# HG changeset patch # User gbcs-embl-heidelberg # Date 1448472997 18000 # Node ID 111ba118031801bef246dc51e1fa644b71488837 Initial upload diff -r 000000000000 -r 111ba1180318 je --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/je Wed Nov 25 12:36:37 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 111ba1180318 je-demultiplex-illu.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/je-demultiplex-illu.xml Wed Nov 25 12:36:37 2015 -0500 @@ -0,0 +1,428 @@ + + demultiplexes fastq files using Illumina Index file + + macros.xml + + + + + echo '1.0' + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff -r 000000000000 -r 111ba1180318 je_1.0_bundle.jar Binary file je_1.0_bundle.jar has changed diff -r 000000000000 -r 111ba1180318 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Wed Nov 25 12:36:37 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 111ba1180318 test-data/barcodes_PE.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/barcodes_PE.txt Wed Nov 25 12:36:37 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 111ba1180318 test-data/barcodes_SE.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/barcodes_SE.txt Wed Nov 25 12:36:37 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 111ba1180318 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 12:36:37 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 111ba1180318 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 12:36:37 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 111ba1180318 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 12:36:37 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 111ba1180318 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 12:36:37 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 111ba1180318 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 12:36:37 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 111ba1180318 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 12:36:37 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 111ba1180318 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 12:36:37 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 111ba1180318 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 12:36:37 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 111ba1180318 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 12:36:37 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 111ba1180318 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 12:36:37 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 111ba1180318 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 12:36:37 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 111ba1180318 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 12:36:37 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 111ba1180318 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 12:36:37 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 111ba1180318 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 12:36:37 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