From bfe0d46c9b0414b53fc99240e614965e4b3cb972 Mon Sep 17 00:00:00 2001 From: Nils Homer Date: Thu, 17 Nov 2016 12:56:26 -0700 Subject: [PATCH 1/2] The molecular indexes should be joined with hyphens rather than concatenated. --- .../picard/illumina/ClusterDataToSamConverter.java | 5 +- .../sams/nonBarcodedWithMolecularIndex4M4M.sam | 360 ++++++++++----------- ...nonBarcodedWithTagPerMolecularIndex2M2M2M2M.sam | 360 ++++++++++----------- .../nonBarcodedWithTagPerMolecularIndex4M4M.sam | 360 ++++++++++----------- .../illumina/25T8B25T/sams_with_4M4M/AACAATGG.sam | 16 +- .../illumina/25T8B25T/sams_with_4M4M/AACGCATT.sam | 28 +- .../illumina/25T8B25T/sams_with_4M4M/ACAGGTAT.sam | 16 +- .../illumina/25T8B25T/sams_with_4M4M/ACAGTTGA.sam | 8 +- .../illumina/25T8B25T/sams_with_4M4M/ACTAAGAC.sam | 16 +- .../illumina/25T8B25T/sams_with_4M4M/ACTGTATC.sam | 16 +- .../illumina/25T8B25T/sams_with_4M4M/AGCATGGA.sam | 12 +- .../illumina/25T8B25T/sams_with_4M4M/AGGTAAGG.sam | 16 +- .../illumina/25T8B25T/sams_with_4M4M/AGGTCGCA.sam | 16 +- .../illumina/25T8B25T/sams_with_4M4M/ATTATCAA.sam | 20 +- .../illumina/25T8B25T/sams_with_4M4M/ATTCCTCT.sam | 16 +- .../illumina/25T8B25T/sams_with_4M4M/CAACTCTC.sam | 20 +- .../illumina/25T8B25T/sams_with_4M4M/CAATAGTC.sam | 28 +- .../illumina/25T8B25T/sams_with_4M4M/CAGCGGTA.sam | 20 +- .../illumina/25T8B25T/sams_with_4M4M/CCAACATT.sam | 28 +- .../illumina/25T8B25T/sams_with_4M4M/CCAGCACC.sam | 12 +- .../illumina/25T8B25T/sams_with_4M4M/CGCCTTCC.sam | 8 +- .../illumina/25T8B25T/sams_with_4M4M/CGCTATGT.sam | 20 +- .../illumina/25T8B25T/sams_with_4M4M/CTAACTCG.sam | 16 +- .../illumina/25T8B25T/sams_with_4M4M/CTATGCGT.sam | 28 +- .../illumina/25T8B25T/sams_with_4M4M/CTGCGGAT.sam | 12 +- .../illumina/25T8B25T/sams_with_4M4M/CTGTAATC.sam | 24 +- .../illumina/25T8B25T/sams_with_4M4M/GAAGGAAG.sam | 12 +- .../illumina/25T8B25T/sams_with_4M4M/GACCAGGA.sam | 28 +- .../illumina/25T8B25T/sams_with_4M4M/GACCGTTG.sam | 16 +- .../illumina/25T8B25T/sams_with_4M4M/GACCTAAC.sam | 4 +- .../illumina/25T8B25T/sams_with_4M4M/GATATCCA.sam | 12 +- .../illumina/25T8B25T/sams_with_4M4M/GCCGTCGA.sam | 20 +- .../illumina/25T8B25T/sams_with_4M4M/GCCTAGCC.sam | 20 +- .../illumina/25T8B25T/sams_with_4M4M/GTAACATC.sam | 8 +- .../illumina/25T8B25T/sams_with_4M4M/GTCCACAG.sam | 8 +- .../picard/illumina/25T8B25T/sams_with_4M4M/N.sam | 64 ++-- .../illumina/25T8B25T/sams_with_4M4M/TAAGCACA.sam | 8 +- .../illumina/25T8B25T/sams_with_4M4M/TATCCAGG.sam | 16 +- .../illumina/25T8B25T/sams_with_4M4M/TATCTGCC.sam | 28 +- .../illumina/25T8B25T/sams_with_4M4M/TCGCTAGA.sam | 20 +- .../illumina/25T8B25T/sams_with_4M4M/TCTGCAAG.sam | 4 +- .../illumina/25T8B25T/sams_with_4M4M/TGCAAGTA.sam | 8 +- .../illumina/25T8B25T/sams_with_4M4M/TGCTGCTG.sam | 16 +- .../illumina/25T8B25T/sams_with_4M4M/TGTAACTC.sam | 4 +- .../illumina/25T8B25T/sams_with_4M4M/TGTAATCA.sam | 12 +- .../illumina/25T8B25T/sams_with_4M4M/TTGTCTAT.sam | 16 +- 46 files changed, 903 insertions(+), 902 deletions(-) diff --git a/src/main/java/picard/illumina/ClusterDataToSamConverter.java b/src/main/java/picard/illumina/ClusterDataToSamConverter.java index 43556226a..487cb4d6c 100644 --- a/src/main/java/picard/illumina/ClusterDataToSamConverter.java +++ b/src/main/java/picard/illumina/ClusterDataToSamConverter.java @@ -74,6 +74,7 @@ // TODO: - https://github.com/samtools/hts-specs/pull/119 private String molecularIndexTag = "RX"; private String molecularIndexQualityTag = "QX"; + private String molecularIndexDelimiter = "-"; private List tagPerMolecularIndex = Collections.emptyList(); /** @@ -178,10 +179,10 @@ private SAMRecord createSamRecord(final ReadData readData, final String readName if (!molecularIndexes.isEmpty()) { if (!this.molecularIndexTag.isEmpty()) { - sam.setAttribute(this.molecularIndexTag, String.join("", molecularIndexes)); + sam.setAttribute(this.molecularIndexTag, String.join(molecularIndexDelimiter, molecularIndexes)); } if (!this.molecularIndexQualityTag.isEmpty()) { - sam.setAttribute(this.molecularIndexQualityTag, String.join("", molecularIndexQualities)); + sam.setAttribute(this.molecularIndexQualityTag, String.join(molecularIndexDelimiter, molecularIndexQualities)); } if (!this.tagPerMolecularIndex.isEmpty()) { if (tagPerMolecularIndex.size() != molecularIndexes.size()) { diff --git a/testdata/picard/illumina/25T8B25T/sams/nonBarcodedWithMolecularIndex4M4M.sam b/testdata/picard/illumina/25T8B25T/sams/nonBarcodedWithMolecularIndex4M4M.sam index 3b70d878a..ab0d8f62c 100644 --- a/testdata/picard/illumina/25T8B25T/sams/nonBarcodedWithMolecularIndex4M4M.sam +++ b/testdata/picard/illumina/25T8B25T/sams/nonBarcodedWithMolecularIndex4M4M.sam @@ -1,182 +1,182 @@ @HD VN:1.5 SO:queryname @RG ID:HiMom.1 SM:HiDad LB:Hello, World PL:illumina PU:HiMom.1 CN:BI -HiMom:1:1101:1031:2224 516 * 0 0 * * 0 0 ......................... ######################### RG:Z:HiMom.1 XN:i:1 QX:Z:######## RX:Z:NNNNNNNN -HiMom:1:1101:1039:2147 516 * 0 0 * * 0 0 ......................... ######################### RG:Z:HiMom.1 XN:i:1 QX:Z:######## RX:Z:NNNNNNNN -HiMom:1:1101:1046:2175 516 * 0 0 * * 0 0 ..GGA.................... ######################### RG:Z:HiMom.1 QX:Z:######## RX:Z:NNNNNNNN -HiMom:1:1101:1047:2122 516 * 0 0 * * 0 0 ..TCA.................... ######################### RG:Z:HiMom.1 QX:Z:######## RX:Z:NNNANNNN -HiMom:1:1101:1048:2197 516 * 0 0 * * 0 0 ..GTG.................... ######################### RG:Z:HiMom.1 QX:Z:######## RX:Z:NNNCNNNN -HiMom:1:1101:1065:2193 4 * 0 0 * * 0 0 .CTTG.................... ######################### RG:Z:HiMom.1 QX:Z:######## RX:Z:GAACGATN -HiMom:1:1101:1069:2159 4 * 0 0 * * 0 0 GACGT.................... <<<@?#################### RG:Z:HiMom.1 QX:Z:@BBFFFFF RX:Z:GTCCACAG -HiMom:1:1101:1071:2233 4 * 0 0 * * 0 0 GTTTG.................... <<<@@#################### RG:Z:HiMom.1 QX:Z:CCCFFFFF RX:Z:TATCCAGG -HiMom:1:1101:1083:2193 4 * 0 0 * * 0 0 AGGCT.................... ######################### RG:Z:HiMom.1 QX:Z:?@;DD?BD RX:Z:CCAACATT -HiMom:1:1101:1084:2136 4 * 0 0 * * 0 0 TTTCT.................... <<<@@#################### RG:Z:HiMom.1 QX:Z:CCCFFFFF RX:Z:TGCTGCTG -HiMom:1:1101:1089:2172 4 * 0 0 * * 0 0 TCCGG.................... :<7+@A7A7 RX:Z:ACTAAGAC -HiMom:1:1101:1263:2236 516 * 0 0 * * 0 0 AGTTCTTCAGTAATTTTAGTACTGC ######################### RG:Z:HiMom.1 QX:Z:######## RX:Z:AGGTAAGG -HiMom:1:1101:1267:2209 4 * 0 0 * * 0 0 GGCAGAGTCTCCAACAGCCCCGTAC =;?DDDD?CCFHAIIIGGIIGE@EG RG:Z:HiMom.1 QX:Z:?@@D;ADD RX:Z:TATCAGCC -HiMom:1:1101:1269:2170 4 * 0 0 * * 0 0 TTCCAAGCCTGTGCTTTAAGGAAAA @@>7A### RX:Z:CAATAGAC -HiMom:1:1101:1327:2200 516 * 0 0 * * 0 0 GTCATCTGGGCTGTCGACAGGTGTC @B@FFFFFHHHHGIJJJJJJIFHHI RG:Z:HiMom.1 QX:Z:BCCFDFFD RX:Z:GCCGTCGA -HiMom:1:1101:1328:2225 4 * 0 0 * * 0 0 AGGAAATTAGGACTTACCTGACATA ######################### RG:Z:HiMom.1 QX:Z:??;=A:B= RX:Z:CAACTCTC -HiMom:1:1101:1338:2175 4 * 0 0 * * 0 0 GCTTGTTGGCTTTAACATCCACAAT CCCFFFFFHHHHHJJJJJJJJJJJJ RG:Z:HiMom.1 QX:Z:CCCFFFFF RX:Z:GAAGGAAG -HiMom:1:1101:1347:2149 4 * 0 0 * * 0 0 GCTCTTCCGATCTGTGCTCTTCCGA CCCFFFFFDFHHFIJDGIGGHGIGH RG:Z:HiMom.1 QX:Z:CC@DFFFD RX:Z:GACCAGGA -HiMom:1:1101:1353:2226 4 * 0 0 * * 0 0 GTGCTCTTCCGATCTTCAGGTTACC BBBFFFFFHHHHHJJJJJJJIJJJJ RG:Z:HiMom.1 QX:Z:@B@FFEFF RX:Z:TATCTGCC -HiMom:1:1101:1363:2138 4 * 0 0 * * 0 0 GTTCTTAAACCTGTTAGAACTTCTG C@@FFFFFHHHHHJJJJJJJJJJJJ RG:Z:HiMom.1 QX:Z:CCCFFFFF RX:Z:CTAACTCG -HiMom:1:1101:1399:2128 4 * 0 0 * * 0 0 ACAAACCCTTGTGTCGAGGGCTGAC CCCFFFFFHHHHHIJJJJJJJJJJJ RG:Z:HiMom.1 QX:Z:CCCFFFFF RX:Z:CAATAGTC -HiMom:1:1101:1403:2194 4 * 0 0 * * 0 0 ACATGGTGAAACCCTGTCTCTACTA CCCFFFDDHHHHHJJJJJJJJJJJJ RG:Z:HiMom.1 QX:Z:CCCFFFFF RX:Z:CTGTAATC -HiMom:1:1101:1406:2222 4 * 0 0 * * 0 0 GGCTGGACTCCCCTGGTTCTGGGCA ;?@DDDBD?FHDFGIIIGIGHHIII RG:Z:HiMom.1 QX:Z:C@@DBFEF RX:Z:AGCATGGA -HiMom:1:1101:1419:2119 4 * 0 0 * * 0 0 ACTTTCCTTTTTTGTTTTACTTTAA ######################### RG:Z:HiMom.1 QX:Z:@@@DFDFD RX:Z:TGTAATCA -HiMom:1:1101:1420:2213 4 * 0 0 * * 0 0 TTCACTGTACCGGCCGTGCGTACTT @CCFFFFDHHHFGIJJJJJJGHIGG RG:Z:HiMom.1 QX:Z:@C@FFFDF RX:Z:CAGCGGTA -HiMom:1:1101:1435:2194 4 * 0 0 * * 0 0 TTTTGTTTTCTTTTACTGAAGTGTA CCCFFDFFHHHHHJJJJIHIJHHHJ RG:Z:HiMom.1 QX:Z:CCCFFFFF RX:Z:TATCTGCC -HiMom:1:1101:1441:2148 4 * 0 0 * * 0 0 TTTTGGCTCTAGAGGGGGTAGAGGG CCCFFFFFHHDFBHIIJJ1?FGHIJ RG:Z:HiMom.1 QX:Z:@@BFFDDD RX:Z:CGCTATGT -HiMom:1:1101:1452:2132 4 * 0 0 * * 0 0 ACAAACCCTTGTGTCGAGGGCTGAC CCCFFFFFHHHHHJJJJJJJIJJJJ RG:Z:HiMom.1 QX:Z:@CCFFFFF RX:Z:AACGCATT -HiMom:1:1101:1460:2176 4 * 0 0 * * 0 0 AGGAAAAAGACACAACAAGTCCAAC ######################### RG:Z:HiMom.1 QX:Z:CCCFFFFF RX:Z:GATATCCA -HiMom:1:1101:1479:2221 4 * 0 0 * * 0 0 GGGGAAATCTATTTTTATGTAAAAA @CCFFFFFHHHHHJIGIJJJJJJJJ RG:Z:HiMom.1 QX:Z:@BCFFFFF RX:Z:TCGCTAGA -HiMom:1:1101:1491:2120 4 * 0 0 * * 0 0 GGCCAGGCTGAACTTCTGAGCTGCT CCCFFFFFHHHGHJJJJJJJJJJJJ RG:Z:HiMom.1 QX:Z:BCCDFFFF RX:Z:AGGTCGCA -HiMom:1:1201:1018:2133 4 * 0 0 * * 0 0 ......................... ######################### RG:Z:HiMom.1 XN:i:1 QX:Z:8??