Mercurial > repos > devteam > picard1106
changeset 49:2bfb9ce28275 draft
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/AsMetrics Mon Feb 17 00:02:22 2014 -0500 @@ -0,0 +1,12 @@ +## net.sf.picard.metrics.StringHeader +# net.sf.picard.analysis.CollectAlignmentSummaryMetrics INPUT=picard_input_tiny.sam OUTPUT=AsMetrics REFERENCE_SEQUENCE=picard_input_hg18.trimmed.fasta MAX_INSERT_SIZE=100000 ADAPTER_SEQUENCE=[AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG] METRIC_ACCUMULATION_LEVEL=[ALL_READS] IS_BISULFITE_SEQUENCED=false ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false +## net.sf.picard.metrics.StringHeader +# Started on: Tue Feb 11 21:51:51 EST 2014 + +## METRICS CLASS net.sf.picard.analysis.AlignmentSummaryMetrics +CATEGORY TOTAL_READS PF_READS PCT_PF_READS PF_NOISE_READS PF_READS_ALIGNED PCT_PF_READS_ALIGNED PF_ALIGNED_BASES PF_HQ_ALIGNED_READS PF_HQ_ALIGNED_BASES PF_HQ_ALIGNED_Q20_BASES PF_HQ_MEDIAN_MISMATCHES PF_MISMATCH_RATE PF_HQ_ERROR_RATE PF_INDEL_RATE MEAN_READ_LENGTH READS_ALIGNED_IN_PAIRS PCT_READS_ALIGNED_IN_PAIRS BAD_CYCLES STRAND_BALANCE PCT_CHIMERAS PCT_ADAPTER SAMPLE LIBRARY READ_GROUP +FIRST_OF_PAIR 4 4 1 0 4 1 404 4 404 28 78 0,777228 0,777228 0 101 3 0,75 63 0,25 0 0 +SECOND_OF_PAIR 4 4 1 0 3 0,75 298 3 298 45 75 0,758389 0,758389 0,006711 101 3 1 7 0,666667 0 0 +PAIR 8 8 1 0 7 0,875 702 7 702 73 78 0,769231 0,769231 0,002849 101 6 0,857143 70 0,428571 0 0 + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bfast_out1.sam Mon Feb 17 00:02:22 2014 -0500 @@ -0,0 +1,23 @@ +@HD VN:0.1.2 SO:unsorted GO:none +@SQ SN:phiX174 LN:5386 +@PG ID:bfast VN:0.6.4d +random_phiX_region_0 0 phiX174 553 255 50M * 0 0 TTGAGGCTTGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTT ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0 +random_phiX_region_1 0 phiX174 3693 255 50M * 0 0 GTTAGTGCTGAGGTTGACTTAGTTCATCAGCAAACGCAGAATCAGCGGTA ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0 +random_phiX_region_2 0 phiX174 375 255 50M * 0 0 AATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTTTCCA ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0 +random_phiX_region_3 0 phiX174 3168 255 50M * 0 0 GGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTC ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0 +random_phiX_region_4 0 phiX174 5254 255 50M * 0 0 ACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTAGCCGAC ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0 +random_phiX_region_5 0 phiX174 5066 255 50M * 0 0 AGCTAAAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACTTCCCA ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0 +random_phiX_region_6 0 phiX174 1226 255 50M * 0 0 CACGTTTATGGTGAACAGTGGATTAAGTTCATGAAGGATGGTGTTAATGC ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0 +random_phiX_region_7 0 phiX174 1096 255 50M * 0 0 AACTACTCCGGTTATCGCTGGCGACTCCTTCGAGATGGACGCCGTTGGCG ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0 +random_phiX_region_8 0 phiX174 535 255 50M * 0 0 CTCGTGCTCGTCGCTGCGTTGAGGCTTGCGTTTATGGTACGCTGGACTTT ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0 +random_phiX_region_9 0 phiX174 3669 255 50M * 0 0 CAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGACTTAGTTCA ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0 +random_phiX_region_10 0 phiX174 4887 255 50M * 0 0 TACAGTATGCCCATCGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTC ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0 +random_phiX_region_11 0 phiX174 1849 255 50M * 0 0 TATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGACTAAAGAGA ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0 +random_phiX_region_12 0 phiX174 4145 255 50M * 0 0 AGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATA ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0 +random_phiX_region_13 0 phiX174 1853 255 50M * 0 0 TTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGACTAAAGAGATTCA ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0 +random_phiX_region_14 0 phiX174 2800 255 50M * 0 0 CCGGGCAATAACGTTTATGTTGGTTTCATGGTTTGGTCTAACTTTACCGC ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2300 NM:i:1 NH:i:1 IH:i:1 HI:i:1 MD:Z:11T38 XA:i:0 +random_phiX_region_15 0 phiX174 1910 255 50M * 0 0 AACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTT ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0 +random_phiX_region_16 0 phiX174 3366 255 50M * 0 0 GCCGGATTTGAGAATCAAAAAGAGCTTACTAAAATGCAACTGGACAATCA ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0 +random_phiX_region_17 0 phiX174 2165 255 50M * 0 0 CATGATTATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAG ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0 +random_phiX_region_18 0 phiX174 2051 255 50M * 0 0 TGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGA ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0 +random_phiX_region_19 0 phiX174 5099 255 50M * 0 0 GCTGTCGCTACTTCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACT ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bwa_wrapper_in2.fastqsanger Mon Feb 17 00:02:22 2014 -0500 @@ -0,0 +1,120 @@ +@seq1/1 +GGACTCAGATAGTAATCC ++ +II#IIIIIII$5+.(9II +@seq2/1 +ATTCGACCTATCCTTGCG ++ +IIIIIIIIIIIIIIIIII +@seq3/1 +GTAACAAAGTTTGGATTG ++ +IIIIIIIIIIIIIIIIII +@seq4/1 +AGCCGCTCGTCTTTTATG ++ +IIIIIIIIIIIIIIIIII +@seq5/1 +CAGTTATATGGCTTTTGG ++ +IIIIIIIIIIIIIIIIII +@seq6/1 +AGGCGCTCGTCTTGGTAT ++ +IIIIIIIIIIIIIIIIII +@seq7/1 +TGTAGGTGGTCAACCAAT ++ +IIIIIIIIIIIIIIIIII +@seq8/1 +ACACCCGTCCTTTACGTC ++ +IIIIIIIIIIIIIIIIII +@seq9/1 +GCCGCTATTCAGGTTGTT ++ +IIIIIIIIIIIIIIIIII +@seq10/1 +ATTCTTTCTTTTCGTATC ++ +IIIIIIIIIIIIIIIIII +@seq11/1 +GCATTTCTACTCCTTCTC ++ +II#IIIIIII$5+.(9II +@seq12/1 +CGCGCTTCGATAAAAATG ++ +IIIIIIIIIIIIIIIIII +@seq13/1 +ATTTCTACTCTTTCTCAT ++ +IIIIIIIIIIIIIIIIII +@seq14/1 +CCCTTTTGAATGTCACGC ++ +IIIIIIIIIIIIIIIIII +@seq15/1 +CCAACTTACCAAGGTGGG ++ +IIIIIIIIIIIIIIIIII +@seq16/1 +TCAGGGTATTAAAAGAGA ++ +IIIIIIIIIIIIIIIIII +@seq17/1 +GTGATGTGCTTGCTACCG ++ +IIIIIIIIIIIIIIIIII +@seq18/1 +TCAATCCCCCATGCTTGG ++ +IIIIIIIIIIIIIIIIII +@seq19/1 +TTCCTGCGCTTAATGCTT ++ +IIIIIIIIIIIIIIIIII +@seq20/1 +CTTATTACCATTTCAACT ++ +IIIIIIIIIIIIIIIIII +@seq21/1 +CTGATACCAATAAAACCC ++ +II#IIIIIII$5+.(9II +@seq22/1 +AATCAAACTTACCAAGGG ++ +IIIIIIIIIIIIIIIIII +@seq23/1 +TGTGCTTCCCCAACTTGA ++ +IIIIIIIIIIIIIIIIII +@seq24/1 +TTTCTCAATCCCCAATGC ++ +IIIIIIIIIIIIIIIIII +@seq25/1 +TTGCTACTGACCGCTCTT ++ +IIIIIIIIIIIIIIIIII +@seq26/1 +CCGCGTGAAATTTCTATG ++ +IIIIIIIIIIIIIIIIII +@seq27/1 +CGCTAATCAAGTTGTTTC ++ +IIIIIIIIIIIIIIIIII +@seq28/1 +AAAGAGATTATTTGTCGG ++ +IIIIIIIIIIIIIIIIII +@seq29/1 +CAAATTAATGCGCGCTTC ++ +IIIIIIIIIIIIIIIIII +@seq30/1 +ATCCCCTATGCTTGGCTT ++ +IIIIIIIIIIIIIIIIII
