552:2151:4:N:0:CACTGT
+ACATACTCAATATGTTTTACATATTTATGACAGACCTTCTCAAACAGAATATTTTACATNNNTTNNNCATTACCGTTTNNNCACAACACATTTT
++
+:@?@?@@@?????@@@@@@?@??@@@???@@?????????????????????@@@@@@@###-8###--=?????==?################
+@D3FCO8P1:229:C49NHACXX:8:1101:1700:2159:4:N:0:CACTGT
+GGCATACCTGCTGCCATTGGTCACACTGGCAGATTACGCGATTATTTTTTTTACGGAAANNNTGNNNTTTCCCTTCCGGNNTGAATTGCCTGGA
++
+:@@?@@@@@@@@@?@?@??@??@@@@?????????????????????=########################################
+@D3FCO8P1:229:C49NHACXX:8:1101:1652:2170:4:N:0:CACTGT
+GACCTACTAAACCTAACAATTCCAGCTATATTAACATTAGCTGAAGACACTAATCAGGAANAATTTAAAACAGAAAACATAATGGCACAGTCCA
++
+AACCCCCCBCCCBBB7CCCCCCBCCBBAABBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB#.;AAABBAAAAA@AA@@@@@@B>==?AA????A
+@D3FCO8P1:229:C49NHACXX:8:1101:1537:2174:4:N:0:CACTGT
+AAGTCTTTGCGCAGACGGATCACCTCCTCGTTTGCAAGTGTGATAGGTACATCATGCTTTNTGTTCAAATCTTGGAAAATGAAATGTGCATGTA
++
+BB?FCBFG4?@@1?CAAC??9?B@9??C:(:@A::@CC:4+:>@C@AAC(>9?
+@D3FCO8P1:229:C49NHACXX:8:1101:1497:2240:1:N:0:CGTACTAG:TAGATCGC:GTCGTTGG
+CATCGTTGCTGCTCTTAACGTCCAAATGGACGGGCGACTCCCCGAACATTGCCTCGAGTCGTGTCTCCACGGATTTCTGGACGTCCG
++
+HHHHHJJJIIIJIHGIJJIHHJJJHIJJJFHIJJBHGGHHHHFEDDDDDDDDDDDDDDCCBDDDDDDDDDDDDDDDDEDD@BDDDDB
diff -r 000000000000 -r 424f44e2124e test-data/emb6801m1_CGTACTAGTAGATCGC_2.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/emb6801m1_CGTACTAGTAGATCGC_2.txt Wed Nov 25 12:37:28 2015 -0500
@@ -0,0 +1,8 @@
+@D3FCO8P1:229:C49NHACXX:8:1101:1385:2179:4:N:0:CGTACTAG:TAGATCGC:CTTCTCAG
+AGATCTGCATCTAATCTAGCTGCTCCCATGCTACCCCTGAATACCCTACACGGCCTGAACAGTCGCCCCACAAGTCTGGCGTGGGG
++
+HF?HHGBHHIJJIGIIIJGIJBEHIGID<9EHIIJJI@;?BGGHIIIIIIIIIIIAGE@HHH?EDFDDB?B?9?:ACCC(85>>B>
+@D3FCO8P1:229:C49NHACXX:8:1101:1497:2240:4:N:0:CGTACTAG:TAGATCGC:CATATGCA
+GCAATCGCAGCAACAACTAAATGGAAACCAACAGCATCTGCCCATCAATCGTCAACCGGCGCCACAGCAATCACACTTCCTGGACA
++
+HDHHHIGJIJJJJJJJIJJIJJJJJIJJJIIJJJJJJIIJJJHHGGGEGIJEHIJGHFFDDDDD@BBDCDDDDDDDDDDDDDDBDD
diff -r 000000000000 -r 424f44e2124e test-data/emb6801m2_AGGCAGAATAGATCGC_1.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/emb6801m2_AGGCAGAATAGATCGC_1.txt Wed Nov 25 12:37:28 2015 -0500
@@ -0,0 +1,8 @@
+@D3FCO8P1:229:C49NHACXX:8:1101:1370:2193:1:N:0:AGGCAGAA:TAGATCGC:TTCCTTGC
+GAGTGTTTGCACGATTATCTCATATTCAAACTGGTCAACATGGGCATACGATTTCTTGCGCTCCTTGCTTTCAAACAGCCTGTCTCT
++
+CFHFHIIJJJJJJIJJIJJJJJJJJJJIJJJJJJBGIJJJJJJJJJJJJJJJJIJJJJHHFFFDEEEDDDDDDDDDDDBBDDDDDDD
+@D3FCO8P1:229:C49NHACXX:8:1101:1399:2245:1:N:0:AGGCAGAA:TAGATCGC:GAATATAA
+ATATAAAGTATAAGCAGCTCTAAAAAAAGATAAAAAAGATAATAAAATTATAGAAATTCAAGATCAAGAAACAATTCTATTTAATAA
++
+FBDFHGIGHGJIJJJJJIIDHHIJJIGGHEEGGIIIIGGDHIGE@FHHIIJJFGGHGHCAHH@D;CD;CCCECDDCCDDDCD3>ACA
diff -r 000000000000 -r 424f44e2124e test-data/emb6801m2_AGGCAGAATAGATCGC_2.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/emb6801m2_AGGCAGAATAGATCGC_2.txt Wed Nov 25 12:37:28 2015 -0500
@@ -0,0 +1,8 @@
+@D3FCO8P1:229:C49NHACXX:8:1101:1370:2193:4:N:0:AGGCAGAA:TAGATCGC:GCTGTTTG
+AAAGCAAGGAGCGCAAGAAATCGTATGCCCATGTTGACCAGTTTGAATATGAGATAATCGTGCAAACACTCCCAAGGAACTGTCTC
++
+HHHHHJJJJJJJJJJJJJJJJJJJJJJJJJIJJJJJHJJJJJGHIIIIIJJIJIJEEEEHHFFFEEEEDED3=CDDDDDDDDCDDD
+@D3FCO8P1:229:C49NHACXX:8:1101:1399:2245:4:N:0:AGGCAGAA:TAGATCGC:AATTTCTT
+TATTAAATAGAATTGTTTCTTGATCTTGAATTTCTATAATTTTATTATCTTTTTTATCTTTTTTTAGAGCTGCTTATACTTTATAT
++
+HFHHGJIIHIEEHIIIIJIJJJ?FFHGHFGHIJHGGIGDFFIG9EHGHEHIJJJJGIFHIGIJJA=;?>CEBBEECCC;>CDCA;B
diff -r 000000000000 -r 424f44e2124e test-data/emb681m1_TAAGGCGACTCTCTAT_1.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/emb681m1_TAAGGCGACTCTCTAT_1.txt Wed Nov 25 12:37:28 2015 -0500
@@ -0,0 +1,8 @@
+@D3FCO8P1:229:C49NHACXX:8:1101:1460:2207:1:N:0:TAAGGCGA:CTCTCTAT:TTACTTGT
+CGTTGTGATACTAAACTTTCTCAAATAATAAAAAAAAAGAATAAAATTCCTAATAATGAAATAGTTGATCCAATAGTTGATACAATA
++
+HHHGHIIGIJJIIJJJJJJIIHIIJHGIHGJIJIJJJHGCCHIGGEHH>EEFFFFFFFACCEACEDCDCCCCCDCDEEDDDE(:ACC
+@D3FCO8P1:229:C49NHACXX:8:1101:1402:2222:1:N:0:TAAGGCGA:CTCTCTAT:GTTAAAAT
+AGTAATAATATTACCTAATACAAATAATGAAATATCATATTGATGAAATCATTTTACTATACCTGATACAGTTGTTATAGCTCCGAT
++
+FHHHHJJIIJJJGJIIJJIIJHIJIJIJIIJJJJJJJIIJJIGGHIJJJIJGJJIIIHIIHJ>GHIIIIIIGGGIIJJJJIH)=ABD
diff -r 000000000000 -r 424f44e2124e test-data/emb681m1_TAAGGCGACTCTCTAT_2.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/emb681m1_TAAGGCGACTCTCTAT_2.txt Wed Nov 25 12:37:28 2015 -0500
@@ -0,0 +1,8 @@
+@D3FCO8P1:229:C49NHACXX:8:1101:1460:2207:4:N:0:TAAGGCGA:CTCTCTAT:CATTATTA
+TATTTATTGGAGTTAATTTAACATTTTTTCCTCAACATTTTTTAGGATTGGCTGGAATACCTCGACGTTATTCAGATTACCCAGAT
++
+HDHHHIJJJJEHHHIIIIJIJHIHIJJJJIGHEIIIJJIJJJHHGIIIJIJIJIJEHGHGFHFH8?ABC?BC>>AADDCACDDDDD