=BBBA RX:Z:ATTCCTCT -HiMom:1:1201:1018:2217 516 * 0 0 * * 0 0 ......................... ######################### RG:Z:HiMom.1 XN:i:1 QX:Z:;<;:BBDD RX:Z:ATTATCAA -HiMom:1:1201:1028:2202 4 * 0 0 * * 0 0 ..AAAC.C.T.......GG..TG.. ##42@?################### RG:Z:HiMom.1 QX:Z:CCCFFDFF RX:Z:GAAGGAAG -HiMom:1:1201:1042:2174 4 * 0 0 * * 0 0 .TCAGGAAGGC..CAAAAAAAGAAA #0;@@@?@?<@##3<@@?@@????? RG:Z:HiMom.1 QX:Z:CCCFFFFF RX:Z:TCTGCAAG -HiMom:1:1201:1043:2246 4 * 0 0 * * 0 0 .GCATCATTTC..GCTTCTCTCTGT #0;@@??@=@>##22=;@??><@?? RG:Z:HiMom.1 QX:Z:@A# RG:Z:HiMom.1 QX:Z:?;@DFDFF RX:Z:GACCAGGA -HiMom:1:1201:1127:2112 516 * 0 0 * * 0 0 TAATCACCTGAGCAGTGAAGCCAGC @<@?BDDDHD?FDBHI?AHGGGDFH RG:Z:HiMom.1 QX:Z:=??BA?BD RX:Z:CAACTCTC -HiMom:1:1201:1134:2144 4 * 0 0 * * 0 0 AGTGTGAGTAATGGTTGAGAGGTGG B@?DDDFFFHHGHJHHGFIHHIFGI RG:Z:HiMom.1 QX:Z:CCCFFFFD RX:Z:CGCTATGT -HiMom:1:1201:1138:2227 516 * 0 0 * * 0 0 GACAAATATAGGAAATAGAAGCTAT =1=A=AAA,2?4>7C<<4B6=BBBB RG:Z:HiMom.1 QX:Z:######## RX:Z:AGAAAAGA -HiMom:1:1201:1416:2128 4 * 0 0 * * 0 0 TTGGTGTGGAGGCGGTGGCGGGATC @@@DDDDDHHFHHII:?GGHIIB6? RG:Z:HiMom.1 QX:Z:CCCFFFFF RX:Z:TCGCTAGA -HiMom:1:1201:1421:2154 4 * 0 0 * * 0 0 TGTGCTCTTCCGATCTTGTGCTCTT BC@DFFFFHHHHHJJJJFHIHHIJJ RG:Z:HiMom.1 QX:Z:@@@FFFFF RX:Z:TGTAACTC -HiMom:1:1201:1439:2156 4 * 0 0 * * 0 0 GGAGATTATTTGCCTTGAAGTAAGC -;(22<>>@>8@>8;@######### RG:Z:HiMom.1 QX:Z:1;;=#### RX:Z:GACCAGGC -HiMom:1:1201:1452:2143 4 * 0 0 * * 0 0 TTTTAGTCTTAGCATTTACTTTCCC CCCFFFFFHHHHHJJJJJJJJJJJJ RG:Z:HiMom.1 QX:Z:BC@DDFFF RX:Z:CAACTCTC -HiMom:1:1201:1458:2109 4 * 0 0 * * 0 0 GATACGAACACACAAGAACTTTTTT CCCFFFFFHHHHHJJJJJJJJJJJI RG:Z:HiMom.1 QX:Z:CCCFFFFF RX:Z:ACTGTATC -HiMom:1:1201:1472:2121 516 * 0 0 * * 0 0 GTGTGCTCTTCCGATCTGGAGGATG =+=??A4A==A@7A??@@??@?????????>?@ RG:Z:HiMom.1 QX:Z:@CCDFFFF RX:Z:ACTAAGAC -HiMom:1:2101:1023:2237 516 * 0 0 * * 0 0 ..TTTGTTTGAGTTCCTTGTAGATT ##0:=@?>?@???@:>?@??>?;?< RG:Z:HiMom.1 QX:Z:=:1<#### RX:Z:GCCTAGCC -HiMom:1:2101:1031:2163 4 * 0 0 * * 0 0 ..ACATTTGTCACCACTAGCCACCA ##0<@?@@@@@@@@@@?@@@@@@@? RG:Z:HiMom.1 QX:Z:B@BFFFFF RX:Z:GATATCCA -HiMom:1:2101:1036:2087 4 * 0 0 * * 0 0 .GTCCACTTACGAAGCAAATACTTT #4=DDFFFHHHHHJJJJJJJJJJJJ RG:Z:HiMom.1 QX:Z:B@CFFDFF RX:Z:GACCGTTG -HiMom:1:2101:1040:2208 516 * 0 0 * * 0 0 .CTGATAGTCACTGAAATGAATTCA #-0=>(2@.22@@############ RG:Z:HiMom.1 QX:Z:######## RX:Z:ACGAAATC -HiMom:1:2101:1048:2238 4 * 0 0 * * 0 0 .GTCACATCGTTGAAGCACTGGATC #11ADDDB?4:>?@###### RG:Z:HiMom.1 QX:Z:1+8?ADD8 RX:Z:ACTAAGAC -HiMom:1:2101:1273:2119 516 * 0 0 * * 0 0 ATGATGGATCTTCTCTAACTTGTCA >=>=>>?############## RG:Z:HiMom.1 QX:Z:####227+@-A7A7 RX:Z:ACTA-AGAC +HiMom:1:1101:1263:2236 516 * 0 0 * * 0 0 AGTTCTTCAGTAATTTTAGTACTGC ######################### RG:Z:HiMom.1 QX:Z:####-#### RX:Z:AGGT-AAGG +HiMom:1:1101:1267:2209 4 * 0 0 * * 0 0 GGCAGAGTCTCCAACAGCCCCGTAC =;?DDDD?CCFHAIIIGGIIGE@EG RG:Z:HiMom.1 QX:Z:?@@D-;ADD RX:Z:TATC-AGCC +HiMom:1:1101:1269:2170 4 * 0 0 * * 0 0 TTCCAAGCCTGTGCTTTAAGGAAAA @@>7-A### RX:Z:CAAT-AGAC +HiMom:1:1101:1327:2200 516 * 0 0 * * 0 0 GTCATCTGGGCTGTCGACAGGTGTC @B@FFFFFHHHHGIJJJJJJIFHHI RG:Z:HiMom.1 QX:Z:BCCF-DFFD RX:Z:GCCG-TCGA +HiMom:1:1101:1328:2225 4 * 0 0 * * 0 0 AGGAAATTAGGACTTACCTGACATA ######################### RG:Z:HiMom.1 QX:Z:??;=-A:B= RX:Z:CAAC-TCTC +HiMom:1:1101:1338:2175 4 * 0 0 * * 0 0 GCTTGTTGGCTTTAACATCCACAAT CCCFFFFFHHHHHJJJJJJJJJJJJ RG:Z:HiMom.1 QX:Z:CCCF-FFFF RX:Z:GAAG-GAAG +HiMom:1:1101:1347:2149 4 * 0 0 * * 0 0 GCTCTTCCGATCTGTGCTCTTCCGA CCCFFFFFDFHHFIJDGIGGHGIGH RG:Z:HiMom.1 QX:Z:CC@D-FFFD RX:Z:GACC-AGGA +HiMom:1:1101:1353:2226 4 * 0 0 * * 0 0 GTGCTCTTCCGATCTTCAGGTTACC BBBFFFFFHHHHHJJJJJJJIJJJJ RG:Z:HiMom.1 QX:Z:@B@F-FEFF RX:Z:TATC-TGCC +HiMom:1:1101:1363:2138 4 * 0 0 * * 0 0 GTTCTTAAACCTGTTAGAACTTCTG C@@FFFFFHHHHHJJJJJJJJJJJJ RG:Z:HiMom.1 QX:Z:CCCF-FFFF RX:Z:CTAA-CTCG +HiMom:1:1101:1399:2128 4 * 0 0 * * 0 0 ACAAACCCTTGTGTCGAGGGCTGAC CCCFFFFFHHHHHIJJJJJJJJJJJ RG:Z:HiMom.1 QX:Z:CCCF-FFFF RX:Z:CAAT-AGTC +HiMom:1:1101:1403:2194 4 * 0 0 * * 0 0 ACATGGTGAAACCCTGTCTCTACTA CCCFFFDDHHHHHJJJJJJJJJJJJ RG:Z:HiMom.1 QX:Z:CCCF-FFFF RX:Z:CTGT-AATC +HiMom:1:1101:1406:2222 4 * 0 0 * * 0 0 GGCTGGACTCCCCTGGTTCTGGGCA ;?@DDDBD?FHDFGIIIGIGHHIII RG:Z:HiMom.1 QX:Z:C@@D-BFEF RX:Z:AGCA-TGGA +HiMom:1:1101:1419:2119 4 * 0 0 * * 0 0 ACTTTCCTTTTTTGTTTTACTTTAA ######################### RG:Z:HiMom.1 QX:Z:@@@D-FDFD RX:Z:TGTA-ATCA +HiMom:1:1101:1420:2213 4 * 0 0 * * 0 0 TTCACTGTACCGGCCGTGCGTACTT @CCFFFFDHHHFGIJJJJJJGHIGG RG:Z:HiMom.1 QX:Z:@C@F-FFDF RX:Z:CAGC-GGTA +HiMom:1:1101:1435:2194 4 * 0 0 * * 0 0 TTTTGTTTTCTTTTACTGAAGTGTA CCCFFDFFHHHHHJJJJIHIJHHHJ RG:Z:HiMom.1 QX:Z:CCCF-FFFF RX:Z:TATC-TGCC +HiMom:1:1101:1441:2148 4 * 0 0 * * 0 0 TTTTGGCTCTAGAGGGGGTAGAGGG CCCFFFFFHHDFBHIIJJ1?FGHIJ RG:Z:HiMom.1 QX:Z:@@BF-FDDD RX:Z:CGCT-ATGT +HiMom:1:1101:1452:2132 4 * 0 0 * * 0 0 ACAAACCCTTGTGTCGAGGGCTGAC CCCFFFFFHHHHHJJJJJJJIJJJJ RG:Z:HiMom.1 QX:Z:@CCF-FFFF RX:Z:AACG-CATT +HiMom:1:1101:1460:2176 4 * 0 0 * * 0 0 AGGAAAAAGACACAACAAGTCCAAC ######################### RG:Z:HiMom.1 QX:Z:CCCF-FFFF RX:Z:GATA-TCCA +HiMom:1:1101:1479:2221 4 * 0 0 * * 0 0 GGGGAAATCTATTTTTATGTAAAAA @CCFFFFFHHHHHJIGIJJJJJJJJ RG:Z:HiMom.1 QX:Z:@BCF-FFFF RX:Z:TCGC-TAGA +HiMom:1:1101:1491:2120 4 * 0 0 * * 0 0 GGCCAGGCTGAACTTCTGAGCTGCT CCCFFFFFHHHGHJJJJJJJJJJJJ RG:Z:HiMom.1 QX:Z:BCCD-FFFF RX:Z:AGGT-CGCA +HiMom:1:1201:1018:2133 4 * 0 0 * * 0 0 ......................... ######################### RG:Z:HiMom.1 XN:i:1 QX:Z:8??=-BBBA RX:Z:ATTC-CTCT +HiMom:1:1201:1018:2217 516 * 0 0 * * 0 0 ......................... ######################### RG:Z:HiMom.1 XN:i:1 QX:Z:;<;:-BBDD RX:Z:ATTA-TCAA +HiMom:1:1201:1028:2202 4 * 0 0 * * 0 0 ..AAAC.C.T.......GG..TG.. ##42@?################### RG:Z:HiMom.1 QX:Z:CCCF-FDFF RX:Z:GAAG-GAAG +HiMom:1:1201:1042:2174 4 * 0 0 * * 0 0 .TCAGGAAGGC..CAAAAAAAGAAA #0;@@@?@?<@##3<@@?@@????? RG:Z:HiMom.1 QX:Z:CCCF-FFFF RX:Z:TCTG-CAAG +HiMom:1:1201:1043:2246 4 * 0 0 * * 0 0 .GCATCATTTC..GCTTCTCTCTGT #0;@@??@=@>##22=;@??><@?? RG:Z:HiMom.1 QX:Z:@A# RG:Z:HiMom.1 QX:Z:?;@D-FDFF RX:Z:GACC-AGGA +HiMom:1:1201:1127:2112 516 * 0 0 * * 0 0 TAATCACCTGAGCAGTGAAGCCAGC @<@?BDDDHD?FDBHI?AHGGGDFH RG:Z:HiMom.1 QX:Z:=??B-A?BD RX:Z:CAAC-TCTC +HiMom:1:1201:1134:2144 4 * 0 0 * * 0 0 AGTGTGAGTAATGGTTGAGAGGTGG B@?DDDFFFHHGHJHHGFIHHIFGI RG:Z:HiMom.1 QX:Z:CCCF-FFFD RX:Z:CGCT-ATGT +HiMom:1:1201:1138:2227 516 * 0 0 * * 0 0 GACAAATATAGGAAATAGAAGCTAT =1=A=AAA,2?4>7C<<4B6=BBBB RG:Z:HiMom.1 QX:Z:####-#### RX:Z:AGAA-AAGA +HiMom:1:1201:1416:2128 4 * 0 0 * * 0 0 TTGGTGTGGAGGCGGTGGCGGGATC @@@DDDDDHHFHHII:?GGHIIB6? RG:Z:HiMom.1 QX:Z:CCCF-FFFF RX:Z:TCGC-TAGA +HiMom:1:1201:1421:2154 4 * 0 0 * * 0 0 TGTGCTCTTCCGATCTTGTGCTCTT BC@DFFFFHHHHHJJJJFHIHHIJJ RG:Z:HiMom.1 QX:Z:@@@F-FFFF RX:Z:TGTA-ACTC +HiMom:1:1201:1439:2156 4 * 0 0 * * 0 0 GGAGATTATTTGCCTTGAAGTAAGC -;(22<>>@>8@>8;@######### RG:Z:HiMom.1 QX:Z:1;;=-#### RX:Z:GACC-AGGC +HiMom:1:1201:1452:2143 4 * 0 0 * * 0 0 TTTTAGTCTTAGCATTTACTTTCCC CCCFFFFFHHHHHJJJJJJJJJJJJ RG:Z:HiMom.1 QX:Z:BC@D-DFFF RX:Z:CAAC-TCTC +HiMom:1:1201:1458:2109 4 * 0 0 * * 0 0 GATACGAACACACAAGAACTTTTTT CCCFFFFFHHHHHJJJJJJJJJJJI RG:Z:HiMom.1 QX:Z:CCCF-FFFF RX:Z:ACTG-TATC +HiMom:1:1201:1472:2121 516 * 0 0 * * 0 0 GTGTGCTCTTCCGATCTGGAGGATG =+=??A4A==A@7A??@@??@?????????>?@ RG:Z:HiMom.1 QX:Z:@CCD-FFFF RX:Z:ACTA-AGAC +HiMom:1:2101:1023:2237 516 * 0 0 * * 0 0 ..TTTGTTTGAGTTCCTTGTAGATT ##0:=@?>?@???@:>?@??>?;?< RG:Z:HiMom.1 QX:Z:=:1<-#### RX:Z:GCCT-AGCC +HiMom:1:2101:1031:2163 4 * 0 0 * * 0 0 ..ACATTTGTCACCACTAGCCACCA ##0<@?@@@@@@@@@@?@@@@@@@? RG:Z:HiMom.1 QX:Z:B@BF-FFFF RX:Z:GATA-TCCA +HiMom:1:2101:1036:2087 4 * 0 0 * * 0 0 .GTCCACTTACGAAGCAAATACTTT #4=DDFFFHHHHHJJJJJJJJJJJJ RG:Z:HiMom.1 QX:Z:B@CF-FDFF RX:Z:GACC-GTTG +HiMom:1:2101:1040:2208 516 * 0 0 * * 0 0 .CTGATAGTCACTGAAATGAATTCA #-0=>(2@.22@@############ RG:Z:HiMom.1 QX:Z:####-#### RX:Z:ACGA-AATC +HiMom:1:2101:1048:2238 4 * 0 0 * * 0 0 .GTCACATCGTTGAAGCACTGGATC #11ADDDB?4:>?@###### RG:Z:HiMom.1 QX:Z:1+8?-ADD8 RX:Z:ACTA-AGAC +HiMom:1:2101:1273:2119 516 * 0 0 * * 0 0 ATGATGGATCTTCTCTAACTTGTCA >=>=>>?############## RG:Z:HiMom.1 QX:Z:####-227+@A7A7 RX:Z:ACTAAGAC -HiMom:1:1101:1263:2236 516 * 0 0 * * 0 0 AGTTCTTCAGTAATTTTAGTACTGC ######################### ZA:Z:AG ZB:Z:GT ZC:Z:AA ZD:Z:GG RG:Z:HiMom.1 QX:Z:######## RX:Z:AGGTAAGG -HiMom:1:1101:1267:2209 4 * 0 0 * * 0 0 GGCAGAGTCTCCAACAGCCCCGTAC =;?DDDD?CCFHAIIIGGIIGE@EG ZA:Z:TA ZB:Z:TC ZC:Z:AG ZD:Z:CC RG:Z:HiMom.1 QX:Z:?