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bwa_wrapper_in3.fastqsanger Mon Feb 17 00:02:22 2014 -0500 @@ -0,0 +1,120 @@ +@seq1/2 +ACGCTCCTTTAAAATATC ++ +IIIII$%*$G$A31I&&B +@seq2/2 +CAGCTCGAGAAGCTCTTA ++ +IIIIIIIIIIIIIIIIII +@seq3/2 +CTACTGACCGCTCTCGTG ++ +IIIIIIIIIIIIIIIIII +@seq4/2 +TAGGTGGTCAACCATTTT ++ +IIIIIIIIIIIIIIIIII +@seq5/2 +TTTCTATGTGGCTTAATA ++ +IIIIIIIIIIIIIIIIII +@seq6/2 +GTAGGTGGTCAACAATTT ++ +IIIIIIIIIIIIIIIIII +@seq7/2 +TTTAATTGCAGGGGCTTC ++ +IIIIIIIIIIIIIIIIII +@seq8/2 +ATGCGCTCTATTCTCTGG ++ +IIIIIIIIIIIIIIIIII +@seq9/2 +TTCTGTTGGTGCTGATAT ++ +IIIIIIIIIIIIIIIIII +@seq10/2 +AGGGCGTTGAGTTCGATA ++ +IIIIIIIIIIIIIIIIII +@seq11/2 +ATCCCCAATGCTTGGCTT ++ +IIIII$%*$G$A31I&&B +@seq12/2 +GGATTGGCGTTTCCAACC ++ +IIIIIIIIIIIIIIIIII +@seq13/2 +CCCCAATCCTTGCCTTCC ++ +IIIAAIIIIIIIIIIIII +@seq14/2 +TGATATTTTGACTTTGAG ++ +IIIIIIIIIIIIIIIIII +@seq15/2 +TTACGAAACGCGACGCCG ++ +IIIIIIIIIIIIIIIIII +@seq16/2 +TTATTTTTCTCCAGCCAC ++ +IIIIIIIIIIIIIIIIII +@seq17/2 +AAACAATACTTTAGGCAT ++ +IIIIIIIIIIIIIIIIII +@seq18/2 +CCGTTCCATAAGCAGATG ++ +IIIIIIIIIIIIIIIIII +@seq19/2 +GAGCGTCCTGGTGCTGAT ++ +IIIIIIIIIIIIIIIIII +@seq20/2 +ACTCCGGTTATCGCTGGC ++ +IIIIIIIIIIIIIIIIII +@seq21/2 +TAAGCATTTGGTTCAGGG ++ +IIIII$%*$G$A31I&&B +@seq22/2 +GTTACGACGCGACGCCGT ++ +IIIIIIIIIIIIIIIIII +@seq23/2 +TTTAATAACCCTATAGAC ++ +IIIIIIIIIIIIIIIIII +@seq24/2 +CTTGGCTTCCCTAAGCAG ++ +IIIIIIIIIIIIIIIIII +@seq25/2 +CGTGCTCGTTGCTGCGTT ++ +IIIIIIIIIIIIIIIIII +@seq26/2 +AAGGATGTTTTCCGTTCT ++ +IIIIIIIIIIIIIIIIII +@seq27/2 +TGTTTGGTGCTGATATTG ++ +IIIIIIIIIIIIIIIIII +@seq28/2 +TCCAGCCACTAAAGTGAG ++ +IIIIIIIIIIIIIIIIII +@seq29/2 +GATAATGATTGGGGTATC ++ +IIIIIIIIIIIIIIIIII +@seq30/2 +ACCATAAGCAGATGGATA ++ +IIIIIIIIIIIIIIIIII
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bwa_wrapper_out3.sam Mon Feb 17 00:02:22 2014 -0500 @@ -0,0 +1,63 @@ +@SQ SN:phiX174 LN:5386 +@RG ID:abcdefg LB:lib-mom-A PL:ILLUMINA SM:mom DS:descrip DT:2010-11-01 PI:400 +@PG ID:bwa PN:bwa VN:0.5.9-r16 +seq1 113 phiX174 340 37 18M = 322 -18 GGATTACTATCTGAGTCC II9(.+5$IIIIIII#II RG:Z:abcdefg XT:A:U NM:i:0 SM:i:37 AM:i:25 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 +seq1 177 phiX174 322 25 18M = 340 18 GATATTTTAAAGGAGCGT B&&I13A$G$*%$IIIII RG:Z:abcdefg XT:A:U NM:i:2 SM:i:25 AM:i:25 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:2C8A6 +seq2 65 phiX174 141 37 18M = 159 18 ATTCGACCTATCCTTGCG IIIIIIIIIIIIIIIIII RG:Z:abcdefg XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 +seq2 129 phiX174 159 37 18M = 141 -18 CAGCTCGAGAAGCTCTTA IIIIIIIIIIIIIIIIII RG:Z:abcdefg XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 +seq3 65 phiX174 505 37 18M = 523 18 GTAACAAAGTTTGGATTG IIIIIIIIIIIIIIIIII RG:Z:abcdefg XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 +seq3 129 phiX174 523 37 18M = 505 -18 CTACTGACCGCTCTCGTG IIIIIIIIIIIIIIIIII RG:Z:abcdefg XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 +seq4 69 phiX174 945 0 * = 945 0 AGCCGCTCGTCTTTTATG IIIIIIIIIIIIIIIIII RG:Z:abcdefg +seq4 137 phiX174 945 23 18M = 945 0 TAGGTGGTCAACCATTTT IIIIIIIIIIIIIIIIII RG:Z:abcdefg XT:A:U NM:i:1 SM:i:23 AM:i:0 X0:i:1 X1:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:12A5 XA:Z:phiX174,+945,17M1S,2; +seq5 65 phiX174 4985 37 18M = 5003 18 CAGTTATATGGCTTTTGG IIIIIIIIIIIIIIIIII RG:Z:abcdefg XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:13G4 +seq5 129 phiX174 5003 37 18M = 4985 -18 TTTCTATGTGGCTTAATA IIIIIIIIIIIIIIIIII RG:Z:abcdefg XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:13A4 +seq6 65 phiX174 925 37 11M1D7M = 944 19 AGGCGCTCGTCTTGGTAT IIIIIIIIIIIIIIIIII RG:Z:abcdefg XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:0 XO:i:1 XG:i:1 MD:Z:11^T7 +seq6 129 phiX174 944 37 18M = 925 -19 GTAGGTGGTCAACAATTT IIIIIIIIIIIIIIIIII RG:Z:abcdefg XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 +seq7 65 phiX174 943 25 18M = 960 17 TGTAGGTGGTCAACCAAT IIIIIIIIIIIIIIIIII RG:Z:abcdefg XT:A:U NM:i:2 SM:i:25 AM:i:25 X0:i:1 X1:i:1 XM:i:2 XO:i:0 XG:i:0 MD:Z:14A1T1 XA:Z:phiX174,+943,13M1I4M,2; +seq7 129 phiX174 960 37 18M = 943 -17 TTTAATTGCAGGGGCTTC IIIIIIIIIIIIIIIIII RG:Z:abcdefg XT:A:U NM:i:0 SM:i:37 AM:i:25 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 +seq8 69 phiX174 1715 0 * = 1715 0 ACACCCGTCCTTTACGTC IIIIIIIIIIIIIIIIII RG:Z:abcdefg +seq8 137 phiX174 1715 37 18M = 1715 0 ATGCGCTCTATTCTCTGG IIIIIIIIIIIIIIIIII RG:Z:abcdefg XT:A:U NM:i:1 SM:i:37 AM:i:0 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:10A7 +seq9 65 phiX174 2596 37 18M = 2613 17 GCCGCTATTCAGGTTGTT IIIIIIIIIIIIIIIIII RG:Z:abcdefg XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:7A10 +seq9 129 phiX174 2613 37 18M = 2596 -17 TTCTGTTGGTGCTGATAT IIIIIIIIIIIIIIIIII RG:Z:abcdefg XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 +seq10 65 phiX174 4149 25 18M = 4168 19 ATTCTTTCTTTTCGTATC IIIIIIIIIIIIIIIIII RG:Z:abcdefg XT:A:U NM:i:2 SM:i:25 AM:i:25 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:5G11G0 +seq10 129 phiX174 4168 37 18M = 4149 -19 AGGGCGTTGAGTTCGATA IIIIIIIIIIIIIIIIII RG:Z:abcdefg XT:A:U NM:i:0 SM:i:37 AM:i:25 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 +seq11 65 phiX174 4072 37 18M = 4091 19 GCATTTCTACTCCTTCTC II#IIIIIII$5+.(9II RG:Z:abcdefg XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:12T5 +seq11 129 phiX174 4091 37 18M = 4072 -19 ATCCCCAATGCTTGGCTT IIIII$%*$G$A31I&&B RG:Z:abcdefg XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 +seq12 65 phiX174 5349 37 18M = 5365 16 CGCGCTTCGATAAAAATG IIIIIIIIIIIIIIIIII RG:Z:abcdefg XT:A:U NM:i:0 SM:i:37 AM:i:25 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 +seq12 129 phiX174 5365 25 18M = 5349 -16 GGATTGGCGTTTCCAACC IIIIIIIIIIIIIIIIII RG:Z:abcdefg XT:A:U NM:i:2 SM:i:25 AM:i:25 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:0T9A7 +seq13 65 phiX174 4074 37 18M = 4093 19 ATTTCTACTCTTTCTCAT IIIIIIIIIIIIIIIIII RG:Z:abcdefg XT:A:U NM:i:1 SM:i:37 AM:i:25 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:17A0 +seq13 129 phiX174 4093 25 18M = 4074 -19 CCCCAATCCTTGCCTTCC IIIAAIIIIIIIIIIIII RG:Z:abcdefg XT:A:U NM:i:2 SM:i:25 AM:i:25 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:7G4G5 +seq14 65 phiX174 3998 37 18M = 4016 18 CCCTTTTGAATGTCACGC IIIIIIIIIIIIIIIIII RG:Z:abcdefg XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:5C12 +seq14 129 phiX174 4016 37 3M1D15M = 3998 -18 TGATATTTTGACTTTGAG IIIIIIIIIIIIIIIIII RG:Z:abcdefg XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:0 XO:i:1 XG:i:1 MD:Z:3^T15 +seq15 65 phiX174 5198 37 18M = 5216 18 CCAACTTACCAAGGTGGG IIIIIIIIIIIIIIIIII RG:Z:abcdefg XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:13C4 +seq15 129 phiX174 5216 37 5M2I11M = 5198 -18 TTACGAAACGCGACGCCG IIIIIIIIIIIIIIIIII RG:Z:abcdefg XT:A:U NM:i:2 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:0 XO:i:1 XG:i:2 