+@D3FCO8P1:229:C49NHACXX:8:1101:1402:2222:4:N:0:TAAGGCGA:CTCTCTAT:GTCCATGA
+CCATTAACAGGAGCTATCGGAGCTATAACAACTGTATCAGGTATAGTAAAATGATTTCATCAATATGATATTTCATTATTTGTATT
++
+HHFHGJJJJJJIIJJGJIIJGHGHIIIJIJJIGIHIIGIIJBFDIIGHJJIJJGIEIEGHIJCH@EHFHGHHHGFFFFFFFFFDDE
diff -r 000000000000 -r 424f44e2124e test-data/emb681m4_TCCTGAGCCTCTCTAT_1.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/emb681m4_TCCTGAGCCTCTCTAT_1.txt Wed Nov 25 12:37:28 2015 -0500
@@ -0,0 +1,8 @@
+@D3FCO8P1:229:C49NHACXX:8:1101:1452:2184:1:N:0:TCCTGAGC:CTCTCTAT:GGTAGAGT
+GGGAAAGGGAAGGGCAAGGGGGAGGGGAAGAATTTAACCGGGCGGGAGGAGAATCGGGCAGGGAAGAATGGTTGGTTGGTGGAACAA
++
+HHHDHJJGIGIJCBDHEHGJJJBGEHIBGGHFGFFGGHFFDD>?BDBBDDDDDD@ADD;>@D98AB?CCDD:CBBACCCCAC
+@D3FCO8P1:229:C49NHACXX:8:1101:1388:2233:4:N:0:TCCTGAGC:CTCTCTAT:GAAATAAA
+CCAAGATACCTTGTGTTTCTTGGCAAGAAAGCAAAACATTGATGCAATTATTGGTATAATAACTTGTAAGATTGGTAATTGCATTA
++
+DB?:3E3+2AEAHHFIIIIIIIE9?9?3DGFF>;;F;D9BD9?@DCFFICFGF@FCF@@F@C@DF<7C@E3?ECC>7@DDBAADA;
diff -r 000000000000 -r 424f44e2124e test-data/emb681m5_GGACTCCTCTCTCTAT_1.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/emb681m5_GGACTCCTCTCTCTAT_1.txt Wed Nov 25 12:37:28 2015 -0500
@@ -0,0 +1,8 @@
+@D3FCO8P1:229:C49NHACXX:8:1101:1486:2204:1:N:0:GGACTCCT:CTCTCTAT:CTTATTCA
+TCTGTTGCTCATATAGGAATTGTTCTATCAGGACTTTTAACTATAACTTATTGAGGTTTATGTGGTTCTTATACATTAATAATTGCT
++
+HHHGHJJIJJJJJJJJJJJJJJJJJJIJJJJJJJIJJJIJJJJJJIJJJJJJIJJJHIJJJJHIIHHHHIJJJIJJHHHHHHFFFFE
+@D3FCO8P1:229:C49NHACXX:8:1101:1587:2187:1:N:0:GGACTCCT:CTCTCTAT:ATATAAAA
+ATAATCAAACTACATCGACAAAATGTCAATATCATGCAGCTGCTTCAAAACCAAAATGATGATTTTTTGAGAAGTGATTATTTAAAT
++
+HHHHHJJJJJJJJJJJJJJJJJIJJIJJJJJJJJJJJJJJJJJJJJJJJJJJIJIJJJJJJJJJJHHFFDDDEDCDDFEEDFEEEDE
diff -r 000000000000 -r 424f44e2124e test-data/emb681m5_GGACTCCTCTCTCTAT_2.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/emb681m5_GGACTCCTCTCTCTAT_2.txt Wed Nov 25 12:37:28 2015 -0500
@@ -0,0 +1,8 @@
+@D3FCO8P1:229:C49NHACXX:8:1101:1486:2204:4:N:0:GGACTCCT:CTCTCTAT:TTAATATT
+CTTCGACTTCCAAGACGTTCATAAGATACATTAGCTAAACAAAATAACCCAGAAGAACATAAACCATGAGCAATTATTAATGTATA
++
+HHHFHIJJJJJJJJJJIIGIIIJJIIGHJJJJIJJIIJIJJJIJJIJJJJJJJJIGIJIIJJHHFHHFFFFFEDEEEFFFEDDDEF
+@D3FCO8P1:229:C49NHACXX:8:1101:1587:2187:4:N:0:GGACTCCT:CTCTCTAT:ATTTATGG
+ATCAACATTTTTTATAGCAACAGGATTTCACGGAATTCATGTATTAATCGGAACAACTTTTTTATTAGTATGTTTACTACGACATT
++
+HHHHHJJJJJJJJJJJJJJJJJJJIJJJJJJJJIJJJJJJJIHGIGIIJJJIJJJJHHHHHHDDEEEEDEFEFEEDDDEDDDDDDD
diff -r 000000000000 -r 424f44e2124e test-data/file_1_sequence.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/file_1_sequence.txt Wed Nov 25 12:37:28 2015 -0500
@@ -0,0 +1,100 @@
+@D3FCO8P1:229:C49NHACXX:8:1101:1347:2097 1:N:0:
+CACTGTTCAATGCCAATAGCAATGAAACCACCCATANAANNNNNACGGCTGAACANNNNNNNACNNGATATAGCATAAATGNANNNTNNNNANTNNNNNN
++
+CCCFFFFFHHHHHJJJJJJJJJJJIJJJIJJJJJJI#1?#####00?FHIJJJJI#######--##,,=A=CDDDDDDDEE###################
+@D3FCO8P1:229:C49NHACXX:8:1101:1406:2140 1:N:0:
+CACTGTAATTTATCTCTTTTCATATAACTCTCTGGTAATNNNNAACATAAAACCGANCGCACATGATAATTCTTCCAAATTTATATATNAATTTTATANN
++
+BBCFFFDFHHHGHHIJJJJJJIJIJIGHHHIJJJJGGIJ####11?DHHIIIIGHI#-?CAAC??9?B@9??C:(:@A::@CC:4+:>@C@AAC(>9?CCCC@
+@D3FCO8P1:229:C49NHACXX:8:1101:1452:2184 1:N:0:
+CACTGTGTGGGAAAGGGAAGGGCAAGGGGGAGGGGAAGAATTTAACCGGGCGGGAGGAGAATCGGGCAGGGAAGAATGGTTGGTTGGTGGAACAACTGAA
++
+BB=DDDEDHHHDHJJGIGIJCBDHEHGJJJBGEHIBGGHFGFFGGHFFDD>?BDBBDDDDDD@ADD;>@D98AB?CCDD:CBBEEFFFFFFFACCEACEDCDCCCCCDCDEEDDDE(:ACCD:@D@
+@D3FCO8P1:229:C49NHACXX:8:1101:1339:2211 1:N:0:
+ATTCCGAGTAAATTAAATGCGAAAATAAAAGGCAGCATGAGNTANTTACTNAAANGGGGTCATNAACAGTACTTGTGCTCCNCCANGTCGNCGNTNCNCT
++
+@@CFFFFFFHHHHJJJIJJJJJJJIJIJJJJJJJJJJJJJJ#0?#0?DHI#-;F#-;DH?EFH#,;BCDEEEEEDDCCCDD#,8?#,5?B##########
+@D3FCO8P1:229:C49NHACXX:8:1101:1402:2222 1:N:0:
+ATTCCGATAGTAATAATATTACCTAATACAAATAATGAAATATCATATTGATGAAATCATTTTACTATACCTGATACAGTTGTTATAGCTCCGATAGCTC
++
+CCCFFFFDFHHHHJJIIJJJGJIIJJIIJHIJIJIJIIJJJJJJJIIJJIGGHIJJJIJGJJIIIHIIHJ>GHIIIIIIGGGIIJJJJIH)=ABDDDDEE
+@D3FCO8P1:229:C49NHACXX:8:1101:1388:2233 1:N:0:
+ATTCCGAATTTAATGCAATTACCAATCTTACAAGTTATTATACCAATAATTGCATCTATGTTTTGCTTTCTTGACAAGAAACACAAGGTAACTTGGGTTA
++
+1?8ADDDDACAA:@?C
+@D3FCO8P1:229:C49NHACXX:8:1101:1664:2088 1:N:0:
+GCTACCAAGTTTATAAATGGCAACCTTAAGTGTAANNNANNNNNTATGCACAGNANNNNNNNNANNNATGCAAAACGACTCNNNNNNNNNNNNCNNNNNN
++
+CCCFFFFFHHHHHJJJJJJJJJJJJJJJJJIIHIJ###1#####20?FHJJJJ#.########-###--;BDFEEECDDDD###################
+@D3FCO8P1:229:C49NHACXX:8:1101:1512:2095 1:N:0:
+GCTACCACGTTCATAAGATACATTAGCTAAACAAAANAANNNNNAAGAACATAAANNNNNNNCANNTATTAATGTATAAGANCNNNANNNNCNTNNNNNN
++