@@D;ADD RX:Z:TATCAGCC -HiMom:1:1101:1269:2170 4 * 0 0 * * 0 0 TTCCAAGCCTGTGCTTTAAGGAAAA @@>7A7## RX:Z:CAATAGAC -HiMom:1:1101:1327:2200 516 * 0 0 * * 0 0 GTCATCTGGGCTGTCGACAGGTGTC @B@FFFFFHHHHGIJJJJJJIFHHI ZA:Z:GC ZB:Z:CG ZC:Z:TC ZD:Z:GA RG:Z:HiMom.1 QX:Z:BCCFDFFD RX:Z:GCCGTCGA -HiMom:1:1101:1328:2225 4 * 0 0 * * 0 0 AGGAAATTAGGACTTACCTGACATA ######################### ZA:Z:CA ZB:Z:AC ZC:Z:TC ZD:Z:TC RG:Z:HiMom.1 QX:Z:??;=A:B= RX:Z:CAACTCTC -HiMom:1:1101:1338:2175 4 * 0 0 * * 0 0 GCTTGTTGGCTTTAACATCCACAAT CCCFFFFFHHHHHJJJJJJJJJJJJ ZA:Z:GA ZB:Z:AG ZC:Z:GA ZD:Z:AG RG:Z:HiMom.1 QX:Z:CCCFFFFF RX:Z:GAAGGAAG -HiMom:1:1101:1347:2149 4 * 0 0 * * 0 0 GCTCTTCCGATCTGTGCTCTTCCGA CCCFFFFFDFHHFIJDGIGGHGIGH ZA:Z:GA ZB:Z:CC ZC:Z:AG ZD:Z:GA RG:Z:HiMom.1 QX:Z:CC@DFFFD RX:Z:GACCAGGA -HiMom:1:1101:1353:2226 4 * 0 0 * * 0 0 GTGCTCTTCCGATCTTCAGGTTACC BBBFFFFFHHHHHJJJJJJJIJJJJ ZA:Z:TA ZB:Z:TC ZC:Z:TG ZD:Z:CC RG:Z:HiMom.1 QX:Z:@B@FFEFF RX:Z:TATCTGCC -HiMom:1:1101:1363:2138 4 * 0 0 * * 0 0 GTTCTTAAACCTGTTAGAACTTCTG C@@FFFFFHHHHHJJJJJJJJJJJJ ZA:Z:CT ZB:Z:AA ZC:Z:CT ZD:Z:CG RG:Z:HiMom.1 QX:Z:CCCFFFFF RX:Z:CTAACTCG -HiMom:1:1101:1399:2128 4 * 0 0 * * 0 0 ACAAACCCTTGTGTCGAGGGCTGAC CCCFFFFFHHHHHIJJJJJJJJJJJ ZA:Z:CA ZB:Z:AT ZC:Z:AG ZD:Z:TC RG:Z:HiMom.1 QX:Z:CCCFFFFF RX:Z:CAATAGTC -HiMom:1:1101:1403:2194 4 * 0 0 * * 0 0 ACATGGTGAAACCCTGTCTCTACTA CCCFFFDDHHHHHJJJJJJJJJJJJ ZA:Z:CT ZB:Z:GT ZC:Z:AA ZD:Z:TC RG:Z:HiMom.1 QX:Z:CCCFFFFF RX:Z:CTGTAATC -HiMom:1:1101:1406:2222 4 * 0 0 * * 0 0 GGCTGGACTCCCCTGGTTCTGGGCA ;?@DDDBD?FHDFGIIIGIGHHIII ZA:Z:AG ZB:Z:CA ZC:Z:TG ZD:Z:GA RG:Z:HiMom.1 QX:Z:C@@DBFEF RX:Z:AGCATGGA -HiMom:1:1101:1419:2119 4 * 0 0 * * 0 0 ACTTTCCTTTTTTGTTTTACTTTAA ######################### ZA:Z:TG ZB:Z:TA ZC:Z:AT ZD:Z:CA RG:Z:HiMom.1 QX:Z:@@@DFDFD RX:Z:TGTAATCA -HiMom:1:1101:1420:2213 4 * 0 0 * * 0 0 TTCACTGTACCGGCCGTGCGTACTT @CCFFFFDHHHFGIJJJJJJGHIGG ZA:Z:CA ZB:Z:GC ZC:Z:GG ZD:Z:TA RG:Z:HiMom.1 QX:Z:@C@FFFDF RX:Z:CAGCGGTA -HiMom:1:1101:1435:2194 4 * 0 0 * * 0 0 TTTTGTTTTCTTTTACTGAAGTGTA CCCFFDFFHHHHHJJJJIHIJHHHJ ZA:Z:TA ZB:Z:TC ZC:Z:TG ZD:Z:CC RG:Z:HiMom.1 QX:Z:CCCFFFFF RX:Z:TATCTGCC -HiMom:1:1101:1441:2148 4 * 0 0 * * 0 0 TTTTGGCTCTAGAGGGGGTAGAGGG CCCFFFFFHHDFBHIIJJ1?FGHIJ ZA:Z:CG ZB:Z:CT ZC:Z:AT ZD:Z:GT RG:Z:HiMom.1 QX:Z:@@BFFDDD RX:Z:CGCTATGT -HiMom:1:1101:1452:2132 4 * 0 0 * * 0 0 ACAAACCCTTGTGTCGAGGGCTGAC CCCFFFFFHHHHHJJJJJJJIJJJJ ZA:Z:AA ZB:Z:CG ZC:Z:CA ZD:Z:TT RG:Z:HiMom.1 QX:Z:@CCFFFFF RX:Z:AACGCATT -HiMom:1:1101:1460:2176 4 * 0 0 * * 0 0 AGGAAAAAGACACAACAAGTCCAAC ######################### ZA:Z:GA ZB:Z:TA ZC:Z:TC ZD:Z:CA RG:Z:HiMom.1 QX:Z:CCCFFFFF RX:Z:GATATCCA -HiMom:1:1101:1479:2221 4 * 0 0 * * 0 0 GGGGAAATCTATTTTTATGTAAAAA @CCFFFFFHHHHHJIGIJJJJJJJJ ZA:Z:TC ZB:Z:GC ZC:Z:TA ZD:Z:GA RG:Z:HiMom.1 QX:Z:@BCFFFFF RX:Z:TCGCTAGA -HiMom:1:1101:1491:2120 4 * 0 0 * * 0 0 GGCCAGGCTGAACTTCTGAGCTGCT CCCFFFFFHHHGHJJJJJJJJJJJJ ZA:Z:AG ZB:Z:GT ZC:Z:CG ZD:Z:CA RG:Z:HiMom.1 QX:Z:BCCDFFFF RX:Z:AGGTCGCA -HiMom:1:1201:1018:2133 4 * 0 0 * * 0 0 ......................... ######################### ZA:Z:AT ZB:Z:TC ZC:Z:CT ZD:Z:CT RG:Z:HiMom.1 XN:i:1 QX:Z:8??=BBBA RX:Z:ATTCCTCT -HiMom:1:1201:1018:2217 516 * 0 0 * * 0 0 ......................... ######################### ZA:Z:AT ZB:Z:TA ZC:Z:TC ZD:Z:AA RG:Z:HiMom.1 XN:i:1 QX:Z:;<;:BBDD RX:Z:ATTATCAA -HiMom:1:1201:1028:2202 4 * 0 0 * * 0 0 ..AAAC.C.T.......GG..TG.. ##42@?################### ZA:Z:GA ZB:Z:AG ZC:Z:GA ZD:Z:AG RG:Z:HiMom.1 QX:Z:CCCFFDFF RX:Z:GAAGGAAG -HiMom:1:1201:1042:2174 4 * 0 0 * * 0 0 .TCAGGAAGGC..CAAAAAAAGAAA #0;@@@?@?<@##3<@@?@@????? ZA:Z:TC ZB:Z:TG ZC:Z:CA ZD:Z:AG RG:Z:HiMom.1 QX:Z:CCCFFFFF RX:Z:TCTGCAAG -HiMom:1:1201:1043:2246 4 * 0 0 * * 0 0 .GCATCATTTC..GCTTCTCTCTGT #0;@@??@=@>##22=;@??><@?? ZA:Z:CG ZB:Z:CT ZC:Z:AT ZD:Z:GT RG:Z:HiMom.1 QX:Z:@A# ZA:Z:GA ZB:Z:CC ZC:Z:AG ZD:Z:GA RG:Z:HiMom.1 QX:Z:?;@DFDFF RX:Z:GACCAGGA -HiMom:1:1201:1127:2112 516 * 0 0 * * 0 0 TAATCACCTGAGCAGTGAAGCCAGC @<@?BDDDHD?FDBHI?AHGGGDFH ZA:Z:CA ZB:Z:AC ZC:Z:TC ZD:Z:TC RG:Z:HiMom.1 QX:Z:=??BA?BD RX:Z:CAACTCTC -HiMom:1:1201:1134:2144 4 * 0 0 * * 0 0 AGTGTGAGTAATGGTTGAGAGGTGG B@?DDDFFFHHGHJHHGFIHHIFGI ZA:Z:CG ZB:Z:CT ZC:Z:AT ZD:Z:GT RG:Z:HiMom.1 QX:Z:CCCFFFFD RX:Z:CGCTATGT -HiMom:1:1201:1138:2227 516 * 0 0 * * 0 0 GACAAATATAGGAAATAGAAGCTAT =1=A=AAA,2?4>7C<<4B6=BBBB ZA:Z:AG ZB:Z:AA ZC:Z:AA ZD:Z:GA RG:Z:HiMom.1 QX:Z:####<>## RX:Z:AGAAAAGA -HiMom:1:1201:1416:2128 4 * 0 0 * * 0 0 TTGGTGTGGAGGCGGTGGCGGGATC @@@DDDDDHHFHHII:?GGHIIB6? ZA:Z:TC ZB:Z:GC ZC:Z:TA ZD:Z:GA RG:Z:HiMom.1 QX:Z:CCCFFFFF RX:Z:TCGCTAGA -HiMom:1:1201:1421:2154 4 * 0 0 * * 0 0 TGTGCTCTTCCGATCTTGTGCTCTT BC@DFFFFHHHHHJJJJFHIHHIJJ ZA:Z:TG ZB:Z:TA ZC:Z:AC ZD:Z:TC RG:Z:HiMom.1 QX:Z:@@@FFFFF RX:Z:TGTAACTC -HiMom:1:1201:1439:2156 4 * 0 0 * * 0 0 GGAGATTATTTGCCTTGAAGTAAGC -;(22<>>@>8@>8;@######### ZA:Z:GA ZB:Z:CC ZC:Z:AG ZD:Z:GC RG:Z:HiMom.1 QX:Z:1;;=#### RX:Z:GACCAGGC -HiMom:1:1201:1452:2143 4 * 0 0 * * 0 0 TTTTAGTCTTAGCATTTACTTTCCC CCCFFFFFHHHHHJJJJJJJJJJJJ ZA:Z:CA ZB:Z:AC ZC:Z:TC ZD:Z:TC RG:Z:HiMom.1 QX:Z:BC@DDFFF RX:Z:CAACTCTC -HiMom:1:1201:1458:2109 4 * 0 0 * * 0 0 GATACGAACACACAAGAACTTTTTT CCCFFFFFHHHHHJJJJJJJJJJJI ZA:Z:AC ZB:Z:TG ZC:Z:TA ZD:Z:TC RG:Z:HiMom.1 QX:Z:CCCFFFFF RX:Z:ACTGTATC -HiMom:1:1201:1472:2121 516 * 0 0 * * 0 0 GTGTGCTCTTCCGATCTGGAGGATG =+=??A4A==A@7A??@@??@?????????>?@ ZA:Z:AC ZB:Z:TA ZC:Z:AG ZD:Z:AC RG:Z:HiMom.1 QX:Z:@CCDFFFF RX:Z:ACTAAGAC -HiMom:1:2101:1023:2237 516 * 0 0 * * 0 0 ..TTTGTTTGAGTTCCTTGTAGATT ##0:=@?>?@???@:>?@??>?;?< ZA:Z:GC ZB:Z:CT ZC:Z:AG ZD:Z:CC RG:Z:HiMom.1 QX:Z:=:1<#### RX:Z:GCCTAGCC -HiMom:1:2101:1031:2163 4 * 0 0 * * 0 0 ..ACATTTGTCACCACTAGCCACCA ##0<@?@@@@@@@@@@?@@@@@@@? ZA:Z:GA ZB:Z:TA ZC:Z:TC ZD:Z:CA RG:Z:HiMom.1 QX:Z:B@BFFFFF RX:Z:GATATCCA -HiMom:1:2101:1036:2087 4 * 0 0 * * 0 0 .GTCCACTTACGAAGCAAATACTTT #4=DDFFFHHHHHJJJJJJJJJJJJ ZA:Z:GA ZB:Z:CC ZC:Z:GT ZD:Z:TG RG:Z:HiMom.1 QX:Z:B@CFFDFF RX:Z:GACCGTTG -HiMom:1:2101:1040:2208 516 * 0 0 * * 0 0 .CTGATAGTCACTGAAATGAATTCA #-0=>(2@.22@@############ ZA:Z:AC ZB:Z:GA ZC:Z:AA ZD:Z:TC RG:Z:HiMom.1 QX:Z::1###### RX:Z:ACGAAATC -HiMom:1:2101:1048:2238 4 * 0 0 * * 0 0 .GTCACATCGTTGAAGCACTGGATC #11ADDDB?4:>?@###### ZA:Z:AC ZB:Z:TA ZC:Z:AG ZD:Z:AC RG:Z:HiMom.1 QX:Z:##8?ADD8 RX:Z:ACTAAGAC -HiMom:1:2101:1273:2119 516 * 0 0 * * 0 0 ATGATGGATCTTCTCTAACTTGTCA >=>=>>?############## ZA:Z:AC ZB:Z:TG ZC:Z:TA ZD:Z:TC RG:Z:HiMom.1 QX:Z:=;##227-+@-A7-A7 RX:Z:AC-TA-AG-AC +HiMom:1:1101:1263:2236 516 * 0 0 * * 0 0 AGTTCTTCAGTAATTTTAGTACTGC ######################### ZA:Z:AG ZB:Z:GT ZC:Z:AA ZD:Z:GG RG:Z:HiMom.1 QX:Z:##-##-##-## RX:Z:AG-GT-AA-GG +HiMom:1:1101:1267:2209 4 * 0 0 * * 0 0 GGCAGAGTCTCCAACAGCCCCGTAC =;?DDDD?CCFHAIIIGGIIGE@EG ZA:Z:TA ZB:Z:TC ZC:Z:AG ZD:Z:CC RG:Z:HiMom.1 QX:Z:?@-@D-;A-DD RX:Z:TA-TC-AG-CC +HiMom:1:1101:1269:2170 4 * 0 0 * * 0 0 TTCCAAGCCTGTGCTTTAAGGAAAA @@->7-A7-## RX:Z:CA-AT-AG-AC +HiMom:1:1101:1327:2200 516 * 0 0 * * 0 0 GTCATCTGGGCTGTCGACAGGTGTC @B@FFFFFHHHHGIJJJJJJIFHHI ZA:Z:GC ZB:Z:CG ZC:Z:TC ZD:Z:GA RG:Z:HiMom.1 QX:Z:BC-CF-DF-FD RX:Z:GC-CG-TC-GA +HiMom:1:1101:1328:2225 4 * 0 0 * * 0 0 AGGAAATTAGGACTTACCTGACATA ######################### ZA:Z:CA ZB:Z:AC ZC:Z:TC ZD:Z:TC RG:Z:HiMom.1 QX:Z:??-;=-A:-B= RX:Z:CA-AC-TC-TC +HiMom:1:1101:1338:2175 4 * 0 0 * * 0 0 GCTTGTTGGCTTTAACATCCACAAT CCCFFFFFHHHHHJJJJJJJJJJJJ ZA:Z:GA ZB:Z:AG ZC:Z:GA ZD:Z:AG RG:Z:HiMom.1 QX:Z:CC-CF-FF-FF RX:Z:GA-AG-GA-AG +HiMom:1:1101:1347:2149 4 * 0 0 * * 0 0 GCTCTTCCGATCTGTGCTCTTCCGA CCCFFFFFDFHHFIJDGIGGHGIGH ZA:Z:GA ZB:Z:CC ZC:Z:AG ZD:Z:GA RG:Z:HiMom.1 QX:Z:CC-@D-FF-FD RX:Z:GA-CC-AG-GA +HiMom:1:1101:1353:2226 4 * 0 0 * * 0 0 GTGCTCTTCCGATCTTCAGGTTACC BBBFFFFFHHHHHJJJJJJJIJJJJ ZA:Z:TA ZB:Z:TC ZC:Z:TG ZD:Z:CC RG:Z:HiMom.1 QX:Z:@B-@F-FE-FF RX:Z:TA-TC-TG-CC +HiMom:1:1101:1363:2138 4 * 0 0 * * 0 0 GTTCTTAAACCTGTTAGAACTTCTG C@@FFFFFHHHHHJJJJJJJJJJJJ ZA:Z:CT ZB:Z:AA ZC:Z:CT ZD:Z:CG RG:Z:HiMom.1 QX:Z:CC-CF-FF-FF RX:Z:CT-AA-CT-CG +HiMom:1:1101:1399:2128 4 * 0 0 * * 0 0 ACAAACCCTTGTGTCGAGGGCTGAC CCCFFFFFHHHHHIJJJJJJJJJJJ ZA:Z:CA ZB:Z:AT ZC:Z:AG ZD:Z:TC RG:Z:HiMom.1 QX:Z:CC-CF-FF-FF RX:Z:CA-AT-AG-TC +HiMom:1:1101:1403:2194 4 * 0 0 * * 0 0 ACATGGTGAAACCCTGTCTCTACTA CCCFFFDDHHHHHJJJJJJJJJJJJ ZA:Z:CT ZB:Z:GT ZC:Z:AA ZD:Z:TC RG:Z:HiMom.1 QX:Z:CC-CF-FF-FF RX:Z:CT-GT-AA-TC +HiMom:1:1101:1406:2222 4 * 0 0 * * 0 0 GGCTGGACTCCCCTGGTTCTGGGCA ;?