MD:Z:16 +seq16 65 phiX174 2880 37 10M1I7M = 2897 17 TCAGGGTATTAAAAGAGA IIIIIIIIIIIIIIIIII RG:Z:abcdefg XT:A:U NM:i:2 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:1 XO:i:1 XG:i:1 MD:Z:5T11 +seq16 129 phiX174 2897 37 18M = 2880 -17 TTATTTTTCTCCAGCCAC IIIIIIIIIIIIIIIIII RG:Z:abcdefg XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:6G11 +seq17 65 phiX174 3034 37 18M = 3053 19 GTGATGTGCTTGCTACCG IIIIIIIIIIIIIIIIII RG:Z:abcdefg XT:A:U NM:i:0 SM:i:37 AM:i:25 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 +seq17 129 phiX174 3053 25 18M = 3034 -19 AAACAATACTTTAGGCAT IIIIIIIIIIIIIIIIII RG:Z:abcdefg XT:A:U NM:i:2 SM:i:25 AM:i:25 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:0T9G7 +seq18 73 phiX174 4088 37 18M = 4088 0 TCAATCCCCCATGCTTGG IIIIIIIIIIIIIIIIII RG:Z:abcdefg XT:A:U NM:i:1 SM:i:37 AM:i:0 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:9A8 +seq18 133 phiX174 4088 0 * = 4088 0 CCGTTCCATAAGCAGATG IIIIIIIIIIIIIIIIII RG:Z:abcdefg +seq19 65 phiX174 3304 37 18M = 3324 20 TTCCTGCGCTTAATGCTT IIIIIIIIIIIIIIIIII RG:Z:abcdefg XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:6A11 +seq19 129 phiX174 3324 37 18M = 3304 -20 GAGCGTCCTGGTGCTGAT IIIIIIIIIIIIIIIIII RG:Z:abcdefg XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:6G11 +seq20 65 phiX174 1082 37 18M = 1100 18 CTTATTACCATTTCAACT IIIIIIIIIIIIIIIIII RG:Z:abcdefg XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 +seq20 129 phiX174 1100 37 18M = 1082 -18 ACTCCGGTTATCGCTGGC IIIIIIIIIIIIIIIIII RG:Z:abcdefg XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 +seq21 65 phiX174 1344 23 18M = 1363 19 CTGATACCAATAAAACCC II#IIIIIII$5+.(9II RG:Z:abcdefg XT:A:U NM:i:1 SM:i:23 AM:i:23 X0:i:1 X1:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:15T2 XA:Z:phiX174,+1344,15M1D3M,2; +seq21 129 phiX174 1363 37 18M = 1344 -19 TAAGCATTTGGTTCAGGG IIIII$%*$G$A31I&&B RG:Z:abcdefg XT:A:U NM:i:1 SM:i:37 AM:i:23 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:10T7 +seq22 69 phiX174 5215 0 * = 5215 0 AATCAAACTTACCAAGGG IIIIIIIIIIIIIIIIII RG:Z:abcdefg +seq22 137 phiX174 5215 37 18M = 5215 0 GTTACGACGCGACGCCGT IIIIIIIIIIIIIIIIII RG:Z:abcdefg XT:A:U NM:i:0 SM:i:37 AM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 +seq23 65 phiX174 4289 37 18M = 4308 19 TGTGCTTCCCCAACTTGA IIIIIIIIIIIIIIIIII RG:Z:abcdefg XT:A:U NM:i:1 SM:i:37 AM:i:25 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:6C11 +seq23 129 phiX174 4308 25 18M = 4289 -19 TTTAATAACCCTATAGAC IIIIIIIIIIIIIIIIII RG:Z:abcdefg XT:A:U NM:i:2 SM:i:25 AM:i:25 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:0A8A8 +seq24 65 phiX174 4084 37 18M = 4101 17 TTTCTCAATCCCCAATGC IIIIIIIIIIIIIIIIII RG:Z:abcdefg XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 +seq24 129 phiX174 4101 37 18M = 4084 -17 CTTGGCTTCCCTAAGCAG IIIIIIIIIIIIIIIIII RG:Z:abcdefg XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:10A7 +seq25 65 phiX174 520 37 18M = 537 17 TTGCTACTGACCGCTCTT IIIIIIIIIIIIIIIIII RG:Z:abcdefg XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:17C0 +seq25 129 phiX174 537 37 18M = 520 -17 CGTGCTCGTTGCTGCGTT IIIIIIIIIIIIIIIIII RG:Z:abcdefg XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:9C8 +seq26 65 phiX174 1976 37 18M = 1994 18 CCGCGTGAAATTTCTATG IIIIIIIIIIIIIIIIII RG:Z:abcdefg XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 +seq26 129 phiX174 1994 37 18M = 1976 -18 AAGGATGTTTTCCGTTCT IIIIIIIIIIIIIIIIII RG:Z:abcdefg XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 +seq27 65 phiX174 2598 37 18M = 2614 16 CGCTAATCAAGTTGTTTC IIIIIIIIIIIIIIIIII RG:Z:abcdefg XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:9G8 +seq27 129 phiX174 2614 37 3M1D15M = 2598 -16 TGTTTGGTGCTGATATTG IIIIIIIIIIIIIIIIII RG:Z:abcdefg XT:A:U NM:i:2 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:0 XO:i:1 XG:i:1 MD:Z:1C1^G15 +seq28 65 phiX174 2890 25 18M = 2906 16 AAAGAGATTATTTGTCGG IIIIIIIIIIIIIIIIII RG:Z:abcdefg XT:A:U NM:i:2 SM:i:25 AM:i:25 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:16T0C0 +seq28 129 phiX174 2906 37 18M = 2890 -16 TCCAGCCACTAAAGTGAG IIIIIIIIIIIIIIIIII RG:Z:abcdefg XT:A:U NM:i:1 SM:i:37 AM:i:25 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:10T7 +seq29 73 phiX174 5339 37 18M = 5339 0 CAAATTAATGCGCGCTTC IIIIIIIIIIIIIIIIII RG:Z:abcdefg XT:A:U NM:i:1 SM:i:37 AM:i:0 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:6T11 +seq29 133 phiX174 5339 0 * = 5339 0 GATAATGATTGGGGTATC IIIIIIIIIIIIIIIIII RG:Z:abcdefg +seq30 65 phiX174 4091 37 18M = 4108 17 ATCCCCTATGCTTGGCTT IIIIIIIIIIIIIIIIII RG:Z:abcdefg XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:6A11 +seq30 129 phiX174 4108 37 18M = 4091 -17 ACCATAAGCAGATGGATA IIIIIIIIIIIIIIIIII RG:Z:abcdefg XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:0T17
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/phiX.fasta Mon Feb 17 00:02:22 2014 -0500 @@ -0,0 +1,79 @@ +>phiX174 +GAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAAAAATTATCTT +GATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGGAAAATGAGAAA +ATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATCAACTAACGATTCTG +TCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTA +GATATGAGTCACATTTTGTTCATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATC +TGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTT +TCCAGACCGCTTTGGCCTCTATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTT +CGATTTTCTGACGAGTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCT +TGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCCG +TCATTGCTTATTATGTTCATCCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAATTTAC +GGAAAACATTATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCTTGCGTGTA +CGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAAATTACGTGCAGAAGGAG +TGATGTAATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACT +AAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAATTGCAGGGGCTTCGGC +CCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCCA +TCTTGGCTTCCTTGCTGGTCAGATTGGTCGTCTTATTACCATTTCAACTACTCCGGTTATCGCTGGCGAC +TCCTTCGAGATGGACGCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTA +CTGTAGACATTTTTACTTTTTATGTCCCTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAA +GGATGGTGTTAATGCCACTCCTCTCCCGACTGTTAACACTACTGGTTATATTGACCATGCCGCTTTTCTT +GGCACGATTAACCCTGATACCAATAAAATCCCTAAGCATTTGTTTCAGGGTTATTTGAATATCTATAACA +ACTATTTTAAAGCGCCGTGGATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATCAAGATGATGC +TCGTTATGGTTTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGCTTCCTCCTGAGACTGAGCTT +TCTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGC +ATACTGACCAAGAACGTGATTACTTCATGCAGCGTTACCGTGATGTTATTTCTTCATTTGGAGGTAAAAC +CTCTTATGACGCTGACAACCGTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTT +GATGGAACTGACCAAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGC +CGCGTTTCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGAC +TAAAGAGATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTG +TATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGTCTAAGAAGT +TTAAGATTGCTGAGGGTCAGTGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGA +AGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGAT +TATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTT +ATCGCAATCTGCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTGAGGTTATAAC +GCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACCAAGCGAAGCGCGGTAGGTTTTCTGC +TTAGGAGTTTAATCATGTTTCAGACTTTTATTTCTCGCCATAATTCAAACTTTTTTTCTGATAAGCTGGT +TCTCACTTCTGTTACTCCAGCTTCTTCGGCACCTGTTTTACAGACACCTAAAGCTACATCGTCAACGTTA +TATTTTGATAGTTTGACGGTTAATGCTGGTAATGGTGGTTTTCTTCATTGCATTCAGATGGATACATCTG +TCAACGCCGCTAATCAGGTTGTTTCTGTTGGTGCTGATATTGCTTTTGATGCCGACCCTAAATTTTTTGC +CTGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTCCCGACTGCCTATGATGTTTATCCTTTG +AATGGTCGCCATGATGGTGGTTATTATACCGTCAAGGACTGTGTGACTATTGACGTCCTTCCCCGTACGC +CGGGCAATAATGTTTATGTTGGTTTCATGGTTTGGTCTAACTTTACCGCTACTAAATGCCGCGGATTGGT +TTCGCTGAATCAGGTTATTAAAGAGATTATTTGTCTCCAGCCACTTAAGTGAGGTGATTTATGTTTGGTG +CTATTGCTGGCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAA +AGCCGCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCT +GGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTG +GTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGA +TAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTGATTAT +CTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCTCTGCTGGTATGG +TTGACGCCGGATTTGAGAATCAAAAAGAGCTTACTAAAATGCAACTGGACAATCAGAAAGAGATTGCCGA +GATGCAAAATGAGACTCAAAAAGAGATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGAC +CAGGTATATGCACAAAATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTA +TGGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAAGCTCA +AACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGAC +TTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTTCTCATATTGGCGCTACTGCAAAGGATATTT +CTAATGTCGTCACTGATGCTGCTTCTGGTGTGGTTGATATTTTTCATGGTATTGATAAAGCTGTTGCCGA +TACTTGGAACAATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAACCG +TCAGGATTGACACCCTCCCAATTGTATGTTTTCATGCCTCCAAATCTTGGAGGCTTTTTTATGGTTCGTT +CTTATTACCCTTCTGAATGTCACGCTGATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTAT +TGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATGGATAACCGC +ATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATATGTATG +TTGACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGA +ATTGGCACAATGCTACAATGTGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGG +GACGAAAAATGGTTTTTAGAGAACGAGAAGACGGTTACGCAGTTTTGCCGCAAGCTGGCTGCTGAACGCC +CTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATGAGTGTTCAAGATT +GCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTACTATTCAGCGTTTGATGAATGCAATGCGACAG +GCTCATGCTGATGGTTGGTTTATCGTTTTTGACACTCTCACGTTGGCTGACGACCGATTAGAGGCGTTTT +ATGATAATCCCAATGCTTTGCGTGACTATTTTCGTGATATTGGTCGTATGGTTCTTGCTGCCGAGGGTCG +CAAGGCTAATGATTCACACGCCGACTGCTATCAGTATTTTTGTGTGCCTGAGTATGGTACAGCTAATGGC +CGTCTTCATTTCCATGCGGTGCATTTTATGCGGACACTTCCTACAGGTAGCGTTGACCCTAATTTTGGTC +GTCGGGTACGCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGTGGCCTTATGGTTACAGTATGCCCAT +CGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAG +CCGCTTAAAGCTACCAGTTATATGGCTGTTGGTTTCTATGTGGCTAAATACGTTAACAAAAAGTCAGATA +TGGACCTTGCTGCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACT +TCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAATGACAAATCTG +TCCACGGAGTGCTTAATCCAACTTACCAAGCTGGGTTACGACGCGACGCCGTTCAACCAGATATTGAAGC +AGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTAGCCGACGTTTTGGCGGCGCAACC +TGTGACGACAAATCTGCTCAAATTTATGCGCGCTTCGATAAAAATGATTGGCGTATCCAACCTGCA +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/picard_ARRG_input1.sam Mon Feb 17 00:02:22 2014 -0500 @@ -0,0 +1,25 @@ +@HD VN:1.0 SO:coordinate +@SQ SN:chr1 LN:10001 +@SQ SN:chr2 LN:100001 +@SQ SN:chr3 LN:10001 +@SQ SN:chr4 LN:1001 +@RG ID:rg1 SM:s1 +@RG ID:rg2 SM:s3 +bar:record:4 77 chr1 1 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg1 +bar:record:6 77 chr1 1 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg2 +bar:record:1 77 chr1 10 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg1 +bar:record:3 77 chr1 10 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg2 +bar:record:1 141 chr1 20 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1 +bar:record:7 77 chr1 20 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg2 +bar:record:8 77 chr1 30 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg2 +bar:record:4 141 chr1 40 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1 +bar:record:5 77 chr1 40 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg2 +bar:record:6 141 chr1 50 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg2 +bar:record:2 77 chr2 10 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg1 +bar:record:2 141 chr2 30 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg2 +bar:record:3 141 chr3 20 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1 +bar:record:8 141 chr3 20 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1 +bar:record:5 141 chr3 40 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1 +bar:record:9 77 chr4 10 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg1 +bar:record:7 141 chr4 20 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1 +bar:record:9 141 chr4 60 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/picard_ARRG_input2.sam Mon Feb 17 00:02:22 2014 -0500 @@ -0,0 +1,23 @@ +@HD VN:1.0 SO:coordinate +@SQ SN:chr1 LN:10001 +@SQ SN:chr2 LN:100001 +@SQ SN:chr3 LN:10001 +@SQ SN:chr4 LN:1001 +bar:record:4 77 chr1 1 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 +bar:record:6 77 chr1 1 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 +bar:record:1 77 chr1 10 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 +bar:record:3 77 chr1 10 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 +bar:record:1 141 chr1 20 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 +bar:record:7 77 chr1 20 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 +bar:record:8 77 chr1 30 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 +bar:record:4 141 chr1 40 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 +bar:record:5 77 chr1 40 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 +bar:record:6 141 chr1 50 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 +bar:record:2 77 chr2 10 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 +bar:record:2 141 chr2 30 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 +bar:record:3 141 chr3 20 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 +bar:record:8 141 chr3 20 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 +bar:record:5 141 chr3 40 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 +bar:record:9 77 chr4 10 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 +bar:record:7 141 chr4 20 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 +bar:record:9 141 chr4 60 0 * * 0 0 CCCCCCCCCCCCC 2222222222222