+CC@FFFFFHHHHHJJJJJJIJJJJIJJJJIJJJJJJ#1C#####00?FIJJJJJJ#######--##,5?DDEEEFCFFEDD###################
+@D3FCO8P1:229:C49NHACXX:8:1101:1630:2114 1:N:0:
+GCTACCCGTTGGAGGAGGAGCCGCCATGAATGCCCTGCGNNNNTTCTACCTGGAGANNNCGGTGGTCACACGAGCCTACACCACGGTCNNCGTGCTNNNN
++
+CCCFFFFFHHHHGJJGHJGHIJJJJJJJJJJJJJJJJJJ####.-;DHIJJHHHHH###,,=?BDBDDDDDDDDDDDDDDDDDDDDDD##+28@DD####
+@D3FCO8P1:229:C49NHACXX:8:1101:1540:2119 1:N:0:
+GCTACCTGGACTCAAGACCTAATTGCATTAACCGTCTGTNNNNTACGTAGCGTATGNNATTGCGCACTTCTTCTGCGGATAGTCCTTCNNCATCTCNNNN
++
+CCCFFFFFHHHHHJJJJJJJJJJJJJJJJJJJJJJJJIJ####20?GHIJJJIJIJ##-5CEFHFFDDEEDDDDDDDDDDDDDEDDDD##+2?BDD####
+@D3FCO8P1:229:C49NHACXX:8:1101:1503:2124 1:N:0:
+GCTACCTACATATACTTATAGGCATACTTATACGACTTCNNNNCCCGGTTAATATGNNGTGGCCCGTATAAGTTAATGGGCACAACCGNNTGGGACNNNN
++
+CCCFFFFFHHHHHIJJJJJJJJJJJIJJJJJJJJJJJJJ####00BFHGIIJJJJJ##--BEHJJHDFFEDEEFEEEDDDDDDDDDDD##+2AC@@CB@BBA@?BBBBA@CCDCCCCC<493?CCCCCC>:>A<8???AC####
+@D3FCO8P1:229:C49NHACXX:8:1101:1563:2176 1:N:0:
+CGAAACGGAAGAGAAAAAAATATAAAGTGTCAAGGGGCGTGTGCAGCGACACTTCGCCGACCCCTCCCCACATTATTTTTTTGCCGCCCGCTGGTAGCAG
++
+;@@BDDDA:DBFDF;A@@@@@@####43@#####11=?????????>?????????????????????@?#####################################
+@D3FCO8P1:229:C49NHACXX:8:1101:1406:2140 4:N:0:
+GTATAGTTATATGAAAGNAATATAAAATTTATATATAAATTTGGAAGAATTATCATGTGCGCTCNNNNNNNNNTTANANATNNNNNNAGAGTTATATGAN
++
+#####22@@@@@@@?@@#3=>?@@?@@@?@?@>?????>????????????>??????@?????####################################
+@D3FCO8P1:229:C49NHACXX:8:1101:1418:2170 4:N:0:
+GTATAGGCTATTGGATTATTAGGATTTATTGTATGAGCTCATCATATATTTACCGTTGGAATAGATNTAGATACTCGAGCTTATTTTACCTCAGCTACTA
++
+#4=DFFFFHHHHHJEHIHHJIJJHIJJIJJJIJJJIJJJJIJJJJIJIIJIGJJJJJJJJJJJJJJ#-;CFHIJJJHHHFFFFFEEEEEEEDDDDDDDDD
+@D3FCO8P1:229:C49NHACXX:8:1101:1385:2179 4:N:0:
+GTATAGAGAGATCTGCATCTAATCTAGCTGCTCCCATGCTACCCCTGAATACCCTACACGGCCTGAACAGTCGCCCCACAAGTCTGGCGTGGGGCTGTCT
++
+@@CDFFDFHF?HHGBHHIJJIGIIIJGIJBEHIGID<9EHIIJJI@;?BGGHIIIIIIIIIIIAGE@HHH?EDFDDB?B?9?:ACCC(85>>B>>@BBD@
+@D3FCO8P1:229:C49NHACXX:8:1101:1452:2184 4:N:0:
+GTATAGCATTCTGTATGCCCTTCCCTCTCGCACACTCGACCCAATGACCCGCTTTGCTCTGTTTACCTCTCCGCTCTGTTTTTGCACTTGGAAATTGCTA
++
+B@CFFFFFHGDHHGGIJJIJJJGHIIIGFHHIIGIIIJIJJEHGEGGIJJIIIIGGGHGGFHHFEC@BCEDECDDDDDDDDDD?AC>ACCCCACADCCDD
+@D3FCO8P1:229:C49NHACXX:8:1101:1370:2193 4:N:0:
+GTATAGTGAAAGCAAGGAGCGCAAGAAATCGTATGCCCATGTTGACCAGTTTGAATATGAGATAATCGTGCAAACACTCCCAAGGAACTGTCTCTTATAC
++
+CCCFFFFFHHHHHJJJJJJJJJJJJJJJJJJJJJJJJJIJJJJJHJJJJJGHIIIIIJJIJIJEEEEHHFFFEEEEDED3=CDDDDDDDDCDDDDDDDDD
+@D3FCO8P1:229:C49NHACXX:8:1101:1486:2204 4:N:0:
+TCCGTCTTCTTCGACTTCCAAGACGTTCATAAGATACATTAGCTAAACAAAATAACCCAGAAGAACATAAACCATGAGCAATTATTAATGTATAAGAACC
++
+CCCFFFFFHHHFHIJJJJJJJJJJIIGIIIJJIIGHJJJJIJJIIJIJJJIJJIJJJJJJJJIGIJIIJJHHFHHFFFFFEDEEEFFFEDDDEFEDDDDD
+@D3FCO8P1:229:C49NHACXX:8:1101:1460:2207 4:N:0:
+TCCGTCTATATTTATTGGAGTTAATTTAACATTTTTTCCTCAACATTTTTTAGGATTGGCTGGAATACCTCGACGTTATTCAGATTACCCAGATGCTTAC
++
+@?@DDDFDHDHHHIJJJJEHHHIIIIJIJHIHIJJJJIGHEIIIJJIJJJHHGIIIJIJIJIJEHGHGFHFH8?ABC?BC>>AADDCACDDDDD<@CD>>
+@D3FCO8P1:229:C49NHACXX:8:1101:1339:2211 4:N:0:
+TCCGTCGGCATAGCCATCGAGGTGTGTCCGGTGTCAAATCAAGTGCTGCAACTGGGCGTGGACTATCGGAATCATCCGGCGGCACTGCTGTTGGCCGCCA
++
+C#1ADDFFHHHHGJJJJJJIJJAGHHGIHHIDFGHIJJJGIJJGIJJIIJIJJIJJJJHHFEFEECACDDBB@CCD@?BDDDDDDDDDDDDCDB:@>BBD
+@D3FCO8P1:229:C49NHACXX:8:1101:1402:2222 4:N:0:
+TCCGTCGACCATTAACAGGAGCTATCGGAGCTATAACAACTGTATCAGGTATAGTAAAATGATTTCATCAATATGATATTTCATTATTTGTATTAGGTAA
++
+@BCFFFFFHHFHGJJJJJJIIJJGJIIJGHGHIIIJIJJIGIHIIGIIJBFDIIGHJJIJJGIEIEGHIJCH@EHFHGHHHGFFFFFFFFFDDEEDCAC@
+@D3FCO8P1:229:C49NHACXX:8:1101:1388:2233 4:N:0:
+TCCGTCAACCAAGATACCTTGTGTTTCTTGGCAAGAAAGCAAAACATTGATGCAATTATTGGTATAATAACTTGTAAGATTGGTAATTGCATTAAATTGT
++
+@@;;F;D9BD9?@DCFFICFGF@FCF@@F@C@DF<7C@E3?ECC>7@DDBAADA;;;>A:A
+@D3FCO8P1:229:C49NHACXX:8:1101:1497:2240 4:N:0:
+TCCGTCCAGCAATCGCAGCAACAACTAAATGGAAACCAACAGCATCTGCCCATCAATCGTCAACCGGCGCCACAGCAATCACACTTCCTGGACAATTCAA
++
+@@?DFFFDHDHHHIGJIJJJJJJJIJJIJJJJJIJJJIIJJJJJJIIJJJHHGGGEGIJEHIJGHFFDDDDD@BBDCDDDDDDDDDDDDDDBDDBDDDDE
+@D3FCO8P1:229:C49NHACXX:8:1101:1399:2245 4:N:0:
+TCCGTCTTTATTAAATAGAATTGTTTCTTGATCTTGAATTTCTATAATTTTATTATCTTTTTTATCTTTTTTTAGAGCTGCTTATACTTTATATTTATAT
++
+?@@DFBEDHFHHGJIIHIEEHIIIIJIJJJ?FFHGHFGHIJHGGIGDFFIG9EHGHEHIJJJJGIFHIGIJJA=;?>CEBBEECCC;>CDCA;BDD>@;C
+@D3FCO8P1:229:C49NHACXX:8:1101:1664:2088 4:N:0:
+TGGTCATAATTTGTTNNNNNNNNNNNNTTCACAATTTGGTCAATAGCTTGCATAGAAAAATTANNNNNNNNNNNNNNNNNNNNNNNNNNTAATCCAGCNN
++
+#####42@>@@@@@@############11=???????????????????????>????@@@@@#####################################
+@D3FCO8P1:229:C49NHACXX:8:1101:1512:2095 4:N:0:
+TGGTCATTCTATCAGNNNNTTTNNNNNTAACTTATTGAGGTTTATGTGGTTCTTATACATTAANNNNNNNNNNNNNNNNNNNNNNNNNTGGGTTATTTNN
++
+#####42@@@?@@@@####43@#####11=???????8??>??>??????????????@@@@@#####################################
+@D3FCO8P1:229:C49NHACXX:8:1101:1630:2114 4:N:0:
+TGGTCAAAGTTGGCANNNNATATNNNCGAAGATAATACACGTACACGTCATCCGCGATTTAGAANNNNNNNNNNNNNNNNNNNNNNNNCGCCAAGGTGNN
++
+#####22@@@@@@@?####33@@###14=???????????????????????????????????####################################
+@D3FCO8P1:229:C49NHACXX:8:1101:1540:2119 4:N:0:
+TGGTCACACACCAATNNNATTATNATGTTATTTAATACATTTATTAAAGAGAATAATGAAATTTNNNNNNNNNANNNNNNNNNNNNNNTATATTCTGCNN
++
+#####22@@@@@@@?###34@@@#1@????????????????????????????????@@@@@@####################################
+@D3FCO8P1:229:C49NHACXX:8:1101:1503:2124 4:N:0:
+TGGTCAAAGAGAGTANNNATAAGATACTCCAAGCAAAAGCAGAGTATCTGTAAACACTTCGCTCNNNNNNNNNGNNNNNNNNNNNNNCCGTGCAAGTCNN
++
+#####22@??@?@??###44@@@@?@?@@@????????????>?????????????@@???@####################################
+@D3FCO8P1:229:C49NHACXX:8:1101:1671:2150 4:N:0:
+TGGTCAAAGACAGTGACAATTCAAATTACACATGCGCGTTGCGCACTCACAGATACAAAGATACANNNANNNNCGGGCATACNTNNNAACAGAGCGACTG
++
+###2#4<@@@@@??@@@@?@@@@@@@@@@@@@@@???????????????????????????????###################################
+@D3FCO8P1:229:C49NHACXX:8:1101:1552:2151 4:N:0:
+CACTGTACATACTCAATATGTTTTACATATTTATGACAGACCTTCTCAAACAGAATATTTTACATNNNTTNNNCATTACCGTTTNNNCACAACACATTTT
++
+###2#2:@?@?@@@?????@@@@@@?@??@@@???@@?????????????????????@@@@@@@###-8###--=?????==?################
+@D3FCO8P1:229:C49NHACXX:8:1101:1700:2159 4:N:0:
+CACTGTGGCATACCTGCTGCCATTGGTCACACTGGCAGATTACGCGATTATTTTTTTTACGGAAANNNTGNNNTTTCCCTTCCGGNNTGAATTGCCTGGA
++
+###2#2:@@?@@@@@@@@@?@?@??@??@@@@?????????????????????=########################################
+@D3FCO8P1:229:C49NHACXX:8:1101:1652:2170 4:N:0:
+CACTGTGACCTACTAAACCTAACAATTCCAGCTATATTAACATTAGCTGAAGACACTAATCAGGAANAATTTAAAACAGAAAACATAATGGCACAGTCCA
++
+#4=AAAAACCCCCCBCCCBBB7CCCCCCBCCBBAABBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB#.;AAABBAAAAA@AA@@@@@@B>==?AA????A
+@D3FCO8P1:229:C49NHACXX:8:1101:1537:2174 4:N:0:
+CACTGTAAGTCTTTGCGCAGACGGATCACCTCCTCGTTTGCAAGTGTGATAGGTACATCATGCTTTNTGTTCAAATCTTGGAAAATGAAATGTGCATGTA
++
+#+1=BBBB?FCBFG4?@@1?CAAC??9?B@9??C:(:@A::@CC:4+:>@C@AAC(>9?CCCC@
+@D3FCO8P1:229:C49NHACXX:8:1101:1452:2184 1:N:0:
+GGTAGAGTGGGAAAGGGAAGGGCAAGGGGGAGGGGAAGAATTTAACCGGGCGGGAGGAGAATCGGGCAGGGAAGAATGGTTGGTTGGTGGAACAACTGAA
++
+BB=DDDEDHHHDHJJGIGIJCBDHEHGJJJBGEHIBGGHFGFFGGHFFDD>?BDBBDDDDDD@ADD;>@D98AB?CCDD:CBBEEFFFFFFFACCEACEDCDCCCCCDCDEEDDDE(:ACCD:@D@
+@D3FCO8P1:229:C49NHACXX:8:1101:1339:2211 1:N:0:
+ATTCAAAGTAAATTAAATGCGAAAATAAAAGGCAGCATGAGNTANTTACTNAAANGGGGTCATNAACAGTACTTGTGCTCCNCCANGTCGNCGNTNCNCT
++
+@@CFFFFFFHHHHJJJIJJJJJJJIJIJJJJJJJJJJJJJJ#0?#0?DHI#-;F#-;DH?EFH#,;BCDEEEEEDDCCCDD#,8?#,5?B##########
+@D3FCO8P1:229:C49NHACXX:8:1101:1402:2222 1:N:0:
+GTTAAAATAGTAATAATATTACCTAATACAAATAATGAAATATCATATTGATGAAATCATTTTACTATACCTGATACAGTTGTTATAGCTCCGATAGCTC
++
+CCCFFFFDFHHHHJJIIJJJGJIIJJIIJHIJIJIJIIJJJJJJJIIJJIGGHIJJJIJGJJIIIHIIHJ>GHIIIIIIGGGIIJJJJIH)=ABDDDDEE
+@D3FCO8P1:229:C49NHACXX:8:1101:1388:2233 1:N:0:
+AACAACAATTTAATGCAATTACCAATCTTACAAGTTATTATACCAATAATTGCATCTATGTTTTGCTTTCTTGACAAGAAACACAAGGTAACTTGGGTTA
++
+1?8ADDDDACAA:@?C
+@D3FCO8P1:229:C49NHACXX:8:1101:1664:2088 1:N:0:
+CTATAAAAGTTTATAAATGGCAACCTTAAGTGTAANNNANNNNNTATGCACAGNANNNNNNNNANNNATGCAAAACGACTCNNNNNNNNNNNNCNNNNNN
++
+CCCFFFFFHHHHHJJJJJJJJJJJJJJJJJIIHIJ###1#####20?FHJJJJ#.########-###--;BDFEEECDDDD###################
+@D3FCO8P1:229:C49NHACXX:8:1101:1512:2095 1:N:0:
+TCCAAGACGTTCATAAGATACATTAGCTAAACAAAANAANNNNNAAGAACATAAANNNNNNNCANNTATTAATGTATAAGANCNNNANNNNCNTNNNNNN
++
+CC@FFFFFHHHHHJJJJJJIJJJJIJJJJIJJJJJJ#1C#####00?FIJJJJJJ#######--##,5?DDEEEFCFFEDD###################
+@D3FCO8P1:229:C49NHACXX:8:1101:1630:2114 1:N:0:
+GTCCAACGTTGGAGGAGGAGCCGCCATGAATGCCCTGCGNNNNTTCTACCTGGAGANNNCGGTGGTCACACGAGCCTACACCACGGTCNNCGTGCTNNNN
++
+CCCFFFFFHHHHGJJGHJGHIJJJJJJJJJJJJJJJJJJ####.-;DHIJJHHHHH###,,=?BDBDDDDDDDDDDDDDDDDDDDDDD##+28@DD####
+@D3FCO8P1:229:C49NHACXX:8:1101:1540:2119 1:N:0:
+CATATATGGACTCAAGACCTAATTGCATTAACCGTCTGTNNNNTACGTAGCGTATGNNATTGCGCACTTCTTCTGCGGATAGTCCTTCNNCATCTCNNNN
++
+CCCFFFFFHHHHHJJJJJJJJJJJJJJJJJJJJJJJJIJ####20?GHIJJJIJIJ##-5CEFHFFDDEEDDDDDDDDDDDDDEDDDD##+2?BDD####
+@D3FCO8P1:229:C49NHACXX:8:1101:1503:2124 1:N:0:
+TACTTATACATATACTTATAGGCATACTTATACGACTTCNNNNCCCGGTTAATATGNNGTGGCCCGTATAAGTTAATGGGCACAACCGNNTGGGACNNNN
++
+CCCFFFFFHHHHHIJJJJJJJJJJJIJJJJJJJJJJJJJ####00BFHGIIJJJJJ##--BEHJJHDFFEDEEFEEEDDDDDDDDDDD##+2AC@@CB@BBA@?BBBBA@CCDCCCCC<493?CCCCCC>:>A<8???AC####
+@D3FCO8P1:229:C49NHACXX:8:1101:1563:2176 1:N:0:
+GTCTCAGGAAGAGAAAAAAATATAAAGTGTCAAGGGGCGTGTGCAGCGACACTTCGCCGACCCCTCCCCACATTATTTTTTTGCCGCCCGCTGGTAGCAG
++
+;@@BDDDA:DBFDF;A@@@@@@####43@#####11=?????????>?????????????????????@?#####################################
+@D3FCO8P1:229:C49NHACXX:8:1101:1406:2140 4:N:0:
+NNNNNATTATATGAAAGNAATATAAAATTTATATATAAATTTGGAAGAATTATCATGTGCGCTCNNNNNNNNNTTANANATNNNNNNAGAGTTATATGAN
++
+#####22@@@@@@@?@@#3=>?@@?@@@?@?@>?????>????????????>??????@?????####################################
+@D3FCO8P1:229:C49NHACXX:8:1101:1418:2170 4:N:0:
+NTATTAGCTATTGGATTATTAGGATTTATTGTATGAGCTCATCATATATTTACCGTTGGAATAGATNTAGATACTCGAGCTTATTTTACCTCAGCTACTA
++
+#4=DFFFFHHHHHJEHIHHJIJJHIJJIJJJIJJJIJJJJIJJJJIJIIJIGJJJJJJJJJJJJJJ#-;CFHIJJJHHHFFFFFEEEEEEEDDDDDDDDD
+@D3FCO8P1:229:C49NHACXX:8:1101:1385:2179 4:N:0:
+CTTCTCAGAGATCTGCATCTAATCTAGCTGCTCCCATGCTACCCCTGAATACCCTACACGGCCTGAACAGTCGCCCCACAAGTCTGGCGTGGGGCTGTCT
++
+@@CDFFDFHF?HHGBHHIJJIGIIIJGIJBEHIGID<9EHIIJJI@;?BGGHIIIIIIIIIIIAGE@HHH?EDFDDB?B?9?:ACCC(85>>B>>@BBD@
+@D3FCO8P1:229:C49NHACXX:8:1101:1452:2184 4:N:0:
+CTTTTCCATTCTGTATGCCCTTCCCTCTCGCACACTCGACCCAATGACCCGCTTTGCTCTGTTTACCTCTCCGCTCTGTTTTTGCACTTGGAAATTGCTA
++
+B@CFFFFFHGDHHGGIJJIJJJGHIIIGFHHIIGIIIJIJJEHGEGGIJJIIIIGGGHGGFHHFEC@BCEDECDDDDDDDDDD?AC>ACCCCACADCCDD
+@D3FCO8P1:229:C49NHACXX:8:1101:1370:2193 4:N:0:
+GCTGTTTGAAAGCAAGGAGCGCAAGAAATCGTATGCCCATGTTGACCAGTTTGAATATGAGATAATCGTGCAAACACTCCCAAGGAACTGTCTCTTATAC
++
+CCCFFFFFHHHHHJJJJJJJJJJJJJJJJJJJJJJJJJIJJJJJHJJJJJGHIIIIIJJIJIJEEEEHHFFFEEEEDED3=CDDDDDDDDCDDDDDDDDD
+@D3FCO8P1:229:C49NHACXX:8:1101:1486:2204 4:N:0:
+TTAATATTCTTCGACTTCCAAGACGTTCATAAGATACATTAGCTAAACAAAATAACCCAGAAGAACATAAACCATGAGCAATTATTAATGTATAAGAACC
++
+CCCFFFFFHHHFHIJJJJJJJJJJIIGIIIJJIIGHJJJJIJJIIJIJJJIJJIJJJJJJJJIGIJIIJJHHFHHFFFFFEDEEEFFFEDDDEFEDDDDD
+@D3FCO8P1:229:C49NHACXX:8:1101:1460:2207 4:N:0:
+CATTATTATATTTATTGGAGTTAATTTAACATTTTTTCCTCAACATTTTTTAGGATTGGCTGGAATACCTCGACGTTATTCAGATTACCCAGATGCTTAC
++
+@?@DDDFDHDHHHIJJJJEHHHIIIIJIJHIHIJJJJIGHEIIIJJIJJJHHGIIIJIJIJIJEHGHGFHFH8?ABC?BC>>AADDCACDDDDD<@CD>>
+@D3FCO8P1:229:C49NHACXX:8:1101:1339:2211 4:N:0:
+CNATTGGGCATAGCCATCGAGGTGTGTCCGGTGTCAAATCAAGTGCTGCAACTGGGCGTGGACTATCGGAATCATCCGGCGGCACTGCTGTTGGCCGCCA
++
+C#1ADDFFHHHHGJJJJJJIJJAGHHGIHHIDFGHIJJJGIJJGIJJIIJIJJIJJJJHHFEFEECACDDBB@CCD@?BDDDDDDDDDDDDCDB:@>BBD
+@D3FCO8P1:229:C49NHACXX:8:1101:1402:2222 4:N:0:
+GTCCATGACCATTAACAGGAGCTATCGGAGCTATAACAACTGTATCAGGTATAGTAAAATGATTTCATCAATATGATATTTCATTATTTGTATTAGGTAA
++
+@BCFFFFFHHFHGJJJJJJIIJJGJIIJGHGHIIIJIJJIGIHIIGIIJBFDIIGHJJIJJGIEIEGHIJCH@EHFHGHHHGFFFFFFFFFDDEEDCAC@
+@D3FCO8P1:229:C49NHACXX:8:1101:1388:2233 4:N:0:
+GAAATAAACCAAGATACCTTGTGTTTCTTGGCAAGAAAGCAAAACATTGATGCAATTATTGGTATAATAACTTGTAAGATTGGTAATTGCATTAAATTGT
++
+@@;;F;D9BD9?@DCFFICFGF@FCF@@F@C@DF<7C@E3?ECC>7@DDBAADA;;;>A:A
+@D3FCO8P1:229:C49NHACXX:8:1101:1497:2240 4:N:0:
+CATATGCAGCAATCGCAGCAACAACTAAATGGAAACCAACAGCATCTGCCCATCAATCGTCAACCGGCGCCACAGCAATCACACTTCCTGGACAATTCAA
++
+@@?DFFFDHDHHHIGJIJJJJJJJIJJIJJJJJIJJJIIJJJJJJIIJJJHHGGGEGIJEHIJGHFFDDDDD@BBDCDDDDDDDDDDDDDDBDDBDDDDE
+@D3FCO8P1:229:C49NHACXX:8:1101:1399:2245 4:N:0:
+AATTTCTTTATTAAATAGAATTGTTTCTTGATCTTGAATTTCTATAATTTTATTATCTTTTTTATCTTTTTTTAGAGCTGCTTATACTTTATATTTATAT
++
+?@@DFBEDHFHHGJIIHIEEHIIIIJIJJJ?FFHGHFGHIJHGGIGDFFIG9EHGHEHIJJJJGIFHIGIJJA=;?>CEBBEECCC;>CDCA;BDD>@;C
+@D3FCO8P1:229:C49NHACXX:8:1101:1664:2088 4:N:0:
+NNNNNATAATTTGTTNNNNNNNNNNNNTTCACAATTTGGTCAATAGCTTGCATAGAAAAATTANNNNNNNNNNNNNNNNNNNNNNNNNNTAATCCAGCNN
++
+#####42@>@@@@@@############11=???????????????????????>????@@@@@#####################################
+@D3FCO8P1:229:C49NHACXX:8:1101:1512:2095 4:N:0:
+NNNNNGTTCTATCAGNNNNTTTNNNNNTAACTTATTGAGGTTTATGTGGTTCTTATACATTAANNNNNNNNNNNNNNNNNNNNNNNNNTGGGTTATTTNN
++
+#####42@@@?@@@@####43@#####11=???????8??>??>??????????????@@@@@#####################################
+@D3FCO8P1:229:C49NHACXX:8:1101:1630:2114 4:N:0:
+NNNNNAAAGTTGGCANNNNATATNNNCGAAGATAATACACGTACACGTCATCCGCGATTTAGAANNNNNNNNNNNNNNNNNNNNNNNNCGCCAAGGTGNN
++
+#####22@@@@@@@?####33@@###14=???????????????????????????????????####################################
+@D3FCO8P1:229:C49NHACXX:8:1101:1540:2119 4:N:0:
+NNNNNGCACACCAATNNNATTATNATGTTATTTAATACATTTATTAAAGAGAATAATGAAATTTNNNNNNNNNANNNNNNNNNNNNNNTATATTCTGCNN
++
+#####22@@@@@@@?###34@@@#1@????????????????????????????????@@@@@@####################################
+@D3FCO8P1:229:C49NHACXX:8:1101:1503:2124 4:N:0:
+NNNNNTAAGAGAGTANNNATAAGATACTCCAAGCAAAAGCAGAGTATCTGTAAACACTTCGCTCNNNNNNNNNGNNNNNNNNNNNNNCCGTGCAAGTCNN
++
+#####22@??@?@??###44@@@@?@?@@@????????????>?????????????@@???@####################################