@DDDBD?FHDFGIIIGIGHHIII ZA:Z:AG ZB:Z:CA ZC:Z:TG ZD:Z:GA RG:Z:HiMom.1 QX:Z:C@-@D-BF-EF RX:Z:AG-CA-TG-GA +HiMom:1:1101:1419:2119 4 * 0 0 * * 0 0 ACTTTCCTTTTTTGTTTTACTTTAA ######################### ZA:Z:TG ZB:Z:TA ZC:Z:AT ZD:Z:CA RG:Z:HiMom.1 QX:Z:@@-@D-FD-FD RX:Z:TG-TA-AT-CA +HiMom:1:1101:1420:2213 4 * 0 0 * * 0 0 TTCACTGTACCGGCCGTGCGTACTT @CCFFFFDHHHFGIJJJJJJGHIGG ZA:Z:CA ZB:Z:GC ZC:Z:GG ZD:Z:TA RG:Z:HiMom.1 QX:Z:@C-@F-FF-DF RX:Z:CA-GC-GG-TA +HiMom:1:1101:1435:2194 4 * 0 0 * * 0 0 TTTTGTTTTCTTTTACTGAAGTGTA CCCFFDFFHHHHHJJJJIHIJHHHJ ZA:Z:TA ZB:Z:TC ZC:Z:TG ZD:Z:CC RG:Z:HiMom.1 QX:Z:CC-CF-FF-FF RX:Z:TA-TC-TG-CC +HiMom:1:1101:1441:2148 4 * 0 0 * * 0 0 TTTTGGCTCTAGAGGGGGTAGAGGG CCCFFFFFHHDFBHIIJJ1?FGHIJ ZA:Z:CG ZB:Z:CT ZC:Z:AT ZD:Z:GT RG:Z:HiMom.1 QX:Z:@@-BF-FD-DD RX:Z:CG-CT-AT-GT +HiMom:1:1101:1452:2132 4 * 0 0 * * 0 0 ACAAACCCTTGTGTCGAGGGCTGAC CCCFFFFFHHHHHJJJJJJJIJJJJ ZA:Z:AA ZB:Z:CG ZC:Z:CA ZD:Z:TT RG:Z:HiMom.1 QX:Z:@C-CF-FF-FF RX:Z:AA-CG-CA-TT +HiMom:1:1101:1460:2176 4 * 0 0 * * 0 0 AGGAAAAAGACACAACAAGTCCAAC ######################### ZA:Z:GA ZB:Z:TA ZC:Z:TC ZD:Z:CA RG:Z:HiMom.1 QX:Z:CC-CF-FF-FF RX:Z:GA-TA-TC-CA +HiMom:1:1101:1479:2221 4 * 0 0 * * 0 0 GGGGAAATCTATTTTTATGTAAAAA @CCFFFFFHHHHHJIGIJJJJJJJJ ZA:Z:TC ZB:Z:GC ZC:Z:TA ZD:Z:GA RG:Z:HiMom.1 QX:Z:@B-CF-FF-FF RX:Z:TC-GC-TA-GA +HiMom:1:1101:1491:2120 4 * 0 0 * * 0 0 GGCCAGGCTGAACTTCTGAGCTGCT CCCFFFFFHHHGHJJJJJJJJJJJJ ZA:Z:AG ZB:Z:GT ZC:Z:CG ZD:Z:CA RG:Z:HiMom.1 QX:Z:BC-CD-FF-FF RX:Z:AG-GT-CG-CA +HiMom:1:1201:1018:2133 4 * 0 0 * * 0 0 ......................... ######################### ZA:Z:AT ZB:Z:TC ZC:Z:CT ZD:Z:CT RG:Z:HiMom.1 XN:i:1 QX:Z:8?-?=-BB-BA RX:Z:AT-TC-CT-CT +HiMom:1:1201:1018:2217 516 * 0 0 * * 0 0 ......................... ######################### ZA:Z:AT ZB:Z:TA ZC:Z:TC ZD:Z:AA RG:Z:HiMom.1 XN:i:1 QX:Z:;<-;:-BB-DD RX:Z:AT-TA-TC-AA +HiMom:1:1201:1028:2202 4 * 0 0 * * 0 0 ..AAAC.C.T.......GG..TG.. ##42@?################### ZA:Z:GA ZB:Z:AG ZC:Z:GA ZD:Z:AG RG:Z:HiMom.1 QX:Z:CC-CF-FD-FF RX:Z:GA-AG-GA-AG +HiMom:1:1201:1042:2174 4 * 0 0 * * 0 0 .TCAGGAAGGC..CAAAAAAAGAAA #0;@@@?@?<@##3<@@?@@????? ZA:Z:TC ZB:Z:TG ZC:Z:CA ZD:Z:AG RG:Z:HiMom.1 QX:Z:CC-CF-FF-FF RX:Z:TC-TG-CA-AG +HiMom:1:1201:1043:2246 4 * 0 0 * * 0 0 .GCATCATTTC..GCTTCTCTCTGT #0;@@??@=@>##22=;@??><@?? ZA:Z:CG ZB:Z:CT ZC:Z:AT ZD:Z:GT RG:Z:HiMom.1 QX:Z:@<-?D-D:-B= RX:Z:CG-CT-AT-GT +HiMom:1:1201:1045:2105 516 * 0 0 * * 0 0 .TTTTTTTTTT..TTTTTTTTTTTT #0;@@@@@@@?##0:????????=< ZA:Z:CT ZB:Z:GT ZC:Z:AA ZD:Z:TC RG:Z:HiMom.1 QX:Z:11-12-@A-## RX:Z:CT-GT-AA-TC +HiMom:1:1201:1054:2151 4 * 0 0 * * 0 0 GTCAGGCACTGAGAATATATGGGTG CBCFFFFFHHHHHJJJJJJJJJJEG ZA:Z:CA ZB:Z:AT ZC:Z:AG ZD:Z:TC RG:Z:HiMom.1 QX:Z:CC-CF-FF-DF RX:Z:CA-AT-AG-TC +HiMom:1:1201:1064:2239 4 * 0 0 * * 0 0 GGGATGGGAGGGCGATGAGGACTAG 8?@:DDDACC:FHHGIHA# ZA:Z:GA ZB:Z:CC ZC:Z:AG ZD:Z:GA RG:Z:HiMom.1 QX:Z:?;-@D-FD-FF RX:Z:GA-CC-AG-GA +HiMom:1:1201:1127:2112 516 * 0 0 * * 0 0 TAATCACCTGAGCAGTGAAGCCAGC @<@?BDDDHD?FDBHI?AHGGGDFH ZA:Z:CA ZB:Z:AC ZC:Z:TC ZD:Z:TC RG:Z:HiMom.1 QX:Z:=?-?B-A?-BD RX:Z:CA-AC-TC-TC +HiMom:1:1201:1134:2144 4 * 0 0 * * 0 0 AGTGTGAGTAATGGTTGAGAGGTGG B@?DDDFFFHHGHJHHGFIHHIFGI ZA:Z:CG ZB:Z:CT ZC:Z:AT ZD:Z:GT RG:Z:HiMom.1 QX:Z:CC-CF-FF-FD RX:Z:CG-CT-AT-GT +HiMom:1:1201:1138:2227 516 * 0 0 * * 0 0 GACAAATATAGGAAATAGAAGCTAT =1=A=AAA,2?4>7C<<4B6=BBBB ZA:Z:AG ZB:Z:AA ZC:Z:AA ZD:Z:GA RG:Z:HiMom.1 QX:Z:##-##-<>-## RX:Z:AG-AA-AA-GA +HiMom:1:1201:1416:2128 4 * 0 0 * * 0 0 TTGGTGTGGAGGCGGTGGCGGGATC @@@DDDDDHHFHHII:?GGHIIB6? ZA:Z:TC ZB:Z:GC ZC:Z:TA ZD:Z:GA RG:Z:HiMom.1 QX:Z:CC-CF-FF-FF RX:Z:TC-GC-TA-GA +HiMom:1:1201:1421:2154 4 * 0 0 * * 0 0 TGTGCTCTTCCGATCTTGTGCTCTT BC@DFFFFHHHHHJJJJFHIHHIJJ ZA:Z:TG ZB:Z:TA ZC:Z:AC ZD:Z:TC RG:Z:HiMom.1 QX:Z:@@-@F-FF-FF RX:Z:TG-TA-AC-TC +HiMom:1:1201:1439:2156 4 * 0 0 * * 0 0 GGAGATTATTTGCCTTGAAGTAAGC -;(22<>>@>8@>8;@######### ZA:Z:GA ZB:Z:CC ZC:Z:AG ZD:Z:GC RG:Z:HiMom.1 QX:Z:1;-;=-##-## RX:Z:GA-CC-AG-GC +HiMom:1:1201:1452:2143 4 * 0 0 * * 0 0 TTTTAGTCTTAGCATTTACTTTCCC CCCFFFFFHHHHHJJJJJJJJJJJJ ZA:Z:CA ZB:Z:AC ZC:Z:TC ZD:Z:TC RG:Z:HiMom.1 QX:Z:BC-@D-DF-FF RX:Z:CA-AC-TC-TC +HiMom:1:1201:1458:2109 4 * 0 0 * * 0 0 GATACGAACACACAAGAACTTTTTT CCCFFFFFHHHHHJJJJJJJJJJJI ZA:Z:AC ZB:Z:TG ZC:Z:TA ZD:Z:TC RG:Z:HiMom.1 QX:Z:CC-CF-FF-FF RX:Z:AC-TG-TA-TC +HiMom:1:1201:1472:2121 516 * 0 0 * * 0 0 GTGTGCTCTTCCGATCTGGAGGATG =+=??A4A==A@7A??@@??@?????????>?@ ZA:Z:AC ZB:Z:TA ZC:Z:AG ZD:Z:AC RG:Z:HiMom.1 QX:Z:@C-CD-FF-FF RX:Z:AC-TA-AG-AC +HiMom:1:2101:1023:2237 516 * 0 0 * * 0 0 ..TTTGTTTGAGTTCCTTGTAGATT ##0:=@?>?@???@:>?@??>?;?< ZA:Z:GC ZB:Z:CT ZC:Z:AG ZD:Z:CC RG:Z:HiMom.1 QX:Z:=:-1<-##-## RX:Z:GC-CT-AG-CC +HiMom:1:2101:1031:2163 4 * 0 0 * * 0 0 ..ACATTTGTCACCACTAGCCACCA ##0<@?@@@@@@@@@@?@@@@@@@? ZA:Z:GA ZB:Z:TA ZC:Z:TC ZD:Z:CA RG:Z:HiMom.1 QX:Z:B@-BF-FF-FF RX:Z:GA-TA-TC-CA +HiMom:1:2101:1036:2087 4 * 0 0 * * 0 0 .GTCCACTTACGAAGCAAATACTTT #4=DDFFFHHHHHJJJJJJJJJJJJ ZA:Z:GA ZB:Z:CC ZC:Z:GT ZD:Z:TG RG:Z:HiMom.1 QX:Z:B@-CF-FD-FF RX:Z:GA-CC-GT-TG +HiMom:1:2101:1040:2208 516 * 0 0 * * 0 0 .CTGATAGTCACTGAAATGAATTCA #-0=>(2@.22@@############ ZA:Z:AC ZB:Z:GA ZC:Z:AA ZD:Z:TC RG:Z:HiMom.1 QX:Z::1-##-##-## RX:Z:AC-GA-AA-TC +HiMom:1:2101:1048:2238 4 * 0 0 * * 0 0 .GTCACATCGTTGAAGCACTGGATC #11ADDDB?4:>?@###### ZA:Z:AC ZB:Z:TA ZC:Z:AG ZD:Z:AC RG:Z:HiMom.1 QX:Z:##-8?-AD-D8 RX:Z:AC-TA-AG-AC +HiMom:1:2101:1273:2119 516 * 0 0 * * 0 0 ATGATGGATCTTCTCTAACTTGTCA >=>=>>?############## ZA:Z:AC ZB:Z:TG ZC:Z:TA ZD:Z:TC RG:Z:HiMom.1 QX:Z:=;-##-22-7+@A7A7 RX:Z:ACTAAGAC -HiMom:1:1101:1263:2236 516 * 0 0 * * 0 0 AGTTCTTCAGTAATTTTAGTACTGC ######################### ZA:Z:AGGT ZB:Z:AAGG RG:Z:HiMom.1 QX:Z:######## RX:Z:AGGTAAGG -HiMom:1:1101:1267:2209 4 * 0 0 * * 0 0 GGCAGAGTCTCCAACAGCCCCGTAC =;?DDDD?CCFHAIIIGGIIGE@EG ZA:Z:TATC ZB:Z:AGCC RG:Z:HiMom.1 QX:Z:?@@D;ADD RX:Z:TATCAGCC -HiMom:1:1101:1269:2170 4 * 0 0 * * 0 0 TTCCAAGCCTGTGCTTTAAGGAAAA @@>7A### RX:Z:CAATAGAC -HiMom:1:1101:1327:2200 516 * 0 0 * * 0 0 GTCATCTGGGCTGTCGACAGGTGTC @B@FFFFFHHHHGIJJJJJJIFHHI ZA:Z:GCCG ZB:Z:TCGA RG:Z:HiMom.1 QX:Z:BCCFDFFD RX:Z:GCCGTCGA -HiMom:1:1101:1328:2225 4 * 0 0 * * 0 0 AGGAAATTAGGACTTACCTGACATA ######################### ZA:Z:CAAC ZB:Z:TCTC RG:Z:HiMom.1 QX:Z:??;=A:B= RX:Z:CAACTCTC -HiMom:1:1101:1338:2175 4 * 0 0 * * 0 0 GCTTGTTGGCTTTAACATCCACAAT CCCFFFFFHHHHHJJJJJJJJJJJJ ZA:Z:GAAG ZB:Z:GAAG RG:Z:HiMom.1 QX:Z:CCCFFFFF RX:Z:GAAGGAAG -HiMom:1:1101:1347:2149 4 * 0 0 * * 0 0 GCTCTTCCGATCTGTGCTCTTCCGA CCCFFFFFDFHHFIJDGIGGHGIGH ZA:Z:GACC ZB:Z:AGGA RG:Z:HiMom.1 QX:Z:CC@DFFFD RX:Z:GACCAGGA -HiMom:1:1101:1353:2226 4 * 0 0 * * 0 0 GTGCTCTTCCGATCTTCAGGTTACC BBBFFFFFHHHHHJJJJJJJIJJJJ ZA:Z:TATC ZB:Z:TGCC RG:Z:HiMom.1 QX:Z:@B@FFEFF RX:Z:TATCTGCC -HiMom:1:1101:1363:2138 4 * 0 0 * * 0 0 GTTCTTAAACCTGTTAGAACTTCTG C@@FFFFFHHHHHJJJJJJJJJJJJ ZA:Z:CTAA ZB:Z:CTCG RG:Z:HiMom.1 QX:Z:CCCFFFFF RX:Z:CTAACTCG -HiMom:1:1101:1399:2128 4 * 0 0 * * 0 0 ACAAACCCTTGTGTCGAGGGCTGAC CCCFFFFFHHHHHIJJJJJJJJJJJ ZA:Z:CAAT ZB:Z:AGTC RG:Z:HiMom.1 QX:Z:CCCFFFFF RX:Z:CAATAGTC -HiMom:1:1101:1403:2194 4 * 0 0 * * 0 0 ACATGGTGAAACCCTGTCTCTACTA CCCFFFDDHHHHHJJJJJJJJJJJJ ZA:Z:CTGT ZB:Z:AATC RG:Z:HiMom.1 QX:Z:CCCFFFFF RX:Z:CTGTAATC -HiMom:1:1101:1406:2222 4 * 0 0 * * 0 0 GGCTGGACTCCCCTGGTTCTGGGCA ;?@DDDBD?FHDFGIIIGIGHHIII ZA:Z:AGCA ZB:Z:TGGA RG:Z:HiMom.1 QX:Z:C@@DBFEF RX:Z:AGCATGGA -HiMom:1:1101:1419:2119 4 * 0 0 * * 0 0 ACTTTCCTTTTTTGTTTTACTTTAA ######################### ZA:Z:TGTA ZB:Z:ATCA RG:Z:HiMom.1 QX:Z:@@@DFDFD RX:Z:TGTAATCA -HiMom:1:1101:1420:2213 4 * 0 0 * * 0 0 TTCACTGTACCGGCCGTGCGTACTT @CCFFFFDHHHFGIJJJJJJGHIGG ZA:Z:CAGC ZB:Z:GGTA RG:Z:HiMom.1 QX:Z:@C@FFFDF RX:Z:CAGCGGTA -HiMom:1:1101:1435:2194 4 * 0 0 * * 0 0 TTTTGTTTTCTTTTACTGAAGTGTA CCCFFDFFHHHHHJJJJIHIJHHHJ ZA:Z:TATC ZB:Z:TGCC RG:Z:HiMom.1 QX:Z:CCCFFFFF RX:Z:TATCTGCC -HiMom:1:1101:1441:2148 4 * 0 0 * * 0 0 TTTTGGCTCTAGAGGGGGTAGAGGG CCCFFFFFHHDFBHIIJJ1?FGHIJ ZA:Z:CGCT ZB:Z:ATGT RG:Z:HiMom.1 QX:Z:@@BFFDDD RX:Z:CGCTATGT -HiMom:1:1101:1452:2132 4 * 0 0 * * 0 0 ACAAACCCTTGTGTCGAGGGCTGAC CCCFFFFFHHHHHJJJJJJJIJJJJ ZA:Z:AACG ZB:Z:CATT RG:Z:HiMom.1 QX:Z:@CCFFFFF RX:Z:AACGCATT -HiMom:1:1101:1460:2176 4 * 0 0 * * 0 0 AGGAAAAAGACACAACAAGTCCAAC ######################### ZA:Z:GATA ZB:Z:TCCA RG:Z:HiMom.1 QX:Z:CCCFFFFF RX:Z:GATATCCA -HiMom:1:1101:1479:2221 4 * 0 0 * * 0 0 GGGGAAATCTATTTTTATGTAAAAA @CCFFFFFHHHHHJIGIJJJJJJJJ ZA:Z:TCGC ZB:Z:TAGA RG:Z:HiMom.1 QX:Z:@BCFFFFF RX:Z:TCGCTAGA -HiMom:1:1101:1491:2120 4 * 0 0 * * 0 0 GGCCAGGCTGAACTTCTGAGCTGCT CCCFFFFFHHHGHJJJJJJJJJJJJ ZA:Z:AGGT ZB:Z:CGCA RG:Z:HiMom.1 QX:Z:BCCDFFFF RX:Z:AGGTCGCA -HiMom:1:1201:1018:2133 4 * 0 0 * * 0 0 ......................... ######################### ZA:Z:ATTC ZB:Z:CTCT RG:Z:HiMom.1 XN:i:1 QX:Z:8??=BBBA RX:Z:ATTCCTCT -HiMom:1:1201:1018:2217 516 * 0 0 * * 0 0 ......................... ######################### ZA:Z:ATTA ZB:Z:TCAA RG:Z:HiMom.1 XN:i:1 QX:Z:;<;:BBDD RX:Z:ATTATCAA -HiMom:1:1201:1028:2202 4 * 0 0 * * 0 0 ..AAAC.C.T.......GG..TG.. ##42@?################### ZA:Z:GAAG ZB:Z:GAAG RG:Z:HiMom.1 QX:Z:CCCFFDFF RX:Z:GAAGGAAG -HiMom:1:1201:1042:2174 4 * 0 0 * * 0 0 .TCAGGAAGGC..CAAAAAAAGAAA #0;@@@?@?<@##3<@@?@@????? ZA:Z:TCTG ZB:Z:CAAG RG:Z:HiMom.1 QX:Z:CCCFFFFF RX:Z:TCTGCAAG -HiMom:1:1201:1043:2246 4 * 0 0 * * 0 0 .GCATCATTTC..GCTTCTCTCTGT #0;@@??@=@>##22=;@??