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/picard_ARRG_output1.sam Mon Feb 17 00:02:22 2014 -0500 @@ -0,0 +1,24 @@ +@HD VN:1.0 SO:coordinate +@SQ SN:chr1 LN:10001 +@SQ SN:chr2 LN:100001 +@SQ SN:chr3 LN:10001 +@SQ SN:chr4 LN:1001 +@RG ID:one PL:illumina PU:peaewe LB:lib SM:sam1 +bar:record:4 77 chr1 1 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:one +bar:record:6 77 chr1 1 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:one +bar:record:1 77 chr1 10 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:one +bar:record:3 77 chr1 10 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:one +bar:record:1 141 chr1 20 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:one +bar:record:7 77 chr1 20 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:one +bar:record:8 77 chr1 30 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:one +bar:record:4 141 chr1 40 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:one +bar:record:5 77 chr1 40 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:one +bar:record:6 141 chr1 50 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:one +bar:record:2 77 chr2 10 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:one +bar:record:2 141 chr2 30 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:one +bar:record:3 141 chr3 20 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:one +bar:record:8 141 chr3 20 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:one +bar:record:5 141 chr3 40 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:one +bar:record:9 77 chr4 10 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:one +bar:record:7 141 chr4 20 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:one +bar:record:9 141 chr4 60 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:one
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/picard_ARRG_output2.sam Mon Feb 17 00:02:22 2014 -0500 @@ -0,0 +1,24 @@ +@HD VN:1.0 SO:coordinate +@SQ SN:chr1 LN:10001 +@SQ SN:chr2 LN:100001 +@SQ SN:chr3 LN:10001 +@SQ SN:chr4 LN:1001 +@RG ID:M5 PL:IL PU:PLAT LB:LIB DS:description with spaces SM:smp CN:FamousCenter +bar:record:4 77 chr1 1 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:M5 +bar:record:6 77 chr1 1 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:M5 +bar:record:1 77 chr1 10 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:M5 +bar:record:3 77 chr1 10 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:M5 +bar:record:1 141 chr1 20 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:M5 +bar:record:7 77 chr1 20 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:M5 +bar:record:8 77 chr1 30 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:M5 +bar:record:4 141 chr1 40 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:M5 +bar:record:5 77 chr1 40 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:M5 +bar:record:6 141 chr1 50 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:M5 +bar:record:2 77 chr2 10 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:M5 +bar:record:2 141 chr2 30 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:M5 +bar:record:3 141 chr3 20 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:M5 +bar:record:8 141 chr3 20 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:M5 +bar:record:5 141 chr3 40 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:M5 +bar:record:9 77 chr4 10 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:M5 +bar:record:7 141 chr4 20 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:M5 +bar:record:9 141 chr4 60 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:M5
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/picard_ARRG_output3.sam Mon Feb 17 00:02:22 2014 -0500 @@ -0,0 +1,24 @@ +@HD VN:1.0 SO:coordinate +@SQ SN:chr1 LN:10001 +@SQ SN:chr2 LN:100001 +@SQ SN:chr3 LN:10001 +@SQ SN:chr4 LN:1001 +@RG ID:M6 PL:IL PU:PLAT LB:LIB SM:smp1 +bar:record:4 77 chr1 1 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:M6 +bar:record:6 77 chr1 1 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:M6 +bar:record:1 77 chr1 10 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:M6 +bar:record:3 77 chr1 10 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:M6 +bar:record:1 141 chr1 20 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:M6 +bar:record:7 77 chr1 20 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:M6 +bar:record:8 77 chr1 30 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:M6 +bar:record:4 141 chr1 40 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:M6 +bar:record:5 77 chr1 40 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:M6 +bar:record:6 141 chr1 50 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:M6 +bar:record:2 77 chr2 10 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:M6 +bar:record:2 141 chr2 30 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:M6 +bar:record:3 141 chr3 20 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:M6 +bar:record:8 141 chr3 20 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:M6 +bar:record:5 141 chr3 40 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:M6 +bar:record:9 77 chr4 10 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:M6 +bar:record:7 141 chr4 20 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:M6 +bar:record:9 141 chr4 60 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:M6
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/picard_BIS_input1.sam Mon Feb 17 00:02:22 2014 -0500 @@ -0,0 +1,18 @@ +@HD VN:1.0 SO:coordinate +@SQ SN:chr1 LN:101 +@SQ SN:chr7 LN:404 +@SQ SN:chr8 LN:202 +@SQ SN:chr10 LN:303 +@SQ SN:chr14 LN:505 +@RG ID:0 SM:Hi,Mom! +@RG ID:1 SM:samplesample DS:ClearDescription +@PG ID:1 PN:Hey! VN:2.0 +@CO Just a generic comment to make the header longer +both_reads_align_clip_marked 83 chr7 1 255 101M = 302 201 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 +both_reads_present_only_first_aligns 89 chr7 1 255 101M * 0 0 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 +read_2_too_many_gaps 83 chr7 1 255 101M = 302 201 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 +both_reads_align_clip_adapter 147 chr7 16 255 101M = 21 -96 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 +both_reads_align_clip_adapter 99 chr7 21 255 101M = 16 96 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 +both_reads_align_clip_marked 163 chr7 302 255 101M = 1 -201 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA &/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1 RG:Z:0 +read_2_too_many_gaps 163 chr7 302 255 10M1D10M5I76M = 1 -201 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA &/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1 RG:Z:0 +both_reads_present_only_first_aligns 165 * 0 0 * chr7 1 0 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA &/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1 RG:Z:0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/picard_BIS_output1.txt Mon Feb 17 00:02:22 2014 -0500 @@ -0,0 +1,39 @@ +<style type="text/css"> + tr.d0 td {background-color: oldlace; color: black;} + tr.d1 td {background-color: aliceblue; color: black;} + </style><?xml version="1.0" encoding="utf-8" ?