+@D3FCO8P1:229:C49NHACXX:8:1101:1671:2150 4:N:0:
+NNNGNCAAGACAGTGACAATTCAAATTACACATGCGCGTTGCGCACTCACAGATACAAAGATACANNNANNNNCGGGCATACNTNNNAACAGAGCGACTG
++
+###2#4<@@@@@??@@@@?@@@@@@@@@@@@@@@???????????????????????????????###################################
+@D3FCO8P1:229:C49NHACXX:8:1101:1552:2151 4:N:0:
+NNNGNGACATACTCAATATGTTTTACATATTTATGACAGACCTTCTCAAACAGAATATTTTACATNNNTTNNNCATTACCGTTTNNNCACAACACATTTT
++
+###2#2:@?@?@@@?????@@@@@@?@??@@@???@@?????????????????????@@@@@@@###-8###--=?????==?################
+@D3FCO8P1:229:C49NHACXX:8:1101:1700:2159 4:N:0:
+NNNCNCGGCATACCTGCTGCCATTGGTCACACTGGCAGATTACGCGATTATTTTTTTTACGGAAANNNTGNNNTTTCCCTTCCGGNNTGAATTGCCTGGA
++
+###2#2:@@?@@@@@@@@@?@?@??@??@@@@?????????????????????=########################################
+@D3FCO8P1:229:C49NHACXX:8:1101:1652:2170 4:N:0:
+NATAAAGACCTACTAAACCTAACAATTCCAGCTATATTAACATTAGCTGAAGACACTAATCAGGAANAATTTAAAACAGAAAACATAATGGCACAGTCCA
++
+#4=AAAAACCCCCCBCCCBBB7CCCCCCBCCBBAABBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB#.;AAABBAAAAA@AA@@@@@@B>==?AA????A
+@D3FCO8P1:229:C49NHACXX:8:1101:1537:2174 4:N:0:
+NCGTGGAAGTCTTTGCGCAGACGGATCACCTCCTCGTTTGCAAGTGTGATAGGTACATCATGCTTTNTGTTCAAATCTTGGAAAATGAAATGTGCATGTA
++
+#+1=BBBB?FCBFG4?@@1AC@@CB@BBA@?BBBBA@CCDCCCCC<493?CCCCCC>:>A<8???AC####
+@D3FCO8P1:229:C49NHACXX:8:1101:1563:2176 1:N:0:
+GTCTCAGGAAGAGAAAAAAATATAAAGTGTCAAGGGGCGTGTGCAGCGACACTTCGCCGACCCCTCCCCACATTATTTTTTTGCCGCCCGCTGGTAGCAG
++
+;@@BDDDA:DBFDF;A@@@@@@####43@#####11=?????????>?????????????????????@?#####################################
+@D3FCO8P1:229:C49NHACXX:8:1101:1406:2140 4:N:0:
+NNNNNATTATATGAAAGNAATATAAAATTTATATATAAATTTGGAAGAATTATCATGTGCGCTCNNNNNNNNNTTANANATNNNNNNAGAGTTATATGAN
++
+#####22@@@@@@@?@@#3=>?@@?@@@?@?@>?????>????????????>??????@?????####################################
+@D3FCO8P1:229:C49NHACXX:8:1101:1418:2170 4:N:0:
+NTATTAGCTATTGGATTATTAGGATTTATTGTATGAGCTCATCATATATTTACCGTTGGAATAGATNTAGATACTCGAGCTTATTTTACCTCAGCTACTA
++
+#4=DFFFFHHHHHJEHIHHJIJJHIJJIJJJIJJJIJJJJIJJJJIJIIJIGJJJJJJJJJJJJJJ#-;CFHIJJJHHHFFFFFEEEEEEEDDDDDDDDD
+@D3FCO8P1:229:C49NHACXX:8:1101:1339:2211 4:N:0:
+CNATTGGGCATAGCCATCGAGGTGTGTCCGGTGTCAAATCAAGTGCTGCAACTGGGCGTGGACTATCGGAATCATCCGGCGGCACTGCTGTTGGCCGCCA
++
+C#1ADDFFHHHHGJJJJJJIJJAGHHGIHHIDFGHIJJJGIJJGIJJIIJIJJIJJJJHHFEFEECACDDBB@CCD@?BDDDDDDDDDDDDCDB:@>BBD
+@D3FCO8P1:229:C49NHACXX:8:1101:1664:2088 4:N:0:
+NNNNNATAATTTGTTNNNNNNNNNNNNTTCACAATTTGGTCAATAGCTTGCATAGAAAAATTANNNNNNNNNNNNNNNNNNNNNNNNNNTAATCCAGCNN
++
+#####42@>@@@@@@############11=???????????????????????>????@@@@@#####################################
+@D3FCO8P1:229:C49NHACXX:8:1101:1512:2095 4:N:0:
+NNNNNGTTCTATCAGNNNNTTTNNNNNTAACTTATTGAGGTTTATGTGGTTCTTATACATTAANNNNNNNNNNNNNNNNNNNNNNNNNTGGGTTATTTNN
++
+#####42@@@?@@@@####43@#####11=???????8??>??>??????????????@@@@@#####################################
+@D3FCO8P1:229:C49NHACXX:8:1101:1630:2114 4:N:0:
+NNNNNAAAGTTGGCANNNNATATNNNCGAAGATAATACACGTACACGTCATCCGCGATTTAGAANNNNNNNNNNNNNNNNNNNNNNNNCGCCAAGGTGNN
++
+#####22@@@@@@@?####33@@###14=???????????????????????????????????####################################
+@D3FCO8P1:229:C49NHACXX:8:1101:1540:2119 4:N:0:
+NNNNNGCACACCAATNNNATTATNATGTTATTTAATACATTTATTAAAGAGAATAATGAAATTTNNNNNNNNNANNNNNNNNNNNNNNTATATTCTGCNN
++
+#####22@@@@@@@?###34@@@#1@????????????????????????????????@@@@@@####################################
+@D3FCO8P1:229:C49NHACXX:8:1101:1503:2124 4:N:0:
+NNNNNTAAGAGAGTANNNATAAGATACTCCAAGCAAAAGCAGAGTATCTGTAAACACTTCGCTCNNNNNNNNNGNNNNNNNNNNNNNCCGTGCAAGTCNN
++
+#####22@??@?@??###44@@@@?@?@@@????????????>?????????????@@???@####################################
+@D3FCO8P1:229:C49NHACXX:8:1101:1671:2150 4:N:0:
+NNNGNCAAGACAGTGACAATTCAAATTACACATGCGCGTTGCGCACTCACAGATACAAAGATACANNNANNNNCGGGCATACNTNNNAACAGAGCGACTG
++
+###2#4<@@@@@??@@@@?@@@@@@@@@@@@@@@???????????????????????????????###################################
+@D3FCO8P1:229:C49NHACXX:8:1101:1552:2151 4:N:0:
+NNNGNGACATACTCAATATGTTTTACATATTTATGACAGACCTTCTCAAACAGAATATTTTACATNNNTTNNNCATTACCGTTTNNNCACAACACATTTT
++
+###2#2:@?@?@@@?????@@@@@@?@??@@@???@@?????????????????????@@@@@@@###-8###--=?????==?################
+@D3FCO8P1:229:C49NHACXX:8:1101:1700:2159 4:N:0:
+NNNCNCGGCATACCTGCTGCCATTGGTCACACTGGCAGATTACGCGATTATTTTTTTTACGGAAANNNTGNNNTTTCCCTTCCGGNNTGAATTGCCTGGA
++
+###2#2:@@?@@@@@@@@@?@?@??@??@@@@?????????????????????=########################################
+@D3FCO8P1:229:C49NHACXX:8:1101:1652:2170 4:N:0:
+NATAAAGACCTACTAAACCTAACAATTCCAGCTATATTAACATTAGCTGAAGACACTAATCAGGAANAATTTAAAACAGAAAACATAATGGCACAGTCCA
++