><@?? ZA:Z:CGCT ZB:Z:ATGT RG:Z:HiMom.1 QX:Z:@A# ZA:Z:GACC ZB:Z:AGGA RG:Z:HiMom.1 QX:Z:?;@DFDFF RX:Z:GACCAGGA -HiMom:1:1201:1127:2112 516 * 0 0 * * 0 0 TAATCACCTGAGCAGTGAAGCCAGC @<@?BDDDHD?FDBHI?AHGGGDFH ZA:Z:CAAC ZB:Z:TCTC RG:Z:HiMom.1 QX:Z:=??BA?BD RX:Z:CAACTCTC -HiMom:1:1201:1134:2144 4 * 0 0 * * 0 0 AGTGTGAGTAATGGTTGAGAGGTGG B@?DDDFFFHHGHJHHGFIHHIFGI ZA:Z:CGCT ZB:Z:ATGT RG:Z:HiMom.1 QX:Z:CCCFFFFD RX:Z:CGCTATGT -HiMom:1:1201:1138:2227 516 * 0 0 * * 0 0 GACAAATATAGGAAATAGAAGCTAT =1=A=AAA,2?4>7C<<4B6=BBBB ZA:Z:AGAA ZB:Z:AAGA RG:Z:HiMom.1 QX:Z:######## RX:Z:AGAAAAGA -HiMom:1:1201:1416:2128 4 * 0 0 * * 0 0 TTGGTGTGGAGGCGGTGGCGGGATC @@@DDDDDHHFHHII:?GGHIIB6? ZA:Z:TCGC ZB:Z:TAGA RG:Z:HiMom.1 QX:Z:CCCFFFFF RX:Z:TCGCTAGA -HiMom:1:1201:1421:2154 4 * 0 0 * * 0 0 TGTGCTCTTCCGATCTTGTGCTCTT BC@DFFFFHHHHHJJJJFHIHHIJJ ZA:Z:TGTA ZB:Z:ACTC RG:Z:HiMom.1 QX:Z:@@@FFFFF RX:Z:TGTAACTC -HiMom:1:1201:1439:2156 4 * 0 0 * * 0 0 GGAGATTATTTGCCTTGAAGTAAGC -;(22<>>@>8@>8;@######### ZA:Z:GACC ZB:Z:AGGC RG:Z:HiMom.1 QX:Z:1;;=#### RX:Z:GACCAGGC -HiMom:1:1201:1452:2143 4 * 0 0 * * 0 0 TTTTAGTCTTAGCATTTACTTTCCC CCCFFFFFHHHHHJJJJJJJJJJJJ ZA:Z:CAAC ZB:Z:TCTC RG:Z:HiMom.1 QX:Z:BC@DDFFF RX:Z:CAACTCTC -HiMom:1:1201:1458:2109 4 * 0 0 * * 0 0 GATACGAACACACAAGAACTTTTTT CCCFFFFFHHHHHJJJJJJJJJJJI ZA:Z:ACTG ZB:Z:TATC RG:Z:HiMom.1 QX:Z:CCCFFFFF RX:Z:ACTGTATC -HiMom:1:1201:1472:2121 516 * 0 0 * * 0 0 GTGTGCTCTTCCGATCTGGAGGATG =+=??A4A==A@7A??@@??@?????????>?@ ZA:Z:ACTA ZB:Z:AGAC RG:Z:HiMom.1 QX:Z:@CCDFFFF RX:Z:ACTAAGAC -HiMom:1:2101:1023:2237 516 * 0 0 * * 0 0 ..TTTGTTTGAGTTCCTTGTAGATT ##0:=@?>?@???@:>?@??>?;?< ZA:Z:GCCT ZB:Z:AGCC RG:Z:HiMom.1 QX:Z:=:1<#### RX:Z:GCCTAGCC -HiMom:1:2101:1031:2163 4 * 0 0 * * 0 0 ..ACATTTGTCACCACTAGCCACCA ##0<@?@@@@@@@@@@?@@@@@@@? ZA:Z:GATA ZB:Z:TCCA RG:Z:HiMom.1 QX:Z:B@BFFFFF RX:Z:GATATCCA -HiMom:1:2101:1036:2087 4 * 0 0 * * 0 0 .GTCCACTTACGAAGCAAATACTTT #4=DDFFFHHHHHJJJJJJJJJJJJ ZA:Z:GACC ZB:Z:GTTG RG:Z:HiMom.1 QX:Z:B@CFFDFF RX:Z:GACCGTTG -HiMom:1:2101:1040:2208 516 * 0 0 * * 0 0 .CTGATAGTCACTGAAATGAATTCA #-0=>(2@.22@@############ ZA:Z:ACGA ZB:Z:AATC RG:Z:HiMom.1 QX:Z:######## RX:Z:ACGAAATC -HiMom:1:2101:1048:2238 4 * 0 0 * * 0 0 .GTCACATCGTTGAAGCACTGGATC #11ADDDB?4:>?@###### ZA:Z:ACTA ZB:Z:AGAC RG:Z:HiMom.1 QX:Z:1+8?ADD8 RX:Z:ACTAAGAC -HiMom:1:2101:1273:2119 516 * 0 0 * * 0 0 ATGATGGATCTTCTCTAACTTGTCA >=>=>>?############## ZA:Z:ACTG ZB:Z:TATC RG:Z:HiMom.1 QX:Z:####227+@-A7A7 RX:Z:ACTA-AGAC +HiMom:1:1101:1263:2236 516 * 0 0 * * 0 0 AGTTCTTCAGTAATTTTAGTACTGC ######################### ZA:Z:AGGT ZB:Z:AAGG RG:Z:HiMom.1 QX:Z:####-#### RX:Z:AGGT-AAGG +HiMom:1:1101:1267:2209 4 * 0 0 * * 0 0 GGCAGAGTCTCCAACAGCCCCGTAC =;?DDDD?CCFHAIIIGGIIGE@EG ZA:Z:TATC ZB:Z:AGCC RG:Z:HiMom.1 QX:Z:?@@D-;ADD RX:Z:TATC-AGCC +HiMom:1:1101:1269:2170 4 * 0 0 * * 0 0 TTCCAAGCCTGTGCTTTAAGGAAAA @@>7-A### RX:Z:CAAT-AGAC +HiMom:1:1101:1327:2200 516 * 0 0 * * 0 0 GTCATCTGGGCTGTCGACAGGTGTC @B@FFFFFHHHHGIJJJJJJIFHHI ZA:Z:GCCG ZB:Z:TCGA RG:Z:HiMom.1 QX:Z:BCCF-DFFD RX:Z:GCCG-TCGA +HiMom:1:1101:1328:2225 4 * 0 0 * * 0 0 AGGAAATTAGGACTTACCTGACATA ######################### ZA:Z:CAAC ZB:Z:TCTC RG:Z:HiMom.1 QX:Z:??;=-A:B= RX:Z:CAAC-TCTC +HiMom:1:1101:1338:2175 4 * 0 0 * * 0 0 GCTTGTTGGCTTTAACATCCACAAT CCCFFFFFHHHHHJJJJJJJJJJJJ ZA:Z:GAAG ZB:Z:GAAG RG:Z:HiMom.1 QX:Z:CCCF-FFFF RX:Z:GAAG-GAAG +HiMom:1:1101:1347:2149 4 * 0 0 * * 0 0 GCTCTTCCGATCTGTGCTCTTCCGA CCCFFFFFDFHHFIJDGIGGHGIGH ZA:Z:GACC ZB:Z:AGGA RG:Z:HiMom.1 QX:Z:CC@D-FFFD RX:Z:GACC-AGGA +HiMom:1:1101:1353:2226 4 * 0 0 * * 0 0 GTGCTCTTCCGATCTTCAGGTTACC BBBFFFFFHHHHHJJJJJJJIJJJJ ZA:Z:TATC ZB:Z:TGCC RG:Z:HiMom.1 QX:Z:@B@F-FEFF RX:Z:TATC-TGCC +HiMom:1:1101:1363:2138 4 * 0 0 * * 0 0 GTTCTTAAACCTGTTAGAACTTCTG C@@FFFFFHHHHHJJJJJJJJJJJJ ZA:Z:CTAA ZB:Z:CTCG RG:Z:HiMom.1 QX:Z:CCCF-FFFF RX:Z:CTAA-CTCG +HiMom:1:1101:1399:2128 4 * 0 0 * * 0 0 ACAAACCCTTGTGTCGAGGGCTGAC CCCFFFFFHHHHHIJJJJJJJJJJJ ZA:Z:CAAT ZB:Z:AGTC RG:Z:HiMom.1 QX:Z:CCCF-FFFF RX:Z:CAAT-AGTC +HiMom:1:1101:1403:2194 4 * 0 0 * * 0 0 ACATGGTGAAACCCTGTCTCTACTA CCCFFFDDHHHHHJJJJJJJJJJJJ ZA:Z:CTGT ZB:Z:AATC RG:Z:HiMom.1 QX:Z:CCCF-FFFF RX:Z:CTGT-AATC +HiMom:1:1101:1406:2222 4 * 0 0 * * 0 0 GGCTGGACTCCCCTGGTTCTGGGCA ;?@DDDBD?FHDFGIIIGIGHHIII ZA:Z:AGCA ZB:Z:TGGA RG:Z:HiMom.1 QX:Z:C@@D-BFEF RX:Z:AGCA-TGGA +HiMom:1:1101:1419:2119 4 * 0 0 * * 0 0 ACTTTCCTTTTTTGTTTTACTTTAA ######################### ZA:Z:TGTA ZB:Z:ATCA RG:Z:HiMom.1 QX:Z:@@@D-FDFD RX:Z:TGTA-ATCA +HiMom:1:1101:1420:2213 4 * 0 0 * * 0 0 TTCACTGTACCGGCCGTGCGTACTT @CCFFFFDHHHFGIJJJJJJGHIGG ZA:Z:CAGC ZB:Z:GGTA RG:Z:HiMom.1 QX:Z:@C@F-FFDF RX:Z:CAGC-GGTA +HiMom:1:1101:1435:2194 4 * 0 0 * * 0 0 TTTTGTTTTCTTTTACTGAAGTGTA CCCFFDFFHHHHHJJJJIHIJHHHJ ZA:Z:TATC ZB:Z:TGCC RG:Z:HiMom.1 QX:Z:CCCF-FFFF RX:Z:TATC-TGCC +HiMom:1:1101:1441:2148 4 * 0 0 * * 0 0 TTTTGGCTCTAGAGGGGGTAGAGGG CCCFFFFFHHDFBHIIJJ1?FGHIJ ZA:Z:CGCT ZB:Z:ATGT RG:Z:HiMom.1 QX:Z:@@BF-FDDD RX:Z:CGCT-ATGT +HiMom:1:1101:1452:2132 4 * 0 0 * * 0 0 ACAAACCCTTGTGTCGAGGGCTGAC CCCFFFFFHHHHHJJJJJJJIJJJJ ZA:Z:AACG ZB:Z:CATT RG:Z:HiMom.1 QX:Z:@CCF-FFFF RX:Z:AACG-CATT +HiMom:1:1101:1460:2176 4 * 0 0 * * 0 0 AGGAAAAAGACACAACAAGTCCAAC ######################### ZA:Z:GATA ZB:Z:TCCA RG:Z:HiMom.1 QX:Z:CCCF-FFFF RX:Z:GATA-TCCA +HiMom:1:1101:1479:2221 4 * 0 0 * * 0 0 GGGGAAATCTATTTTTATGTAAAAA @CCFFFFFHHHHHJIGIJJJJJJJJ ZA:Z:TCGC ZB:Z:TAGA RG:Z:HiMom.1 QX:Z:@BCF-FFFF RX:Z:TCGC-TAGA +HiMom:1:1101:1491:2120 4 * 0 0 * * 0 0 GGCCAGGCTGAACTTCTGAGCTGCT CCCFFFFFHHHGHJJJJJJJJJJJJ ZA:Z:AGGT ZB:Z:CGCA RG:Z:HiMom.1 QX:Z:BCCD-FFFF RX:Z:AGGT-CGCA +HiMom:1:1201:1018:2133 4 * 0 0 * * 0 0 ......................... ######################### ZA:Z:ATTC ZB:Z:CTCT RG:Z:HiMom.1 XN:i:1 QX:Z:8??=-BBBA RX:Z:ATTC-CTCT +HiMom:1:1201:1018:2217 516 * 0 0 * * 0 0 ......................... ######################### ZA:Z:ATTA ZB:Z:TCAA RG:Z:HiMom.1 XN:i:1 QX:Z:;<;:-BBDD RX:Z:ATTA-TCAA +HiMom:1:1201:1028:2202 4 * 0 0 * * 0 0 ..AAAC.C.T.......GG..TG.. ##42@?################### ZA:Z:GAAG ZB:Z:GAAG RG:Z:HiMom.1 QX:Z:CCCF-FDFF RX:Z:GAAG-GAAG +HiMom:1:1201:1042:2174 4 * 0 0 * * 0 0 .TCAGGAAGGC..CAAAAAAAGAAA #0;@@@?@?<@##3<@@?@@????? ZA:Z:TCTG ZB:Z:CAAG RG:Z:HiMom.1 QX:Z:CCCF-FFFF RX:Z:TCTG-CAAG +HiMom:1:1201:1043:2246 4 * 0 0 * * 0 0 .GCATCATTTC..GCTTCTCTCTGT #0;@@??@=@>##22=;@??><@?? ZA:Z:CGCT ZB:Z:ATGT RG:Z:HiMom.1 QX:Z:@A# ZA:Z:GACC ZB:Z:AGGA RG:Z:HiMom.1 QX:Z:?;@D-FDFF RX:Z:GACC-AGGA +HiMom:1:1201:1127:2112 516 * 0 0 * * 0 0 TAATCACCTGAGCAGTGAAGCCAGC @<@?BDDDHD?FDBHI?AHGGGDFH ZA:Z:CAAC ZB:Z:TCTC RG:Z:HiMom.1 QX:Z:=??B-A?BD RX:Z:CAAC-TCTC +HiMom:1:1201:1134:2144 4 * 0 0 * * 0 0 AGTGTGAGTAATGGTTGAGAGGTGG B@?DDDFFFHHGHJHHGFIHHIFGI ZA:Z:CGCT ZB:Z:ATGT RG:Z:HiMom.1 QX:Z:CCCF-FFFD RX:Z:CGCT-ATGT +HiMom:1:1201:1138:2227 516 * 0 0 * * 0 0 GACAAATATAGGAAATAGAAGCTAT =1=A=AAA,2?4>7C<<4B6=BBBB ZA:Z:AGAA ZB:Z:AAGA RG:Z:HiMom.1 QX:Z:####-#### RX:Z:AGAA-AAGA +HiMom:1:1201:1416:2128 4 * 0 0 * * 0 0 TTGGTGTGGAGGCGGTGGCGGGATC @@@DDDDDHHFHHII:?GGHIIB6? ZA:Z:TCGC ZB:Z:TAGA RG:Z:HiMom.1 QX:Z:CCCF-FFFF RX:Z:TCGC-TAGA +HiMom:1:1201:1421:2154 4 * 0 0 * * 0 0 TGTGCTCTTCCGATCTTGTGCTCTT BC@DFFFFHHHHHJJJJFHIHHIJJ ZA:Z:TGTA ZB:Z:ACTC RG:Z:HiMom.1 QX:Z:@@@F-FFFF RX:Z:TGTA-ACTC +HiMom:1:1201:1439:2156 4 * 0 0 * * 0 0 GGAGATTATTTGCCTTGAAGTAAGC -;(22<>>@>8@>8;@######### ZA:Z:GACC ZB:Z:AGGC RG:Z:HiMom.1 QX:Z:1;;=-#### RX:Z:GACC-AGGC +HiMom:1:1201:1452:2143 4 * 0 0 * * 0 0 TTTTAGTCTTAGCATTTACTTTCCC CCCFFFFFHHHHHJJJJJJJJJJJJ ZA:Z:CAAC ZB:Z:TCTC RG:Z:HiMom.1 QX:Z:BC@D-DFFF RX:Z:CAAC-TCTC +HiMom:1:1201:1458:2109 4 * 0 0 * * 0 0 GATACGAACACACAAGAACTTTTTT CCCFFFFFHHHHHJJJJJJJJJJJI ZA:Z:ACTG ZB:Z:TATC RG:Z:HiMom.1 QX:Z:CCCF-FFFF RX:Z:ACTG-TATC +HiMom:1:1201:1472:2121 516 * 0 0 * * 0 0 GTGTGCTCTTCCGATCTGGAGGATG =+=??A4A==A@7A??@@??@?????????>?@ ZA:Z:ACTA ZB:Z:AGAC RG:Z:HiMom.1 QX:Z:@CCD-FFFF RX:Z:ACTA-AGAC +HiMom:1:2101:1023:2237 516 * 0 0 * * 0 0 ..TTTGTTTGAGTTCCTTGTAGATT ##0:=@?>?@???@:>?@??>?;?< ZA:Z:GCCT ZB:Z:AGCC RG:Z:HiMom.1 QX:Z:=:1<-#### RX:Z:GCCT-AGCC +HiMom:1:2101:1031:2163 4 * 0 0 * * 0 0 ..ACATTTGTCACCACTAGCCACCA ##0<@?@@@@@@@@@@?@@@@@@@? ZA:Z:GATA ZB:Z:TCCA RG:Z:HiMom.1 QX:Z:B@BF-FFFF RX:Z:GATA-TCCA +HiMom:1:2101:1036:2087 4 * 0 0 * * 0 0 .GTCCACTTACGAAGCAAATACTTT #4=DDFFFHHHHHJJJJJJJJJJJJ ZA:Z:GACC ZB:Z:GTTG RG:Z:HiMom.1 QX:Z:B@CF-FDFF RX:Z:GACC-GTTG +HiMom:1:2101:1040:2208 516 * 0 0 * * 0 0 .CTGATAGTCACTGAAATGAATTCA #-0=>(2@.22@@############ ZA:Z:ACGA ZB:Z:AATC RG:Z:HiMom.1 QX:Z:####-#### RX:Z:ACGA-AATC +HiMom:1:2101:1048:2238 4 * 0 0 * * 0 0 .GTCACATCGTTGAAGCACTGGATC #11ADDDB?4:>?@###### ZA:Z:ACTA ZB:Z:AGAC RG:Z:HiMom.1 QX:Z:1+8?-ADD8 RX:Z:ACTA-AGAC +HiMom:1:2101:1273:2119 516 * 0 0 * * 0 0 ATGATGGATCTTCTCTAACTTGTCA >=>=>>?############## ZA:Z:ACTG ZB:Z:TATC RG:Z:HiMom.1 QX:Z:####-22?? RX:Z:NNGGAAGG -HiMom:1:2101:1021:2209 141 * 0 0 * * 0 0 CTGCTAGCTGGCCAGAG @@??@?????????>?@ RG:Z:HiMom.1 QX:Z:####@>?? RX:Z:NNGGAAGG -HiMom:1:2101:1262:2128 589 * 0 0 * * 0 0 AGCAGAAGGGCAAAAGCTGGCTTGA 9;<@:@################### RG:Z:HiMom.1 QX:Z:####-9@; RX:Z:TCTTGTGG -HiMom:1:2101:1262:2128 653 * 0 0 * * 0 0 TAACTTTTCTGACACCT @?:8>?4:>?