> +<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> +<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"> +<head> +<meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> +<meta name="generator" content="Galaxy picard_wrapper tool output - see http://getgalaxy.org/" /> +<title></title> +<link rel="stylesheet" href="/static/style/base.css" type="text/css" /> +</head> +<body> +<div class="document"> +Galaxy tool BamIndexStats run at 12/05/2011 14:18:06</b><br/><b>The following output files were created (click the filename to view/download a copy):</b><hr/><table> +<tr><td><a href="BamIndexStats.log">BamIndexStats.log</a></td></tr> +<tr><td><a href="BamIndexStats.metrics.txt">BamIndexStats.metrics.txt</a></td></tr> +</table><p/> +<b>Picard on line resources</b><ul> +<li><a href="http://picard.sourceforge.net/index.shtml">Click here for Picard Documentation</a></li> +<li><a href="http://picard.sourceforge.net/picard-metric-definitions.shtml">Click here for Picard Metrics definitions</a></li></ul><hr/> +<b>Picard output</b><hr/> +<table cellpadding="3" > +<tr class="d0"><td colspan="2">chr1 length= 101 Aligned= 0 Unaligned= 0</td></tr> +<tr class="d1"><td colspan="2">chr7 length= 404 Aligned= 7 Unaligned= 0</td></tr> +<tr class="d0"><td colspan="2">chr8 length= 202 Aligned= 0 Unaligned= 0</td></tr> +<tr class="d1"><td colspan="2">NoCoordinateCount= 1</td></tr> +</table> +<b>Picard Tool Run Log</b><hr/> +<pre>Thu, 12 May 2011 14:18:06 INFO + ## executing java -Xmx2g -jar /udd/rerla/galaxy-central/tool-data/shared/jars/BamIndexStats.jar VALIDATION_STRINGENCY=LENIENT INPUT=/udd/rerla/galaxy-central/database/job_working_directory/955/dataset_1015_files/tmp45bd_D.bam returned status 0 and stderr: +[Thu May 12 14:18:06 EDT 2011] net.sf.picard.sam.BamIndexStats INPUT=/udd/rerla/galaxy-central/database/job_working_directory/955/dataset_1015_files/tmp45bd_D.bam VALIDATION_STRINGENCY=LENIENT TMP_DIR=/tmp/rerla VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false +[Thu May 12 14:18:06 EDT 2011] net.sf.picard.sam.BamIndexStats done. +Runtime.totalMemory()=9109504 + + +</pre><hr/>The freely available <a href="http://picard.sourceforge.net/command-line-overview.shtml">Picard software</a> +generated all outputs reported here running as a <a href="http://getgalaxy.org">Galaxy</a> tool</div></body></html> +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/picard_BIS_output2.txt Mon Feb 17 00:02:22 2014 -0500 @@ -0,0 +1,41 @@ +<style type="text/css"> + tr.d0 td {background-color: oldlace; color: black;} + tr.d1 td {background-color: aliceblue; color: black;} + </style><?xml version="1.0" encoding="utf-8" ?> +<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> +<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"> +<head> +<meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> +<meta name="generator" content="Galaxy picard_wrapper tool output - see http://getgalaxy.org/" /> +<title></title> +<link rel="stylesheet" href="/static/style/base.css" type="text/css" /> +</head> +<body> +<div class="document"> +Galaxy tool BamIndexStats run at 12/05/2011 14:18:22</b><br/><b>The following output files were created (click the filename to view/download a copy):</b><hr/><table> +<tr><td><a href="BamIndexStats.log">BamIndexStats.log</a></td></tr> +<tr><td><a href="BamIndexStats.metrics.txt">BamIndexStats.metrics.txt</a></td></tr> +</table><p/> +<b>Picard on line resources</b><ul> +<li><a href="http://picard.sourceforge.net/index.shtml">Click here for Picard Documentation</a></li> +<li><a href="http://picard.sourceforge.net/picard-metric-definitions.shtml">Click here for Picard Metrics definitions</a></li></ul><hr/> +<b>Picard output</b><hr/> +<table cellpadding="3" > +<tr class="d0"><td colspan="2">chr1 length= 101 Aligned= 0 Unaligned= 0</td></tr> +<tr class="d1"><td colspan="2">chr7 length= 404 Aligned= 7 Unaligned= 0</td></tr> +<tr class="d0"><td colspan="2">chr8 length= 202 Aligned= 0 Unaligned= 0</td></tr> +<tr class="d1"><td colspan="2">chr10 length= 303 Aligned= 0 Unaligned= 0</td></tr> +<tr class="d0"><td colspan="2">chr14 length= 505 Aligned= 0 Unaligned= 0</td></tr> +<tr class="d1"><td colspan="2">NoCoordinateCount= 1</td></tr> +</table> +<b>Picard Tool Run Log</b><hr/> +<pre>Thu, 12 May 2011 14:18:22 INFO + ## executing java -Xmx2g -jar /udd/rerla/galaxy-central/tool-data/shared/jars/BamIndexStats.jar VALIDATION_STRINGENCY=LENIENT INPUT=/udd/rerla/galaxy-central/database/job_working_directory/957/dataset_1017_files/tmpqXGksN.bam returned status 0 and stderr: +[Thu May 12 14:18:21 EDT 2011] net.sf.picard.sam.BamIndexStats INPUT=/udd/rerla/galaxy-central/database/job_working_directory/957/dataset_1017_files/tmpqXGksN.bam VALIDATION_STRINGENCY=LENIENT TMP_DIR=/tmp/rerla VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false +[Thu May 12 14:18:22 EDT 2011] net.sf.picard.sam.BamIndexStats done. +Runtime.totalMemory()=9109504 + + +</pre><hr/>The freely available <a href="http://picard.sourceforge.net/command-line-overview.shtml">Picard software</a> +generated all outputs reported here running as a <a href="http://getgalaxy.org">Galaxy</a> tool</div></body></html> +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/picard_MD_output1.txt Mon Feb 17 00:02:22 2014 -0500 @@ -0,0 +1,112 @@ +## net.sf.picard.metrics.StringHeader +# net.sf.picard.sam.MarkDuplicates INPUT=picard_input_tiny_coord.bam OUTPUT=picard_MD_output2.bam METRICS_FILE=picard_MD_output1.txt REMOVE_DUPLICATES=false ASSUME_SORTED=true READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).* OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VALIDATION_STRINGENCY=LENIENT MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 TMP_DIR=/tmp/kpvincent VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false +## net.sf.picard.metrics.StringHeader +# Started on: Tue Apr 19 15:28:21 EDT 2011 + +## METRICS CLASS net.sf.picard.sam.DuplicationMetrics +LIBRARY UNPAIRED_READS_EXAMINED READ_PAIRS_EXAMINED UNMAPPED_READS UNPAIRED_READ_DUPLICATES READ_PAIR_DUPLICATES READ_PAIR_OPTICAL_DUPLICATES PERCENT_DUPLICATION ESTIMATED_LIBRARY_SIZE + 1 3 1 1 1 0 0.428571 3 + +## HISTOGRAM java.lang.Double +BIN VALUE +1.0 0.948181 +2.0 1.296997 +3.0 1.425319 +4.0 1.472527 +5.0 1.489893 +6.0 1.496282 +7.0 1.498632 +8.0 1.499497 +9.0 1.499815 +10.0 1.499932 +11.0 1.499975 +12.0 1.499991 +13.0 1.499997 +14.0 1.499999 +15.0 1.5 +16.0 1.5 +17.0 1.5 +18.0 1.5 +19.0 1.5 +20.0 1.5 +21.0 1.5 +22.0 1.5 +23.0 1.5 +24.0 1.5 +25.0 1.5 +26.0 1.5 +27.0 1.5 +28.0 1.5 +29.0 1.5 +30.0 1.5 +31.0 1.5 +32.0 1.5 +33.0 1.5 +34.0 1.5 +35.0 1.5 +36.0 1.5 +37.0 1.5 +38.0 1.5 +39.0 1.5 +40.0 1.5 +41.0 1.5 +42.0 1.5 +43.0 1.5 +44.0 1.5 +45.0 1.5 +46.0 1.5 +47.0 1.5 +48.0 1.5 +49.0 1.5 +50.0 1.5 +51.0 1.5 +52.0 1.5 +53.0 1.5 +54.0 1.5 +55.0 1.5 +56.0 1.5 +57.0 1.5 +58.0 1.5 +59.0 1.5 +60.0 1.5 +61.0 1.5 +62.0 1.5 +63.0 1.5 +64.0 1.5 +65.0 1.5 +66.0 1.5 +67.0 1.5 +68.0 1.5 +69.0 1.5 +70.0 1.5 +71.0 1.5 +72.0 1.5 +73.0 1.5 +74.0 1.5 +75.0 1.5 +76.0 1.5 +77.0 1.5 +78.0 1.5 +79.0 1.5 +80.0 1.5 +81.0 1.5 +82.0 1.5 +83.0 1.5 +84.0 1.5 +85.0 1.5 +86.0 1.5 +87.0 1.5 +88.0 1.5 +89.0 1.5 +90.0 1.5 +91.0 1.5 +92.0 1.5 +93.0 1.5 +94.0 1.5 +95.0 1.5 +96.0 1.5 +97.0 1.5 +98.0 1.5 +99.0 1.5 +100.0 1.5 +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/picard_MD_output3.txt Mon Feb 17 00:02:22 2014 -0500 @@ -0,0 +1,112 @@ +## net.sf.picard.metrics.StringHeader +# net.sf.picard.sam.MarkDuplicates INPUT=picard_input_tiny_coord.sam OUTPUT=picard_MD_output4_.sam METRICS_FILE=picard_MD_output3_.txt REMOVE_DUPLICATES=true ASSUME_SORTED=false READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).* OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VALIDATION_STRINGENCY=LENIENT MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 TMP_DIR=/tmp/kpvincent VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false +## net.sf.picard.metrics.StringHeader +# Started on: Tue Apr 19 15:32:38 EDT 2011 + +## METRICS CLASS net.sf.picard.sam.DuplicationMetrics +LIBRARY UNPAIRED_READS_EXAMINED READ_PAIRS_EXAMINED UNMAPPED_READS UNPAIRED_READ_DUPLICATES READ_PAIR_DUPLICATES READ_PAIR_OPTICAL_DUPLICATES PERCENT_DUPLICATION ESTIMATED_LIBRARY_SIZE + 1 3 1 1 1 0 0.428571 3 + +## HISTOGRAM java.lang.Double +BIN VALUE +1.0 0.948181 +2.0 1.296997 +3.0 1.425319 +4.0 1.472527 +5.0 1.489893 +6.0 1.496282 +7.0 1.498632 +8.0 1.499497 +9.0 1.499815 +10.0 1.499932 +11.0 1.499975 +12.0 1.499991 +13.0 1.499997 +14.0 1.499999 +15.0 1.5 +16.0 1.5 +17.0 1.5 +18.0 1.5 +19.0 1.5 +20.0 1.5 +21.0 1.5 +22.0 1.5 +23.0 1.5 +24.0 1.5 +25.0 1.5 +26.0 1.5 +27.0 1.5 +28.0 1.5 +29.0 1.5 +30.0 1.5 +31.0 1.5 +32.0 1.5 +33.0 1.5 +34.0 1.5 +35.0 1.5 +36.0 1.5 +37.0 1.5 +38.0 1.5 +39.0 1.5 +40.0 1.5 +41.0 1.5 +42.0 1.5 +43.0 1.5 +44.0 1.5 +45.0 1.5 +46.0 1.5 +47.0 1.5 +48.0 1.5 +49.0 1.5 +50.0 1.5 +51.0 1.5 +52.0 1.5 +53.0 1.5 +54.0 1.5 +55.0 1.5 +56.0 1.5 +57.0 1.5 +58.0 1.5 +59.0 1.5 +60.0 1.5 +61.0 1.5 +62.0 1.5 +63.0 1.5 +64.0 1.5 +65.0 1.5 +66.0 1.5 +67.0 1.5 +68.0 1.5 +69.0 1.5 +70.0 1.5 +71.0 1.5 +72.0 1.5 +73.0 1.5 +74.0 1.5 +75.0 1.5 +76.0 1.5 +77.0 1.5 +78.0 1.5 +79.0 1.5 +80.0 1.5 +81.0 1.5 +82.0 1.5 +83.0 1.5 +84.0 1.5 +85.0 1.5 +86.0 1.5 +87.0 1.5 +88.0 1.5 +89.0 1.5 +90.0 1.5 +91.0 1.5 +92.0 1.5 +93.0 1.5 +94.0 1.5 +95.0 1.5 +96.0 1.5 +97.0 1.5 +98.0 1.5 +99.0 1.5 +100.0 1.5 +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/picard_MD_output4.sam Mon Feb 17 00:02:22 2014 -0500 @@ -0,0 +1,11 @@ +@HD VN:1.0 SO:coordinate +@SQ SN:chr1 LN:101 +@SQ SN:chr7 LN:404 +@SQ SN:chr8 LN:202 +@RG ID:0 SM:Hi,Mom! +@PG ID:1 PN:Hey! VN:2.0 +both_reads_align_clip_marked 83 chr7 1 255 101M = 302 201 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 +both_reads_align_clip_adapter 147 chr7 16 255 101M = 21 -96 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 +both_reads_align_clip_adapter 99 chr7 21 255 101M = 16 96 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 +both_reads_align_clip_marked 163 chr7 302 255 101M = 1 -201 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA &/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1 RG:Z:0 +both_reads_present_only_first_aligns 165 * 0 0 * chr7 1 0 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA &/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1 RG:Z:0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/picard_RSH_input1.sam Mon Feb 17 00:02:22 2014 -0500 @@ -0,0 +1,14 @@ +@HD VN:1.0 SO:coordinate +@SQ SN:chr1 LN:101 +@SQ SN:chr7 LN:404 +@SQ SN:chr8 LN:202 +@RG ID:0 SM:What_is_that_sound? +@PG ID:1 PN:Greetings! VN:2.0 +both_reads_align_clip_marked 83 chr7 1 255 101M = 302 201 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 +both_reads_present_only_first_aligns 89 chr7 1 255 101M * 0 0 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 +read_2_too_many_gaps 83 chr7 1 255 101M = 302 201 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 +both_reads_align_clip_adapter 147 chr7 16 255 101M = 21 -96 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 +both_reads_align_clip_adapter 99 chr7 21 255 101M = 16 96 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 +both_reads_align_clip_marked 163 chr7 302 255 101M = 1 -201 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA &/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1 RG:Z:0 +read_2_too_many_gaps 163 chr7 302 255 10M1D10M5I76M = 1 -201 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA &/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1 RG:Z:0 +both_reads_present_only_first_aligns 165 * 0 0 * chr7 1 0 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA &/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1 RG:Z:0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/picard_RSH_output1.sam Mon Feb 17 00:02:22 2014 -0500 @@ -0,0 +1,14 @@ +@HD VN:1.0 SO:coordinate +@SQ SN:chr1 LN:101 +@SQ SN:chr7 LN:404 +@SQ SN:chr8 LN:202 +@RG ID:0 SM:What_is_that_sound? +@PG ID:1 PN:Greetings! VN:2.0 +both_reads_align_clip_marked 83 chr7 1 255 101M = 302 201 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 +both_reads_present_only_first_aligns 89 chr7 1 255 101M * 0 0 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 +read_2_too_many_gaps 83 chr7 1 255 101M = 302 201 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 +both_reads_align_clip_adapter 147 chr7 16 255 101M = 21 -96 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 +both_reads_align_clip_adapter 99 chr7 21 255 101M = 16 96 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 +both_reads_align_clip_marked 163 chr7 302 255 101M = 1 -201 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA &/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1 RG:Z:0 +read_2_too_many_gaps 