+#4=AAAAACCCCCCBCCCBBB7CCCCCCBCCBBAABBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB#.;AAABBAAAAA@AA@@@@@@B>==?AA????A
+@D3FCO8P1:229:C49NHACXX:8:1101:1537:2174 4:N:0:
+NCGTGGAAGTCTTTGCGCAGACGGATCACCTCCTCGTTTGCAAGTGTGATAGGTACATCATGCTTTNTGTTCAAATCTTGGAAAATGAAATGTGCATGTA
++
+#+1=BBBB?FCBFG4?@@1?CAAC??9?B@9??C:(:@A::@CC:4+:>@C@AAC(>9?CCCC@
+@D3FCO8P1:229:C49NHACXX:8:1101:1452:2184:1:N:0:CACTGT
+GTGGGAAAGGGAAGGGCAAGGGGGAGGGGAAGAATTTAACCGGGCGGGAGGAGAATCGGGCAGGGAAGAATGGTTGGTTGGTGGAACAACTGAA
++
+EDHHHDHJJGIGIJCBDHEHGJJJBGEHIBGGHFGFFGGHFFDD>?BDBBDDDDDD@ADD;>@D98AB?CCDD:CBB@@@@@@####43@#####11=?????????>?????????????????????@?#####################################
+@D3FCO8P1:229:C49NHACXX:8:1101:1406:2140:4:N:0:GTATAG
+TTATATGAAAGNAATATAAAATTTATATATAAATTTGGAAGAATTATCATGTGCGCTCNNNNNNNNNTTANANATNNNNNNAGAGTTATATGAN
++
+2@@@@@@@?@@#3=>?@@?@@@?@?@>?????>????????????>??????@?????####################################
+@D3FCO8P1:229:C49NHACXX:8:1101:1418:2170:4:N:0:GTATAG
+GCTATTGGATTATTAGGATTTATTGTATGAGCTCATCATATATTTACCGTTGGAATAGATNTAGATACTCGAGCTTATTTTACCTCAGCTACTA
++
+FFHHHHHJEHIHHJIJJHIJJIJJJIJJJIJJJJIJJJJIJIIJIGJJJJJJJJJJJJJJ#-;CFHIJJJHHHFFFFFEEEEEEEDDDDDDDDD
+@D3FCO8P1:229:C49NHACXX:8:1101:1385:2179:4:N:0:GTATAG
+AGAGATCTGCATCTAATCTAGCTGCTCCCATGCTACCCCTGAATACCCTACACGGCCTGAACAGTCGCCCCACAAGTCTGGCGTGGGGCTGTCT
++
+DFHF?HHGBHHIJJIGIIIJGIJBEHIGID<9EHIIJJI@;?BGGHIIIIIIIIIIIAGE@HHH?EDFDDB?B?9?:ACCC(85>>B>>@BBD@
+@D3FCO8P1:229:C49NHACXX:8:1101:1452:2184:4:N:0:GTATAG
+CATTCTGTATGCCCTTCCCTCTCGCACACTCGACCCAATGACCCGCTTTGCTCTGTTTACCTCTCCGCTCTGTTTTTGCACTTGGAAATTGCTA
++
+FFHGDHHGGIJJIJJJGHIIIGFHHIIGIIIJIJJEHGEGGIJJIIIIGGGHGGFHHFEC@BCEDECDDDDDDDDDD?AC>ACCCCACADCCDD
+@D3FCO8P1:229:C49NHACXX:8:1101:1370:2193:4:N:0:GTATAG
+TGAAAGCAAGGAGCGCAAGAAATCGTATGCCCATGTTGACCAGTTTGAATATGAGATAATCGTGCAAACACTCCCAAGGAACTGTCTCTTATAC
++
+FFHHHHHJJJJJJJJJJJJJJJJJJJJJJJJJIJJJJJHJJJJJGHIIIIIJJIJIJEEEEHHFFFEEEEDED3=CDDDDDDDDCDDDDDDDDD
diff -r 000000000000 -r 424f44e2124e test-data/sample2_ATTCCGTCCGTC_1.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sample2_ATTCCGTCCGTC_1.txt Wed Nov 25 12:37:28 2015 -0500
@@ -0,0 +1,28 @@
+@D3FCO8P1:229:C49NHACXX:8:1101:1486:2204:1:N:0:ATTCCG
+CATCTGTTGCTCATATAGGAATTGTTCTATCAGGACTTTTAACTATAACTTATTGAGGTTTATGTGGTTCTTATACATTAATAATTGCTCATGG
++
+DFHHHGHJJIJJJJJJJJJJJJJJJJJJIJJJJJJJIJJJIJJJJJJIJJJJJJIJJJHIJJJJHIIHHHHIJJJIJJHHHHHHFFFFEFCEEE
+@D3FCO8P1:229:C49NHACXX:8:1101:1460:2207:1:N:0:ATTCCG
+GTCGTTGTGATACTAAACTTTCTCAAATAATAAAAAAAAAGAATAAAATTCCTAATAATGAAATAGTTGATCCAATAGTTGATACAATATTTCA
++
+FFHHHGHIIGIJJIIJJJJJJIIHIIJHGIHGJIJIJJJHGCCHIGGEHH>EEFFFFFFFACCEACEDCDCCCCCDCDEEDDDE(:ACCD:@D@
+@D3FCO8P1:229:C49NHACXX:8:1101:1339:2211:1:N:0:ATTCCG
+AGTAAATTAAATGCGAAAATAAAAGGCAGCATGAGNTANTTACTNAAANGGGGTCATNAACAGTACTTGTGCTCCNCCANGTCGNCGNTNCNCT
++
+FFFHHHHJJJIJJJJJJJIJIJJJJJJJJJJJJJJ#0?#0?DHI#-;F#-;DH?EFH#,;BCDEEEEEDDCCCDD#,8?#,5?B##########
+@D3FCO8P1:229:C49NHACXX:8:1101:1402:2222:1:N:0:ATTCCG
+ATAGTAATAATATTACCTAATACAAATAATGAAATATCATATTGATGAAATCATTTTACTATACCTGATACAGTTGTTATAGCTCCGATAGCTC
++
+FDFHHHHJJIIJJJGJIIJJIIJHIJIJIJIIJJJJJJJIIJJIGGHIJJJIJGJJIIIHIIHJ>GHIIIIIIGGGIIJJJJIH)=ABDDDDEE
+@D3FCO8P1:229:C49NHACXX:8:1101:1388:2233:1:N:0:ATTCCG
+AATTTAATGCAATTACCAATCTTACAAGTTATTATACCAATAATTGCATCTATGTTTTGCTTTCTTGACAAGAAACACAAGGTAACTTGGGTTA
++
+DDACAA:@?C
diff -r 000000000000 -r 424f44e2124e test-data/sample2_ATTCCGTCCGTC_2.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sample2_ATTCCGTCCGTC_2.txt Wed Nov 25 12:37:28 2015 -0500
@@ -0,0 +1,28 @@
+@D3FCO8P1:229:C49NHACXX:8:1101:1486:2204:4:N:0:TCCGTC
+TTCTTCGACTTCCAAGACGTTCATAAGATACATTAGCTAAACAAAATAACCCAGAAGAACATAAACCATGAGCAATTATTAATGTATAAGAACC
++
+FFHHHFHIJJJJJJJJJJIIGIIIJJIIGHJJJJIJJIIJIJJJIJJIJJJJJJJJIGIJIIJJHHFHHFFFFFEDEEEFFFEDDDEFEDDDDD
+@D3FCO8P1:229:C49NHACXX:8:1101:1460:2207:4:N:0:TCCGTC
+TATATTTATTGGAGTTAATTTAACATTTTTTCCTCAACATTTTTTAGGATTGGCTGGAATACCTCGACGTTATTCAGATTACCCAGATGCTTAC
++
+FDHDHHHIJJJJEHHHIIIIJIJHIHIJJJJIGHEIIIJJIJJJHHGIIIJIJIJIJEHGHGFHFH8?ABC?BC>>AADDCACDDDDD<@CD>>
+@D3FCO8P1:229:C49NHACXX:8:1101:1339:2211:4:N:0:TCCGTC
+GGCATAGCCATCGAGGTGTGTCCGGTGTCAAATCAAGTGCTGCAACTGGGCGTGGACTATCGGAATCATCCGGCGGCACTGCTGTTGGCCGCCA
++
+FFHHHHGJJJJJJIJJAGHHGIHHIDFGHIJJJGIJJGIJJIIJIJJIJJJJHHFEFEECACDDBB@CCD@?BDDDDDDDDDDDDCDB:@>BBD
+@D3FCO8P1:229:C49NHACXX:8:1101:1402:2222:4:N:0:TCCGTC
+GACCATTAACAGGAGCTATCGGAGCTATAACAACTGTATCAGGTATAGTAAAATGATTTCATCAATATGATATTTCATTATTTGTATTAGGTAA
++
+FFHHFHGJJJJJJIIJJGJIIJGHGHIIIJIJJIGIHIIGIIJBFDIIGHJJIJJGIEIEGHIJCH@EHFHGHHHGFFFFFFFFFDDEEDCAC@
+@D3FCO8P1:229:C49NHACXX:8:1101:1388:2233:4:N:0:TCCGTC