@###### RG:Z:HiMom.1 QX:Z:####-9@; RX:Z:TCTTGTGG +HiMom:1:1101:1259:2152 77 * 0 0 * * 0 0 CACCTATAATCCCAGCTACTCCAGA CCCFFFFFHHHHHJJJJJJIJJJIJ RG:Z:HiMom.1 QX:Z:CCCF-FFFF RX:Z:ATTT-TTAT +HiMom:1:1101:1259:2152 141 * 0 0 * * 0 0 ATTTTTTTAGACATAGG GHHHHJJJJIGIIJJJJ RG:Z:HiMom.1 QX:Z:CCCF-FFFF RX:Z:ATTT-TTAT +HiMom:1:1101:1261:2127 589 * 0 0 * * 0 0 .TGAAATCTGGATAGGCTGGAGTTA #0-@@@################### RG:Z:HiMom.1 QX:Z:CCCF-FFFF RX:Z:TTTT-TTTT +HiMom:1:1101:1261:2127 653 * 0 0 * * 0 0 TTTTTTTTTTTTTTTTT HGHHHJJIFDDDDDDDD RG:Z:HiMom.1 QX:Z:CCCF-FFFF RX:Z:TTTT-TTTT +HiMom:1:2101:1021:2209 77 * 0 0 * * 0 0 .GGCCCCACCCTCCTCCAGCACGTC #1=DDFFFHHHHHJJJJJJHIIHFH RG:Z:HiMom.1 QX:Z:####-@>?? RX:Z:NNGG-AAGG +HiMom:1:2101:1021:2209 141 * 0 0 * * 0 0 CTGCTAGCTGGCCAGAG @@??@?????????>?@ RG:Z:HiMom.1 QX:Z:####-@>?? RX:Z:NNGG-AAGG +HiMom:1:2101:1262:2128 589 * 0 0 * * 0 0 AGCAGAAGGGCAAAAGCTGGCTTGA 9;<@:@################### RG:Z:HiMom.1 QX:Z:####--9@; RX:Z:TCTT-GTGG +HiMom:1:2101:1262:2128 653 * 0 0 * * 0 0 TAACTTTTCTGACACCT @?:8>?4:>?@###### RG:Z:HiMom.1 QX:Z:####--9@; RX:Z:TCTT-GTGG diff --git a/testdata/picard/illumina/25T8B25T/sams_with_4M4M/ACTGTATC.sam b/testdata/picard/illumina/25T8B25T/sams_with_4M4M/ACTGTATC.sam index dc583f2fb..139c6fc0b 100644 --- a/testdata/picard/illumina/25T8B25T/sams_with_4M4M/ACTGTATC.sam +++ b/testdata/picard/illumina/25T8B25T/sams_with_4M4M/ACTGTATC.sam @@ -1,10 +1,10 @@ @HD VN:1.5 SO:queryname @RG ID:HiMom.1 SM:SA_ACTGTATC LB:LN_ACTGTATC PL:illumina PU:HiMom.1.ACTGTATC CN:BI -HiMom:1:1201:1458:2109 77 * 0 0 * * 0 0 .GAGACCATAGAGCGGATGCTTTCA #1=DDDFFHHGHGIJJIGIIJJJJJ RG:Z:HiMom.1 QX:Z:CCCFFFFF RX:Z:GATACGAA -HiMom:1:1201:1458:2109 141 * 0 0 * * 0 0 CACACAAGAACTTTTTT HHHHHJJJJJJJJJJJI RG:Z:HiMom.1 QX:Z:CCCFFFFF RX:Z:GATACGAA -HiMom:1:2101:1105:2131 77 * 0 0 * * 0 0 TTGGAACACAGCGGGAATCACAGCA CCCFFFFFHHHHHJIJJJJJJJJJJ RG:Z:HiMom.1 QX:Z:CCCFFFFF RX:Z:CAGCAGCA -HiMom:1:2101:1105:2131 141 * 0 0 * * 0 0 GCAACAGCAGAAACATG HHHHHJJJJJIJJJJJJ RG:Z:HiMom.1 QX:Z:CCCFFFFF RX:Z:CAGCAGCA -HiMom:1:2101:1349:2084 77 * 0 0 * * 0 0 .CAAGTAGCAGTGTCACGCCTTAGC #1=DDBDDADFDDBEH@HC=CEGG@ RG:Z:HiMom.1 QX:Z:<5;??=>= RX:Z:AGTCTGAA -HiMom:1:2101:1349:2084 141 * 0 0 * * 0 0 TCATTGGTGTCTGAAGA >>?############## RG:Z:HiMom.1 QX:Z:<5;??=>= RX:Z:AGTCTGAA -HiMom:1:2101:1365:2094 77 * 0 0 * * 0 0 .AAGGTGAAGGCCGGCGCGCTCGCC #1=BDDDFFHHHHJGGGIGFIHIIJ RG:Z:HiMom.1 QX:Z:CCCFFFFD RX:Z:GCTCTTCC -HiMom:1:2101:1365:2094 141 * 0 0 * * 0 0 GATCTTGTGCTCTTCCG HFHHGJJIIJIJJIHII RG:Z:HiMom.1 QX:Z:CCCFFFFD RX:Z:GCTCTTCC +HiMom:1:1201:1458:2109 77 * 0 0 * * 0 0 .GAGACCATAGAGCGGATGCTTTCA #1=DDDFFHHGHGIJJIGIIJJJJJ RG:Z:HiMom.1 QX:Z:CCCF-FFFF RX:Z:GATA-CGAA +HiMom:1:1201:1458:2109 141 * 0 0 * * 0 0 CACACAAGAACTTTTTT HHHHHJJJJJJJJJJJI RG:Z:HiMom.1 QX:Z:CCCF-FFFF RX:Z:GATA-CGAA +HiMom:1:2101:1105:2131 77 * 0 0 * * 0 0 TTGGAACACAGCGGGAATCACAGCA CCCFFFFFHHHHHJIJJJJJJJJJJ RG:Z:HiMom.1 QX:Z:CCCF-FFFF RX:Z:CAGC-AGCA +HiMom:1:2101:1105:2131 141 * 0 0 * * 0 0 GCAACAGCAGAAACATG HHHHHJJJJJIJJJJJJ RG:Z:HiMom.1 QX:Z:CCCF-FFFF RX:Z:CAGC-AGCA +HiMom:1:2101:1349:2084 77 * 0 0 * * 0 0 .CAAGTAGCAGTGTCACGCCTTAGC #1=DDBDDADFDDBEH@HC=CEGG@ RG:Z:HiMom.1 QX:Z:<5;?-?=>= RX:Z:AGTC-TGAA +HiMom:1:2101:1349:2084 141 * 0 0 * * 0 0 TCATTGGTGTCTGAAGA >>?############## RG:Z:HiMom.1 QX:Z:<5;?-?=>= RX:Z:AGTC-TGAA +HiMom:1:2101:1365:2094 77 * 0 0 * * 0 0 .AAGGTGAAGGCCGGCGCGCTCGCC #1=BDDDFFHHHHJGGGIGFIHIIJ RG:Z:HiMom.1 QX:Z:CCCF-FFFD RX:Z:GCTC-TTCC +HiMom:1:2101:1365:2094 141 * 0 0 * * 0 0 GATCTTGTGCTCTTCCG HFHHGJJIIJIJJIHII RG:Z:HiMom.1 QX:Z:CCCF-FFFD RX:Z:GCTC-TTCC diff --git a/testdata/picard/illumina/25T8B25T/sams_with_4M4M/AGCATGGA.sam b/testdata/picard/illumina/25T8B25T/sams_with_4M4M/AGCATGGA.sam index e77d45d98..b87bc9baf 100644 --- a/testdata/picard/illumina/25T8B25T/sams_with_4M4M/AGCATGGA.sam +++ b/testdata/picard/illumina/25T8B25T/sams_with_4M4M/AGCATGGA.sam @@ -1,8 +1,8 @@ @HD VN:1.5 SO:queryname @RG ID:HiMom.1 SM:SA_AGCATGGA LB:LN_AGCATGGA PL:illumina PU:HiMom.1.AGCATGGA CN:BI -HiMom:1:1101:1406:2222 77 * 0 0 * * 0 0 CTCCCCCCGGGCTGAACCAGGGTAC CCCFFDDDDHDFHIIIIIIIII9DG RG:Z:HiMom.1 QX:Z:;?@DDDBD RX:Z:GGCTGGAC -HiMom:1:1101:1406:2222 141 * 0 0 * * 0 0 TCCCCTGGTTCTGGGCA ?FHDFGIIIGIGHHIII RG:Z:HiMom.1 QX:Z:;?@DDDBD RX:Z:GGCTGGAC -HiMom:1:1201:1291:2158 77 * 0 0 * * 0 0 AGAAGGGGAAAGCCTTCATCTTGGC BCBFFFFFHHHHHJJJJJIIFIJIJ RG:Z:HiMom.1 QX:Z:@CCFFFDD RX:Z:CGTGTGCT -HiMom:1:1201:1291:2158 141 * 0 0 * * 0 0 CTTCCGATCTGATGGGC ?FHHFGEHHIIDHIIII RG:Z:HiMom.1 QX:Z:@CCFFFDD RX:Z:CGTGTGCT -HiMom:1:2101:1370:2116 77 * 0 0 * * 0 0 .TGGTGGTCCATAGAGATTTGAAAC #1:4BD7DACF?FCA:4+>6=?> RG:Z:HiMom.1 QX:Z:######## RX:Z:NNNNNNNN -HiMom:1:1201:1018:2217 653 * 0 0 * * 0 0 ................. ################# RG:Z:HiMom.1 XN:i:1 QX:Z:######## RX:Z:NNNNNNNN -HiMom:1:1201:1118:2198 77 * 0 0 * * 0 0 CAAGTGTACAGGATTAGACTGGGTT BCCFDEBDHHHHHIJJJGIIIJJGH RG:Z:HiMom.1 QX:Z:C@CFFFFF RX:Z:AATAAACT -HiMom:1:1201:1118:2198 141 * 0 0 * * 0 0 TTATTAAAGCAGTTAAA HDHHHGIIIJJJIJJJJ RG:Z:HiMom.1 QX:Z:C@CFFFFF RX:Z:AATAAACT +HiMom:1:1101:1100:2207 77 * 0 0 * * 0 0 ACGACAGACGTTCTTTCTTTGCTGC CCCFFFFFHHFHHJIJJJJJHIJJH RG:Z:HiMom.1 QX:Z:####-#### RX:Z:AGGC-TNNN +HiMom:1:1101:1100:2207 141 * 0 0 * * 0 0 .........G....... ################# RG:Z:HiMom.1 QX:Z:####-#### RX:Z:AGGC-TNNN +HiMom:1:1101:1157:2135 77 * 0 0 * * 0 0 .GGACATTGTAATCATTTCTTACAA #1=DD?DDHHHHHGGHIIIIIIIII RG:Z:HiMom.1 QX:Z:CCCF-FFFF RX:Z:TTTA-AAGT +HiMom:1:1101:1157:2135 141 * 0 0 * * 0 0 CTTAATCAAAGATGATA HHHHHJJJJJJJJJJJJ RG:Z:HiMom.1 QX:Z:CCCF-FFFF RX:Z:TTTA-AAGT +HiMom:1:1101:1269:2170 77 * 0 0 * * 0 0 ACAGTGTGGGAGGCAGACGAAGAGA @@@DDDDDFA:C@EGA?FD>6=?> RG:Z:HiMom.1 QX:Z:####-#### RX:Z:NNNN-NNNN +HiMom:1:1201:1018:2217 653 * 0 0 * * 0 0 ................. ################# RG:Z:HiMom.1 XN:i:1 QX:Z:####-#### RX:Z:NNNN-NNNN +HiMom:1:1201:1118:2198 77 * 0 0 * * 0 0 CAAGTGTACAGGATTAGACTGGGTT BCCFDEBDHHHHHIJJJGIIIJJGH RG:Z:HiMom.1 QX:Z:C@CF-FFFF RX:Z:AATA-AACT +HiMom:1:1201:1118:2198 141 * 0 0 * * 0 0 TTATTAAAGCAGTTAAA HDHHHGIIIJJJIJJJJ RG:Z:HiMom.1 QX:Z:C@CF-FFFF RX:Z:AATA-AACT diff --git a/testdata/picard/illumina/25T8B25T/sams_with_4M4M/ATTCCTCT.sam b/testdata/picard/illumina/25T8B25T/sams_with_4M4M/ATTCCTCT.sam index 56dafa335..367825fe2 100644 --- a/testdata/picard/illumina/25T8B25T/sams_with_4M4M/ATTCCTCT.sam +++ b/testdata/picard/illumina/25T8B25T/sams_with_4M4M/ATTCCTCT.sam @@ -1,10 +1,10 @@ @HD VN:1.5 SO:queryname @RG ID:HiMom.1 SM:SA_ATTCCTCT LB:LN_ATTCCTCT PL:illumina PU:HiMom.1.ATTCCTCT CN:BI -HiMom:1:1101:1309:2210 77 * 0 0 * * 0 0 ACACCAACCACCCAACTATCTATAA CCCFFFFFHHHHHJJJJJJJJJJJJ RG:Z:HiMom.1 QX:Z:@@?DFFDF RX:Z:AGTGGGCT -HiMom:1:1101:1309:2210 141 * 0 0 * * 0 0 AGGGCATTTTTAATCTT HHHDFHJIJJIJGIIIJ RG:Z:HiMom.1 QX:Z:@@?DFFDF RX:Z:AGTGGGCT -HiMom:1:1201:1018:2133 77 * 0 0 * * 0 0 .AAAACTTGAGGATGCTATGCAAGC #1:B:ADDDDDDDEEAEBF9FFEBF RG:Z:HiMom.1 QX:Z:######## RX:Z:NNNNNNNN -HiMom:1:1201:1018:2133 141 * 0 0 * * 0 0 ................. ################# RG:Z:HiMom.1 XN:i:1 QX:Z:######## RX:Z:NNNNNNNN -HiMom:1:1201:1073:2225 77 * 0 0 * * 0 0 GGGGCTGAGACCTTTGCTGATGGTG @@@FFFFFHHHGHJJJJJIIIGICH RG:Z:HiMom.1 QX:Z:@BBDFFFF RX:Z:CGTGTGCT -HiMom:1:1201:1073:2225 141 * 0 0 * * 0 0 CTTCCGATCTGGAGGGT HHHHHJJJJJJJJJJJ: RG:Z:HiMom.1 QX:Z:@BBDFFFF RX:Z:CGTGTGCT -HiMom:1:1201:1242:2207 77 * 0 0 * * 0 0 ATGGCAAAGTGGTGTCTGAGACCAA BCCFFFFFGHHHHHIIIJFHIJJJJ RG:Z:HiMom.1 QX:Z:CCCFFFFF RX:Z:ATCTTTTA -HiMom:1:1201:1242:2207 141 * 0 0 * * 0 0 TTGGCCTCCTGCTCCCC HHHHHJJJJJJJJJJJJ RG:Z:HiMom.1 QX:Z:CCCFFFFF RX:Z:ATCTTTTA +HiMom:1:1101:1309:2210 77 * 0 0 * * 0 0 ACACCAACCACCCAACTATCTATAA CCCFFFFFHHHHHJJJJJJJJJJJJ RG:Z:HiMom.1 QX:Z:@@?D-FFDF RX:Z:AGTG-GGCT +HiMom:1:1101:1309:2210 141 * 0 0 * * 0 0 AGGGCATTTTTAATCTT HHHDFHJIJJIJGIIIJ RG:Z:HiMom.1 QX:Z:@@?D-FFDF RX:Z:AGTG-GGCT +HiMom:1:1201:1018:2133 77 * 0 0 * * 0 0 .AAAACTTGAGGATGCTATGCAAGC #1:B:ADDDDDDDEEAEBF9FFEBF RG:Z:HiMom.1 QX:Z:####-#### RX:Z:NNNN-NNNN +HiMom:1:1201:1018:2133 141 * 0 0 * * 0 0 ................. ################# RG:Z:HiMom.1 XN:i:1 QX:Z:####-#### RX:Z:NNNN-NNNN +HiMom:1:1201:1073:2225 77 * 0 0 * * 0 0 GGGGCTGAGACCTTTGCTGATGGTG @@@FFFFFHHHGHJJJJJIIIGICH RG:Z:HiMom.1 QX:Z:@BBD-FFFF RX:Z:CGTG-TGCT +HiMom:1:1201:1073:2225 141 * 0 0 * * 0 0 CTTCCGATCTGGAGGGT HHHHHJJJJJJJJJJJ: RG:Z:HiMom.1 QX:Z:@BBD-FFFF RX:Z:CGTG-TGCT +HiMom:1:1201:1242:2207 77 * 0 0 * * 0 0 ATGGCAAAGTGGTGTCTGAGACCAA BCCFFFFFGHHHHHIIIJFHIJJJJ RG:Z:HiMom.1 QX:Z:CCCF-FFFF RX:Z:ATCT-TTTA +HiMom:1:1201:1242:2207 141 * 0 0 * * 0 0 TTGGCCTCCTGCTCCCC HHHHHJJJJJJJJJJJJ RG:Z:HiMom.1 QX:Z:CCCF-FFFF RX:Z:ATCT-TTTA diff --git a/testdata/picard/illumina/25T8B25T/sams_with_4M4M/CAACTCTC.sam b/testdata/picard/illumina/25T8B25T/sams_with_4M4M/CAACTCTC.sam index b09417076..f00384359 100644 --- a/testdata/picard/illumina/25T8B25T/sams_with_4M4M/CAACTCTC.sam +++ b/testdata/picard/illumina/25T8B25T/sams_with_4M4M/CAACTCTC.sam @@ -1,12 +1,12 @@ @HD VN:1.5 SO:queryname @RG ID:HiMom.1 SM:SA_CAACTCTC LB:LN_CAACTCTC PL:illumina PU:HiMom.1.CAACTCTC CN:BI -HiMom:1:1101:1140:2120 77 * 0 0 * * 0 0 .CCCCAACATTCTAATTATGCCTCA #1:BDFFDHFFDFIJJJIIJIIIII RG:Z:HiMom.1 QX:Z:@@@DDDDD RX:Z:TTTTTTTT -HiMom:1:1101:1140:2120 141 * 0 0 * * 0 0 TTTTTAACTTTGCAAAT HHHHFB@9FHI@BFH@@ RG:Z:HiMom.1 QX:Z:@@@DDDDD RX:Z:TTTTTTTT -HiMom:1:1101:1328:2225 77 * 0 0 * * 0 0 GAAATGCATCTGTCTTAGAAACTGG ??