# 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 + + + + + echo '1.0' + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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=${library.SAME_HEADERS} + #end if + + + + + + + + + + + + + + + + + + @single_or_paired_cmd@ + I1=$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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + #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 + + + + + + + + + + + + + + + + + + + + + + + + + + #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 + + + + + + + + + + + ADD=${ADD} + MM=$MM + MMD=$MMD + Q=$MIN_BASE_QUALITY + QUALITY_FORMAT=$QUALITY_FORMAT + + + + + + + + + + + + + + + + + + + KEEP_UNASSIGNED_READ=$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=${GZ} + OUTPUT_DIR=results + + + + + + + + + + + + METRICS_FILE_NAME=$METRICS_FILE_NAME + + + + + + + + (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@@@@?@?@@@????????????>?==?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@@@@?@?@@@????????????>?==?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@@@@?@?@@@????????????>?==?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@@@@?@?@@@????????????>?==?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@@@@?@?@@@????????????>?AC@@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