+AACCAAGATACCTTGTGTTTCTTGGCAAGAAAGCAAAACATTGATGCAATTATTGGTATAATAACTTGTAAGATTGGTAATTGCATTAAATTGT
++
+D4DB?:3E3+2AEAHHFIIIIIIIE9?9?3DGFF>;;F;D9BD9?@DCFFICFGF@FCF@@F@C@DF<7C@E3?ECC>7@DDBAADA;;;>A:A
+@D3FCO8P1:229:C49NHACXX:8:1101:1497:2240:4:N:0:TCCGTC
+CAGCAATCGCAGCAACAACTAAATGGAAACCAACAGCATCTGCCCATCAATCGTCAACCGGCGCCACAGCAATCACACTTCCTGGACAATTCAA
++
+FDHDHHHIGJIJJJJJJJIJJIJJJJJIJJJIIJJJJJJIIJJJHHGGGEGIJEHIJGHFFDDDDD@BBDCDDDDDDDDDDDDDDBDDBDDDDE
+@D3FCO8P1:229:C49NHACXX:8:1101:1399:2245:4:N:0:TCCGTC
+TTTATTAAATAGAATTGTTTCTTGATCTTGAATTTCTATAATTTTATTATCTTTTTTATCTTTTTTTAGAGCTGCTTATACTTTATATTTATAT
++
+EDHFHHGJIIHIEEHIIIIJIJJJ?FFHGHFGHIJHGGIGDFFIG9EHGHEHIJJJJGIFHIGIJJA=;?>CEBBEECCC;>CDCA;BDD>@;C
diff -r 000000000000 -r 424f44e2124e test-data/sample3_GCTACCTGGTCA_1.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sample3_GCTACCTGGTCA_1.txt Wed Nov 25 12:37:28 2015 -0500
@@ -0,0 +1,24 @@
+@D3FCO8P1:229:C49NHACXX:8:1101:1664:2088:1:N:0:GCTACC
+AAGTTTATAAATGGCAACCTTAAGTGTAANNNANNNNNTATGCACAGNANNNNNNNNANNNATGCAAAACGACTCNNNNNNNNNNNNCNNNNNN
++
+FFHHHHHJJJJJJJJJJJJJJJJJIIHIJ###1#####20?FHJJJJ#.########-###--;BDFEEECDDDD###################
+@D3FCO8P1:229:C49NHACXX:8:1101:1512:2095:1:N:0:GCTACC
+ACGTTCATAAGATACATTAGCTAAACAAAANAANNNNNAAGAACATAAANNNNNNNCANNTATTAATGTATAAGANCNNNANNNNCNTNNNNNN
++
+FFHHHHHJJJJJJIJJJJIJJJJIJJJJJJ#1C#####00?FIJJJJJJ#######--##,5?DDEEEFCFFEDD###################
+@D3FCO8P1:229:C49NHACXX:8:1101:1630:2114:1:N:0:GCTACC
+CGTTGGAGGAGGAGCCGCCATGAATGCCCTGCGNNNNTTCTACCTGGAGANNNCGGTGGTCACACGAGCCTACACCACGGTCNNCGTGCTNNNN
++
+FFHHHHGJJGHJGHIJJJJJJJJJJJJJJJJJJ####.-;DHIJJHHHHH###,,=?BDBDDDDDDDDDDDDDDDDDDDDDD##+28@DD####
+@D3FCO8P1:229:C49NHACXX:8:1101:1540:2119:1:N:0:GCTACC
+TGGACTCAAGACCTAATTGCATTAACCGTCTGTNNNNTACGTAGCGTATGNNATTGCGCACTTCTTCTGCGGATAGTCCTTCNNCATCTCNNNN
++
+FFHHHHHJJJJJJJJJJJJJJJJJJJJJJJJIJ####20?GHIJJJIJIJ##-5CEFHFFDDEEDDDDDDDDDDDDDEDDDD##+2?BDD####
+@D3FCO8P1:229:C49NHACXX:8:1101:1503:2124:1:N:0:GCTACC
+TACATATACTTATAGGCATACTTATACGACTTCNNNNCCCGGTTAATATGNNGTGGCCCGTATAAGTTAATGGGCACAACCGNNTGGGACNNNN
++
+FFHHHHHIJJJJJJJJJJJIJJJJJJJJJJJJJ####00BFHGIIJJJJJ##--BEHJJHDFFEDEEFEEEDDDDDDDDDDD##+2@@@@@@############11=???????????????????????>????@@@@@#####################################
+@D3FCO8P1:229:C49NHACXX:8:1101:1512:2095:4:N:0:TGGTCA
+TTCTATCAGNNNNTTTNNNNNTAACTTATTGAGGTTTATGTGGTTCTTATACATTAANNNNNNNNNNNNNNNNNNNNNNNNNTGGGTTATTTNN
++
+2@@@?@@@@####43@#####11=???????8??>??>??????????????@@@@@#####################################
+@D3FCO8P1:229:C49NHACXX:8:1101:1630:2114:4:N:0:TGGTCA
+AAGTTGGCANNNNATATNNNCGAAGATAATACACGTACACGTCATCCGCGATTTAGAANNNNNNNNNNNNNNNNNNNNNNNNCGCCAAGGTGNN
++
+2@@@@@@@?####33@@###14=???????????????????????????????????####################################
+@D3FCO8P1:229:C49NHACXX:8:1101:1540:2119:4:N:0:TGGTCA
+CACACCAATNNNATTATNATGTTATTTAATACATTTATTAAAGAGAATAATGAAATTTNNNNNNNNNANNNNNNNNNNNNNNTATATTCTGCNN
++
+2@@@@@@@?###34@@@#1@????????????????????????????????@@@@@@####################################
+@D3FCO8P1:229:C49NHACXX:8:1101:1503:2124:4:N:0:TGGTCA
+AAGAGAGTANNNATAAGATACTCCAAGCAAAAGCAGAGTATCTGTAAACACTTCGCTCNNNNNNNNNGNNNNNNNNNNNNNCCGTGCAAGTCNN
++
+2@??@?@??###44@@@@?@?@@@????????????>?????????????@@???@####################################
+@D3FCO8P1:229:C49NHACXX:8:1101:1671:2150:4:N:0:TGGTCA
+AAGACAGTGACAATTCAAATTACACATGCGCGTTGCGCACTCACAGATACAAAGATACANNNANNNNCGGGCATACNTNNNAACAGAGCGACTG
++
+<@@@@@??@@@@?@@@@@@@@@@@@@@@???????????????????????????????###################################
diff -r 000000000000 -r 424f44e2124e test-data/sample4_CGAAACCACTGT_1.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sample4_CGAAACCACTGT_1.txt Wed Nov 25 12:37:28 2015 -0500
@@ -0,0 +1,24 @@
+@D3FCO8P1:229:C49NHACXX:8:1101:1552:2151:1:N:0:CGAAAC
+AACTTAAGGCTGAAAATTATTTATTTGACTTGTGTCAAATATAAAAATGTNTTGTGTAGAAACGGTAATGTGAAATTAATGTNAAATATTCTNN
++
+FFHHHHHJJJJJJJJJJJJJJJJJJIIIJJJJHIJJJJIJIJJJIJIJJI#0?FGIIJJJJJJIIEIJJHHHGHHHFFFFFF#,;ABDEDEE##
+@D3FCO8P1:229:C49NHACXX:8:1101:1700:2159:1:N:0:CGAAAC
+TGCAATGCAAGTGGATTAGAGGATTGCAGCTGGAGGGGTAACAGCAGTGCNTTCGAAATATGTATCTTACAGCATTTCTGGGNTCCTCGTCCGN
++
+FFHHHHHJJJJHIIIIJIJIJJJJJJJJJJJJJFHJJJ?FHCFFHGIGHC#-5;DHHFHHHFCDFFFFFEEEECEDCDCCDC#,8AC@@CB@BBA@?BBBBA@CCDCCCCC<493?CCCCCC>:>A<8???AC####
+@D3FCO8P1:229:C49NHACXX:8:1101:1563:2176:1:N:0:CGAAAC
+GGAAGAGAAAAAAATATAAAGTGTCAAGGGGCGTGTGCAGCGACACTTCGCCGACCCCTCCCCACATTATTTTTTTGCCGCCCGCTGGTAGCAG
++
+DA:DBFDF;A==?AA????A
+@D3FCO8P1:229:C49NHACXX:8:1101:1537:2174:4:N:0:CACTGT
+AAGTCTTTGCGCAGACGGATCACCTCCTCGTTTGCAAGTGTGATAGGTACATCATGCTTTNTGTTCAAATCTTGGAAAATGAAATGTGCATGTA
++
+BB?FCBFG4?@@1