@=BDDDFDD<<,<2:C@?ACB RG:Z:HiMom.1 QX:Z:<<<@??@? RX:Z:TTTTTTTT -HiMom:1:1201:1486:2146 653 * 0 0 * * 0 0 TTTTTTTTTTTTTGGGC ?@???????######## RG:Z:HiMom.1 QX:Z:<<<@??@? RX:Z:TTTTTTTT +HiMom:1:1101:1140:2120 77 * 0 0 * * 0 0 .CCCCAACATTCTAATTATGCCTCA #1:BDFFDHFFDFIJJJIIJIIIII RG:Z:HiMom.1 QX:Z:@@@D-DDDD RX:Z:TTTT-TTTT +HiMom:1:1101:1140:2120 141 * 0 0 * * 0 0 TTTTTAACTTTGCAAAT HHHHFB@9FHI@BFH@@ RG:Z:HiMom.1 QX:Z:@@@D-DDDD RX:Z:TTTT-TTTT +HiMom:1:1101:1328:2225 77 * 0 0 * * 0 0 GAAATGCATCTGTCTTAGAAACTGG ??@=BDDDFDD<<,<2:C@?ACB RG:Z:HiMom.1 QX:Z:<<<@-??@? RX:Z:TTTT-TTTT +HiMom:1:1201:1486:2146 653 * 0 0 * * 0 0 TTTTTTTTTTTTTGGGC ?@???????######## RG:Z:HiMom.1 QX:Z:<<<@-??@? RX:Z:TTTT-TTTT diff --git a/testdata/picard/illumina/25T8B25T/sams_with_4M4M/CAATAGTC.sam b/testdata/picard/illumina/25T8B25T/sams_with_4M4M/CAATAGTC.sam index 93a3709a8..063d2adbd 100644 --- a/testdata/picard/illumina/25T8B25T/sams_with_4M4M/CAATAGTC.sam +++ b/testdata/picard/illumina/25T8B25T/sams_with_4M4M/CAATAGTC.sam @@ -1,16 +1,16 @@ @HD VN:1.5 SO:queryname @RG ID:HiMom.1 SM:SA_CAATAGTC LB:LN_CAATAGTC PL:illumina PU:HiMom.1.CAATAGTC CN:BI -HiMom:1:1101:1316:2126 77 * 0 0 * * 0 0 .AAAAAAAAAAAAAAAAAAAAAAAA #1BDFFFFHHHHHJJJJFDDDDDDD RG:Z:HiMom.1 XN:i:1 QX:Z:CCCFFFFF RX:Z:TCTTTTTT -HiMom:1:1101:1316:2126 141 * 0 0 * * 0 0 TTTTTTTTTTTTTTTTT HHHHHJJJJHFDDDDDD RG:Z:HiMom.1 QX:Z:CCCFFFFF RX:Z:TCTTTTTT -HiMom:1:1101:1399:2128 77 * 0 0 * * 0 0 .TGCCCTTCGTCCTGGGAAACGGGG #1BDFFFFHHHHHJJJJJJJJJJJJ RG:Z:HiMom.1 QX:Z:CCCFFFFF RX:Z:ACAAACCC -HiMom:1:1101:1399:2128 141 * 0 0 * * 0 0 TTGTGTCGAGGGCTGAC HHHHHIJJJJJJJJJJJ RG:Z:HiMom.1 QX:Z:CCCFFFFF RX:Z:ACAAACCC -HiMom:1:1201:1054:2151 77 * 0 0 * * 0 0 .TAGTGCTGGGCACTAAGTAATACC #4=DDDFFHHHHHJJJJJHIJJJJJ RG:Z:HiMom.1 QX:Z:CBCFFFFF RX:Z:GTCAGGCA -HiMom:1:1201:1054:2151 141 * 0 0 * * 0 0 CTGAGAATATATGGGTG HHHHHJJJJJJJJJJEG RG:Z:HiMom.1 QX:Z:CBCFFFFF RX:Z:GTCAGGCA -HiMom:1:1201:1345:2181 77 * 0 0 * * 0 0 GGATAATCCTATTTATTACCTCAGA BBBDDFFFHHHHHJJJJJJJJJIJJ RG:Z:HiMom.1 QX:Z:CCCFFFFF RX:Z:ATACGGAT -HiMom:1:1201:1345:2181 141 * 0 0 * * 0 0 GTGTTTAGGAGTGGGAC HHHHHIIJJHJFHIJIJ RG:Z:HiMom.1 QX:Z:CCCFFFFF RX:Z:ATACGGAT -HiMom:1:1201:1392:2184 77 * 0 0 * * 0 0 TTTCAGATTGGTCATTGTTAGTGTA ??@BDDDEHBHADHHIIEHDHFHFF RG:Z:HiMom.1 QX:Z:@@BFFFFF RX:Z:ATCTTTAT -HiMom:1:1201:1392:2184 141 * 0 0 * * 0 0 TCATTTGTATGATCTTA HFFHFHIHIIJIJJJJI RG:Z:HiMom.1 QX:Z:@@BFFFFF RX:Z:ATCTTTAT -HiMom:1:2101:1172:2152 589 * 0 0 * * 0 0 AACACGGACAAAGGAGTCTAACACG <<F>7C<<4F>7C<<4FCHGGGBFAAED9 RG:Z:HiMom.1 QX:Z:@@ RG:Z:HiMom.1 QX:Z:CCCFFFFF RX:Z:TTTTGGCT -HiMom:1:1101:1441:2148 141 * 0 0 * * 0 0 CTAGAGGGGGTAGAGGG HHDFBHIIJJ1?FGHIJ RG:Z:HiMom.1 QX:Z:CCCFFFFF RX:Z:TTTTGGCT -HiMom:1:1201:1043:2246 77 * 0 0 * * 0 0 .TTCTCGGCTGTCATGTGCAACATT #1=DDBDFHHHDFFBHGHGHIIJEH RG:Z:HiMom.1 QX:Z:#0;@@??@ RX:Z:NGCATCAT -HiMom:1:1201:1043:2246 141 * 0 0 * * 0 0 TTC..GCTTCTCTCTGT =@>##22=;@??><@?? RG:Z:HiMom.1 QX:Z:#0;@@??@ RX:Z:NGCATCAT -HiMom:1:1201:1134:2144 77 * 0 0 * * 0 0 TGCCAGGAAGTGTTTTTTCTGGGTC @CCFFEFFHHFFFGIJJJJJJJJGH RG:Z:HiMom.1 QX:Z:B@?DDDFF RX:Z:AGTGTGAG -HiMom:1:1201:1134:2144 141 * 0 0 * * 0 0 TAATGGTTGAGAGGTGG FHHGHJHHGFIHHIFGI RG:Z:HiMom.1 QX:Z:B@?DDDFF RX:Z:AGTGTGAG +HiMom:1:1101:1291:2150 77 * 0 0 * * 0 0 CGTGGGGAACCTGGCGCTAAACCAT @BBFFFFFHHHHHJJJJIJJJJJIJ RG:Z:HiMom.1 QX:Z:CCCF-FFFF RX:Z:ACAA-ACCC +HiMom:1:1101:1291:2150 141 * 0 0 * * 0 0 TTGTGTCGAGGGCTGAC HHFHHIJJJIIIGIJIJ RG:Z:HiMom.1 QX:Z:CCCF-FFFF RX:Z:ACAA-ACCC +HiMom:1:1101:1314:2233 77 * 0 0 * * 0 0 GTTTATTGGGGCATTCCTTATCCCA @??DDDDBDHF>FCHGGGBFAAED9 RG:Z:HiMom.1 QX:Z:@@ RG:Z:HiMom.1 QX:Z:CCCF-FFFF RX:Z:TTTT-GGCT +HiMom:1:1101:1441:2148 141 * 0 0 * * 0 0 CTAGAGGGGGTAGAGGG HHDFBHIIJJ1?FGHIJ RG:Z:HiMom.1 QX:Z:CCCF-FFFF RX:Z:TTTT-GGCT +HiMom:1:1201:1043:2246 77 * 0 0 * * 0 0 .TTCTCGGCTGTCATGTGCAACATT #1=DDBDFHHHDFFBHGHGHIIJEH RG:Z:HiMom.1 QX:Z:#0;@-@??@ RX:Z:NGCA-TCAT +HiMom:1:1201:1043:2246 141 * 0 0 * * 0 0 TTC..GCTTCTCTCTGT =@>##22=;@??><@?? RG:Z:HiMom.1 QX:Z:#0;@-@??@ RX:Z:NGCA-TCAT +HiMom:1:1201:1134:2144 77 * 0 0 * * 0 0 TGCCAGGAAGTGTTTTTTCTGGGTC @CCFFEFFHHFFFGIJJJJJJJJGH RG:Z:HiMom.1 QX:Z:B@?D-DDFF RX:Z:AGTG-TGAG +HiMom:1:1201:1134:2144 141 * 0 0 * * 0 0 TAATGGTTGAGAGGTGG FHHGHJHHGFIHHIFGI RG:Z:HiMom.1 QX:Z:B@?D-DDFF RX:Z:AGTG-TGAG diff --git a/testdata/picard/illumina/25T8B25T/sams_with_4M4M/CTAACTCG.sam b/testdata/picard/illumina/25T8B25T/sams_with_4M4M/CTAACTCG.sam index 894ad0d80..4c69ed963 100644 --- a/testdata/picard/illumina/25T8B25T/sams_with_4M4M/CTAACTCG.sam +++ b/testdata/picard/illumina/25T8B25T/sams_with_4M4M/CTAACTCG.sam @@ -1,10 +1,10 @@ @HD VN:1.5 SO:queryname @RG ID:HiMom.1 SM:SA_CTAACTCG LB:LN_CTAACTCG PL:illumina PU:HiMom.1.CTAACTCG CN:BI -HiMom:1:1101:1363:2138 77 * 0 0 * * 0 0 .GTCTGGCCTGCACAGACATCCTAC #1=DDFFFHHHHHJJJIJJIJJJIJ RG:Z:HiMom.1 QX:Z:C@@FFFFF RX:Z:GTTCTTAA -HiMom:1:1101:1363:2138 141 * 0 0 * * 0 0 ACCTGTTAGAACTTCTG HHHHHJJJJJJJJJJJJ RG:Z:HiMom.1 QX:Z:C@@FFFFF RX:Z:GTTCTTAA -HiMom:1:1201:1393:2143 77 * 0 0 * * 0 0 TGGTTGATCCTGCCAGTAGCATATG @@@ADADDFHFFDBHE?G@HIIIEE RG:Z:HiMom.1 QX:Z:C@CFFFFF RX:Z:GATAAATG -HiMom:1:1201:1393:2143 141 * 0 0 * * 0 0 CACGCATCCCCCCCGCG GGHHHHJJJJJJJJJJI RG:Z:HiMom.1 QX:Z:C@CFFFFF RX:Z:GATAAATG -HiMom:1:2101:1273:2119 589 * 0 0 * * 0 0 .AGATAAGAGTCCACACAGTTGAGT #11AAAAA=>=>=><-AAAA RX:Z:ATGA-TGGA +HiMom:1:2101:1273:2119 653 * 0 0 * * 0 0 TCTTCTCTAACTTGTCA A+2AA?CB4@@ABB3?A RG:Z:HiMom.1 QX:Z:>=><-AAAA RX:Z:ATGA-TGGA +HiMom:1:2101:1414:2098 77 * 0 0 * * 0 0 .AGGACATCGATAAAGGCGAGGTGT #1=DDFFFHHHHHJJJJJJJJJHHG RG:Z:HiMom.1 QX:Z:CCCF-FFFF RX:Z:TTGG-GGCC +HiMom:1:2101:1414:2098 141 * 0 0 * * 0 0 GGTGCCGTCGGGCCCAA HHHHGJJIJJJJJJJIJ RG:Z:HiMom.1 QX:Z:CCCF-FFFF RX:Z:TTGG-GGCC diff --git a/testdata/picard/illumina/25T8B25T/sams_with_4M4M/CTATGCGT.sam b/testdata/picard/illumina/25T8B25T/sams_with_4M4M/CTATGCGT.sam index 8cc90ea7a..aa83f6be4 100644 --- a/testdata/picard/illumina/25T8B25T/sams_with_4M4M/CTATGCGT.sam +++ b/testdata/picard/illumina/25T8B25T/sams_with_4M4M/CTATGCGT.sam @@ -1,16 +1,16 @@ @HD VN:1.5 SO:queryname @RG ID:HiMom.1 SM:SA_CTATGCGT LB:LN_CTATGCGT PL:illumina PU:HiMom.1.CTATGCGT CN:BI -HiMom:1:1201:1083:2121 77 * 0 0 * * 0 0 .AGAACTGGCGCTGCGGGATGAACC #1=BDFFFHHHHHJJJJJHIJIJJJ RG:Z:HiMom.1 QX:Z:######## RX:Z:ACACACAA -HiMom:1:1201:1083:2121 141 * 0 0 * * 0 0 CACCACCGCCCTCCCCC ################# RG:Z:HiMom.1 QX:Z:######## RX:Z:ACACACAA -HiMom:1:1201:1185:2143 77 * 0 0 * * 0 0 ATCTGCCTGGTTCGGCCCGCCTGCC CCCFFFFFHHHHHJJJJJJJJJJJJ RG:Z:HiMom.1 QX:Z:@CCFFFFF RX:Z:GCTGAAGG -HiMom:1:1201:1185:2143 141 * 0 0 * * 0 0 CCCGTGGGCCAGAGGTG HHHHHJJJJJJJJJJHI RG:Z:HiMom.1 QX:Z:@CCFFFFF RX:Z:GCTGAAGG -HiMom:1:1201:1219:2115 77 * 0 0 * * 0 0 .TATAGTGGAGGCCGGAGCAGGAAC #1:DABADHHHFHIIIGGHGIIIII RG:Z:HiMom.1 QX:Z:???DBDBD RX:Z:TGGGAGTA -HiMom:1:1201:1219:2115 141 * 0 0 * * 0 0 GTTCCCTGCTAAGGGAG ADDDDIEID:AFFD:?8 RG:Z:HiMom.1 QX:Z:???DBDBD RX:Z:TGGGAGTA -HiMom:1:1201:1472:2121 589 * 0 0 * * 0 0 .TAAAGTGTGAACAAGGAAGGTCAT #07>@<9=@################ RG:Z:HiMom.1 QX:Z:=+=??A4A RX:Z:GTGTGCTC -HiMom:1:1201:1472:2121 653 * 0 0 * * 0 0 TTCCGATCTGGAGGATG ==A@7A@<9=@################ RG:Z:HiMom.1 QX:Z:=+=?-?A4A RX:Z:GTGT-GCTC +HiMom:1:1201:1472:2121 653 * 0 0 * * 0 0 TTCCGATCTGGAGGATG ==A@7A? RG:Z:HiMom.1 QX:Z:@@@DDDBB RX:Z:GCATGCAG -HiMom:1:1201:1483:2126 653 * 0 0 * * 0 0 CTGGGTGCTGTGATGCA ? RG:Z:HiMom.1 QX:Z:@@@D-DDBB RX:Z:GCAT-GCAG +HiMom:1:1201:1483:2126 653 * 0 0 * * 0 0 CTGGGTGCTGTGATGCA E@EEF@+A# RG:Z:HiMom.1 QX:Z:===AAAA8 RX:Z:CGTGTGCT -HiMom:1:1201:1439:2156 77 * 0 0 * * 0 0 AGCCGCGAGGTGCTGGCGGACTTCC :;1BDDDAA88A> RX:Z:GGAGATTA -HiMom:1:1201:1439:2156 141 * 0 0 * * 0 0 TTTGCCTTGAAGTAAGC @>8@>8;@######### RG:Z:HiMom.1 QX:Z:####2<>> RX:Z:GGAGATTA -HiMom:1:2101:1207:2084 589 * 0 0 * * 0 0 .TAGATGACCAAAACTTGCAGGGCA #1:AE@EEF@+A# RG:Z:HiMom.1 QX:Z:===A-AAA8 RX:Z:CGTG-TGCT +HiMom:1:1201:1439:2156 77 * 0 0 * * 0 0 AGCCGCGAGGTGCTGGCGGACTTCC :;1BDDDAA88A> RX:Z:GGAG-ATTA +HiMom:1:1201:1439:2156 141 * 0 0 * * 0 0 TTTGCCTTGAAGTAAGC @>8@>8;@######### RG:Z:HiMom.1 QX:Z:####-2<>> RX:Z:GGAG-ATTA +HiMom:1:2101:1207:2084 589 * 0 0 * * 0 0 .TAGATGACCAAAACTTGCAGGGCA #1:AEG RG:Z:HiMom.1 QX:Z:==?BDFFF RX:Z:GCTCTTCC -HiMom:1:2101:1226:2088 141 * 0 0 * * 0 0 GATCTAGGTAATAGCTA DCDDHFFFAFHDHIJGJ RG:Z:HiMom.1 QX:Z:==?BDFFF RX:Z:GCTCTTCC +HiMom:1:1101:1460:2176 77 * 0 0 * * 0 0 AGTCCAGGCTGAGCCCAGGGAAGAA CCCFFFFFHHHHGJIJJIJJHIJJI RG:Z:HiMom.1 QX:Z:####-#### RX:Z:AGGA-AAAA +HiMom:1:1101:1460:2176 141 * 0 0 * * 0 0 GACACAACAAGTCCAAC ################# RG:Z:HiMom.1 QX:Z:####-#### RX:Z:AGGA-AAAA +HiMom:1:2101:1031:2163 77 * 0 0 * * 0 0 .TTTCCATGGCCGTCACCTTTGGGT #4=DDFFFHHHHHJJJJJJJJJJJI RG:Z:HiMom.1 QX:Z:####-@?@@ RX:Z:NNAC-ATTT +HiMom:1:2101:1031:2163 141 * 0 0 * * 0 0 GTCACCACTAGCCACCA @@@@@@@@?@@@@@@@? RG:Z:HiMom.1 QX:Z:####-@?@@ RX:Z:NNAC-ATTT +HiMom:1:2101:1226:2088 77 * 0 0 * * 0 0 .GATCGGAAGAGCACACGTTTGACT #4=DAA=DDFHFHIIBFGHHIG>EG RG:Z:HiMom.1 QX:Z:==?B-DFFF RX:Z:GCTC-TTCC +HiMom:1:2101:1226:2088 141 * 0 0 * * 0 0 GATCTAGGTAATAGCTA DCDDHFFFAFHDHIJGJ RG:Z:HiMom.1 QX:Z:==?B-DFFF RX:Z:GCTC-TTCC diff --git a/testdata/picard/illumina/25T8B25T/sams_with_4M4M/GCCGTCGA.sam b/testdata/picard/illumina/25T8B25T/sams_with_4M4M/GCCGTCGA.sam index 235189ae2..31e7d99f7 100644 --- a/testdata/picard/illumina/25T8B25T/sams_with_4M4M/GCCGTCGA.sam +++ b/testdata/picard/illumina/25T8B25T/sams_with_4M4M/GCCGTCGA.sam @@ -1,12 +1,12 @@ @HD VN:1.5 SO:queryname @RG ID:HiMom.1 SM:SA_GCCGTCGA LB:LN_GCCGTCGA PL:illumina PU:HiMom.1.GCCGTCGA CN:BI -HiMom:1:1101:1111:2148 77 * 0 0 * * 0 0 GTGGAGACCACCTCCGAGGCCTTGT BBCFFFFFHHHHHJJJIJJJJJJJI RG:Z:HiMom.1 QX:Z:######## RX:Z:GCGAANAN -HiMom:1:1101:1111:2148 141 * 0 0 * * 0 0 .........GGACGAC. ################# RG:Z:HiMom.1 QX:Z:######## RX:Z:GCGAANAN -HiMom:1:1101:1221:2143 77 * 0 0 * * 0 0 TTTGGTGGAAATTTTTTGTTATGAT CCCFFBDBHFD?FBFHIIGGIC@EF RG:Z:HiMom.1 QX:Z:@@@FFFFD RX:Z:CAATTGAA -HiMom:1:1101:1221:2143 141 * 0 0 * * 0 0 TGTCTGCACAGCCGCTT HHHHHJJJIIIJGHIJJ RG:Z:HiMom.1 QX:Z:@@@FFFFD RX:Z:CAATTGAA -HiMom:1:1101:1327:2200 589 * 0 0 * * 0 0 AGGGGGATCCGCCGGGGGACCACAA ######################### RG:Z:HiMom.1 QX:Z:@B@FFFFF RX:Z:GTCATCTG -HiMom:1:1101:1327:2200 653 * 0 0 * * 0 0 GGCTGTCGACAGGTGTC HHHHGIJJJJJJIFHHI RG:Z:HiMom.1 QX:Z:@B@FFFFF RX:Z:GTCATCTG -HiMom:1:2101:1122:2136 77 * 0 0 * * 0 0 GTAGGCGCTCAGCAAATACTTGTCG @@@DDDD8?=39>9;<412@?###### RG:Z:HiMom.1 QX:Z:####=@?> RX:Z:NNTTTGTT -HiMom:1:2101:1023:2237 653 * 0 0 * * 0 0 TGAGTTCCTTGTAGATT ?@???@:>?@??>?;?< RG:Z:HiMom.1 QX:Z:####=@?> RX:Z:NNTTTGTT +HiMom:1:1101:1165:2239 77 * 0 0 * * 0 0 GGCGGAGGCAGCATTTCAGCTGTGA CCCFFDFFHHHHHIJJIGHHHJHHF RG:Z:HiMom.1 QX:Z:####-#### RX:Z:ATGG-AAGT +HiMom:1:1101:1165:2239 141 * 0 0 * * 0 0 CGAGACAGAAGTGAGAA ################# RG:Z:HiMom.1 QX:Z:####-#### RX:Z:ATGG-AAGT +HiMom:1:1101:1290:2225 77 * 0 0 * * 0 0 CTTGGGCGCATGGTGAGGGAGGGAG @@@FFDDFHDFH??CBEBHHIGDCD RG:Z:HiMom.1 QX:Z:C@@F-BEDD RX:Z:TCAG-TTCA +HiMom:1:1101:1290:2225 141 * 0 0 * * 0 0 CTGGCAAAGACAGTCAC FHFHGIIICEHGDHBHE RG:Z:HiMom.1 QX:Z:C@@F-BEDD RX:Z:TCAG-TTCA +HiMom:1:1201:1280:2179 77 * 0 0 * * 0 0 TTCAAGGAATCGTCCTGCCTCAGCC BCCFFFFFHHHHHJJJJJJJJJJJJ RG:Z:HiMom.1 QX:Z:@@BF-FDEF RX:Z:GAGG-ACTG +HiMom:1:1201:1280:2179 141 * 0 0 * * 0 0 CTTGAGTCCAGGAGTTC GHHHHIFGCHIJJJGGI RG:Z:HiMom.1 QX:Z:@@BF-FDEF RX:Z:GAGG-ACTG +HiMom:1:1201:1300:2137 77 * 0 0 * * 0 0 .TGTAATCCCAGCTCTCAGGGAGGC #1=ADDDDDDDBBA?@AE?E@FE8; RG:Z:HiMom.1 QX:Z:@@?D-DDDD RX:Z:GCTC-TTCC +HiMom:1:1201:1300:2137 141 * 0 0 * * 0 0 GATCTTTTTTTTAATTT FDHADEHGIGGED3?FD RG:Z:HiMom.1 QX:Z:@@?D-DDDD RX:Z:GCTC-TTCC +HiMom:1:2101:1023:2237 589 * 0 0 * * 0 0 .TAAACAGCTTCTGCACAGCCAAAG #00@@?>=39>9;<412@?###### RG:Z:HiMom.1 QX:Z:####-=@?> RX:Z:NNTT-TGTT +HiMom:1:2101:1023:2237 653 * 0 0 * * 0 0 TGAGTTCCTTGTAGATT ?@???@:>?@??>?;?< RG:Z:HiMom.1 QX:Z:####-=@?> RX:Z:NNTT-TGTT diff --git a/testdata/picard/illumina/25T8B25T/sams_with_4M4M/GTAACATC.sam b/testdata/picard/illumina/25T8B25T/sams_with_4M4M/GTAACATC.sam index fd117a03f..5c70b5f5e 100644 --- a/testdata/picard/illumina/25T8B25T/sams_with_4M4M/GTAACATC.sam +++ b/testdata/picard/illumina/25T8B25T/sams_with_4M4M/GTAACATC.sam @@ -1,6 +1,6 @@ @HD VN:1.5 SO:queryname @RG ID:HiMom.1 SM:SA_GTAACATC LB:LN_GTAACATC PL:illumina PU:HiMom.1.GTAACATC CN:BI -HiMom:1:1101:1188:2237 77 * 0 0 * * 0 0 TCCCCCTCCCTTTTGCGCACACACC @?@DDADDHDHBDHB6=BBBB BC:Z:AGAAAAGA RG:Z:HiMom.1 QX:Z:@;@1BDAD RX:Z:TTTTTTTT -HiMom:1:2101:1040:2208 589 * 0 0 * * 0 0 .ATGCCCACCTCCCTCCTACGCACC ######################### BC:Z:ACGAAATC RG:Z:HiMom.1 QX:Z:####>(2@ RX:Z:NCTGATAG -HiMom:1:2101:1040:2208 653 * 0 0 * * 0 0 TCACTGAAATGAATTCA .22@@############ BC:Z:ACGAAATC RG:Z:HiMom.1 QX:Z:####>(2@ RX:Z:NCTGATAG -HiMom:1:2101:1059:2083 77 * 0 0 * * 0 0 .AAGAGGGGTCAAGAGTTAAACTTA #1=DDFFFHFHHGIGHGHJJJJJJI BC:Z:TACCGTCT RG:Z:HiMom.1 QX:Z:#1=BDDDE RX:Z:NGAATGTC -HiMom:1:2101:1059:2083 141 * 0 0 * * 0 0 TTAGAAGGATGCTTCTC HHGHHJJJJJIJJIIJJ BC:Z:TACCGTCT RG:Z:HiMom.1 QX:Z:#1=BDDDE RX:Z:NGAATGTC -HiMom:1:2101:1143:2137 77 * 0 0 * * 0 0 ATGCAGCAGCTGCCACGGAGCACCA CC@FFDFDFHFHHGIDHEHIGJJJJ BC:Z:TCCGTCTA RG:Z:HiMom.1 QX:Z:@@@DD?=D RX:Z:GCTCTTCA -HiMom:1:2101:1143:2137 141 * 0 0 * * 0 0 GATCTAGGGGGAACAGC CAFFFHIIDG:EFHIII BC:Z:TCCGTCTA RG:Z:HiMom.1 QX:Z:@@@DD?=D RX:Z:GCTCTTCA -HiMom:1:2101:1151:2182 589 * 0 0 * * 0 0 TTGTTTTGGCTTATAATGACAAGAA ;;8-2).2())(<6=@8;?4??>>? BC:Z:GAAAAAAA RG:Z:HiMom.1 QX:Z:9<B6=BBBB BC:Z:AGAAAAGA RG:Z:HiMom.1 QX:Z:@;@1-BDAD RX:Z:TTTT-TTTT +HiMom:1:2101:1040:2208 589 * 0 0 * * 0 0 .ATGCCCACCTCCCTCCTACGCACC ######################### BC:Z:ACGAAATC RG:Z:HiMom.1 QX:Z:####->(2@ RX:Z:NCTG-ATAG +HiMom:1:2101:1040:2208 653 * 0 0 * * 0 0 TCACTGAAATGAATTCA .22@@############ BC:Z:ACGAAATC RG:Z:HiMom.1 QX:Z:####->(2@ RX:Z:NCTG-ATAG +HiMom:1:2101:1059:2083 77 * 0 0 * * 0 0 .AAGAGGGGTCAAGAGTTAAACTTA #1=DDFFFHFHHGIGHGHJJJJJJI BC:Z:TACCGTCT RG:Z:HiMom.1 QX:Z:#1=B-DDDE RX:Z:NGAA-TGTC +HiMom:1:2101:1059:2083 141 * 0 0 * * 0 0 TTAGAAGGATGCTTCTC HHGHHJJJJJIJJIIJJ BC:Z:TACCGTCT RG:Z:HiMom.1 QX:Z:#1=B-DDDE RX:Z:NGAA-TGTC +HiMom:1:2101:1143:2137 77 * 0 0 * * 0 0 ATGCAGCAGCTGCCACGGAGCACCA CC@FFDFDFHFHHGIDHEHIGJJJJ BC:Z:TCCGTCTA RG:Z:HiMom.1 QX:Z:@@@D-D?=D RX:Z:GCTC-TTCA +HiMom:1:2101:1143:2137 141 * 0 0 * * 0 0 GATCTAGGGGGAACAGC CAFFFHIIDG:EFHIII BC:Z:TCCGTCTA RG:Z:HiMom.1 QX:Z:@@@D-D?=D RX:Z:GCTC-TTCA +HiMom:1:2101:1151:2182 589 * 0 0 * * 0 0 TTGTTTTGGCTTATAATGACAAGAA ;;8-2).2())(<6=@8;?4??>>? BC:Z:GAAAAAAA RG:Z:HiMom.1 QX:Z:9<IHHII RG:Z:HiMom.1 QX:Z:BBBFFFFF RX:Z:GTGCTCTT -HiMom:1:1101:1353:2226 141 * 0 0 * * 0 0 CCGATCTTCAGGTTACC HHHHHJJJJJJJIJJJJ RG:Z:HiMom.1 QX:Z:BBBFFFFF RX:Z:GTGCTCTT -HiMom:1:1101:1435:2194 77 * 0 0 * * 0 0 GAGAAAGAACATGACTACAGAGATG CCCFFFFFHHHHHJJJJJJJJJHJJ RG:Z:HiMom.1 QX:Z:CCCFFDFF RX:Z:TTTTGTTT -HiMom:1:1101:1435:2194 141 * 0 0 * * 0 0 TCTTTTACTGAAGTGTA HHHHHJJJJIHIJHHHJ RG:Z:HiMom.1 QX:Z:CCCFFDFF RX:Z:TTTTGTTT -HiMom:1:1201:1084:2204 77 * 0 0 * * 0 0 GGCCCGTGGACGCCGCCGAAGAAGC CCCFFFFFHHHHHJJJJJIJJJJJJ RG:Z:HiMom.1 QX:Z:CCCFFFFF RX:Z:TGGCTCCT -HiMom:1:1201:1084:2204 141 * 0 0 * * 0 0 CAGGCTCTCATCAGTTG HHHHHJJJJJJJJJJJJ RG:Z:HiMom.1 QX:Z:CCCFFFFF RX:Z:TGGCTCCT -HiMom:1:1201:1142:2242 77 * 0 0 * * 0 0 TGTTGATAGTCCTTCTTATCTTAGT ???DB?==CC2IHHII RG:Z:HiMom.1 QX:Z:BBBF-FFFF RX:Z:GTGC-TCTT +HiMom:1:1101:1353:2226 141 * 0 0 * * 0 0 CCGATCTTCAGGTTACC HHHHHJJJJJJJIJJJJ RG:Z:HiMom.1 QX:Z:BBBF-FFFF RX:Z:GTGC-TCTT +HiMom:1:1101:1435:2194 77 * 0 0 * * 0 0 GAGAAAGAACATGACTACAGAGATG CCCFFFFFHHHHHJJJJJJJJJHJJ RG:Z:HiMom.1 QX:Z:CCCF-FDFF RX:Z:TTTT-GTTT +HiMom:1:1101:1435:2194 141 * 0 0 * * 0 0 TCTTTTACTGAAGTGTA HHHHHJJJJIHIJHHHJ RG:Z:HiMom.1 QX:Z:CCCF-FDFF RX:Z:TTTT-GTTT +HiMom:1:1201:1084:2204 77 * 0 0 * * 0 0 GGCCCGTGGACGCCGCCGAAGAAGC CCCFFFFFHHHHHJJJJJIJJJJJJ RG:Z:HiMom.1 QX:Z:CCCF-FFFF RX:Z:TGGC-TCCT +HiMom:1:1201:1084:2204 141 * 0 0 * * 0 0 CAGGCTCTCATCAGTTG HHHHHJJJJJJJJJJJJ RG:Z:HiMom.1 QX:Z:CCCF-FFFF RX:Z:TGGC-TCCT +HiMom:1:1201:1142:2242 77 * 0 0 * * 0 0 TGTTGATAGTCCTTCTTATCTTAGT ???DB?==CC2EFGDHGFGHD RG:Z:HiMom.1 QX:Z:@EFGDHGFGHD RG:Z:HiMom.1 QX:Z:@ Date: Wed, 7 Dec 2016 22:52:32 -0700 Subject: [PATCH 2/2] Squash me: make it final --- src/main/java/picard/illumina/ClusterDataToSamConverter.java | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/src/main/java/picard/illumina/ClusterDataToSamConverter.java b/src/main/java/picard/illumina/ClusterDataToSamConverter.java index 487cb4d6c..fc3517860 100644 --- a/src/main/java/picard/illumina/ClusterDataToSamConverter.java +++ b/src/main/java/picard/illumina/ClusterDataToSamConverter.java @@ -72,10 +72,10 @@ // TODO: - https://github.com/broadinstitute/picard/issues/287 // TODO: - HTS-spec issue: https://github.com/samtools/hts-specs/issues/109 // TODO: - https://github.com/samtools/hts-specs/pull/119 - private String molecularIndexTag = "RX"; - private String molecularIndexQualityTag = "QX"; - private String molecularIndexDelimiter = "-"; - private List tagPerMolecularIndex = Collections.emptyList(); + private String molecularIndexTag = "RX"; + private String molecularIndexQualityTag = "QX"; + private final String molecularIndexDelimiter = "-"; + private List tagPerMolecularIndex = Collections.emptyList(); /** * Constructor