163 chr7 302 255 10M1D10M5I76M = 1 -201 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA &/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1 RG:Z:0 +both_reads_present_only_first_aligns 165 * 0 0 * chr7 1 0 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA &/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1 RG:Z:0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/picard_RSH_output2.sam Mon Feb 17 00:02:22 2014 -0500 @@ -0,0 +1,14 @@ +@HD VN:1.0 SO:coordinate +@SQ SN:chr1 LN:101 +@SQ SN:chr7 LN:404 +@SQ SN:chr8 LN:202 +@RG ID:0 SM:What_is_that_sound? +@PG ID:1 PN:Greetings! VN:2.0 +both_reads_align_clip_marked 83 chr7 1 255 101M = 302 201 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 +both_reads_present_only_first_aligns 89 chr7 1 255 101M * 0 0 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 +read_2_too_many_gaps 83 chr7 1 255 101M = 302 201 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 +both_reads_align_clip_adapter 147 chr7 16 255 101M = 21 -96 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 +both_reads_align_clip_adapter 99 chr7 21 255 101M = 16 96 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 +both_reads_align_clip_marked 163 chr7 302 255 101M = 1 -201 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA &/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1 RG:Z:0 +read_2_too_many_gaps 163 chr7 302 255 10M1D10M5I76M = 1 -201 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA &/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1 RG:Z:0 +both_reads_present_only_first_aligns 165 * 0 0 * chr7 1 0 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA &/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1 RG:Z:0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/picard_RS_input2.sam Mon Feb 17 00:02:22 2014 -0500 @@ -0,0 +1,22 @@ +@HD VN:1.0 SO:unsorted +@SQ SN:phiX174 LN:5386 +@PG ID:Bowtie VN:0.12.7 CL:"bowtie -q -p 4 -S --phred33-quals /genome/phiX/bowtie_index/phiX dataset_437.dat" +HWI-EAS91_1_30788AAXX:1:1:1761:343/1 0 phiX174 5 255 50M * 0 0 TTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGA IIIIIII""IIIIIIIIIII?I0IIIIHIIIGIIIII0II?I""IIIIII XA:i:0 MD:Z:50 NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1647:512/1 0 phiX174 401 255 50M * 0 0 TACTGAACAATCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAAGCTCA IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1578:331/1 0 phiX174 209 255 50M * 0 0 TGTCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGC IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1746:351/1 0 phiX174 1218 255 50M * 0 0 CTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAAGGATGGT IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1582:633/1 0 phiX174 1517 255 50M * 0 0 CCGCTTCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGACTTCTACCAC IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1599:330/1 0 phiX174 803 255 50M * 0 0 AGAAGAAAACGTGCGTCAAAAATTACGTGCAGAAGGAGTGATGTAATGTC IIIIIII""IIIIIIIIIIIIIIIIIII<III@II"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1598:534/1 0 phiX174 1717 255 50M * 0 0 GCGCTCTAATCTCTGGGCATCTGGCTATGATGTTGATGGAACTGACCAAA IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1749:466/1 0 phiX174 2201 255 50M * 0 0 TTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTTATCGCAATCT IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1570:620/1 4 * 0 0 * * 0 0 GAGTAACAAAGTAAAGTTTGGACCGTTTTTGTCTCGTGCTCGTCGCTGCG IIIIIII""IIIIIIIIIIIIIBIIIIIIIIIIII"IIIIIII000IIII XM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1629:446/1 0 phiX174 2301 255 50M * 0 0 AGGTTATAACGCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGT IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1763:587/1 0 phiX174 2501 255 50M * 0 0 AAGCTACATCGTCAACGTTATATTTTGATAGTTTGACGGTTAATGCTGGT IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1616:363/1 0 phiX174 2718 255 50M * 0 0 TGTTTATCCTTTGAATGGTCGCCATGATGGTGGTTATTATACCGTCAAGG IIIIIII""IIIIIIIIIIIIIIIIIIIIIIDIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1572:270/1 0 phiX174 3518 255 50M * 0 0 TGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTA IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1768:715/1 0 phiX174 3118 255 50M * 0 0 ACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTGGTGCTATGGCTAAAGCT IIIIIII""IIIIIIIIIIIIIDIIIIIIIIIIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1785:1272/1 0 phiX174 3818 255 50M * 0 0 TATTTTTCATGGTATTGATAAAGCTGTTGCCGATACTTGGAACAATTTCT III""""""IIIIIIIII""FI"IIII""II+ICI"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1673:514/1 0 phiX174 4018 255 50M * 0 0 ATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTATTGAGGCT IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIII1"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1652:270/1 4 * 0 0 * * 0 0 AGCGTAAAGGCGCTCGTCTTTGGTATGTAGGACTTTGCATTGTTTAATTG IIIIIII""IIIIIIIIIIIIIIIIIIIIIII6II"IIIIIII000IIII XM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1572:324/1 4 * 0 0 * * 0 0 AAGGTGCTTAAATTCGTGGGTCCTGAGCTGGCGACCCTGTTTTGTATGGC IIIIIII""IIIIIIIIIIIIIIIIIIII+7I05I"IIIIIII000IIII XM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1634:330/1 0 phiX174 4418 255 50M * 0 0 GGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATG IIIIIII""IIIIIIIIIIIIIIIIIIIIIII8II"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/picard_RS_input3.sam Mon Feb 17 00:02:22 2014 -0500 @@ -0,0 +1,26 @@ +@HD VN:1.0 SO:unsorted +@SQ SN:phiX1 LN:1120 +@SQ SN:phiX2 LN:1190 +@SQ SN:phiX3 LN:1330 +@SQ SN:phiX4 LN:910 +@SQ SN:phiX5 LN:828 +@PG ID:Bowtie VN:0.12.7 CL:"bowtie -q -p 4 -S --phred33-quals /tmp/tmp1E6jpl/tmpDg42o9 dataset_437.dat" +HWI-EAS91_1_30788AAXX:1:1:1578:331/1 0 phiX1 209 255 50M * 0 0 TGTCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGC IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1761:343/1 0 phiX1 5 255 50M * 0 0 TTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGA IIIIIII""IIIIIIIIIII?I0IIIIHIIIGIIIII0II?I""IIIIII XA:i:0 MD:Z:50 NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1647:512/1 0 phiX1 401 255 50M * 0 0 TACTGAACAATCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAAGCTCA IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1746:351/1 0 phiX2 98 255 50M * 0 0 CTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAAGGATGGT IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1582:633/1 0 phiX2 397 255 50M * 0 0 CCGCTTCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGACTTCTACCAC IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1570:620/1 4 * 0 0 * * 0 0 GAGTAACAAAGTAAAGTTTGGACCGTTTTTGTCTCGTGCTCGTCGCTGCG IIIIIII""IIIIIIIIIIIIIBIIIIIIIIIIII"IIIIIII000IIII XM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1598:534/1 0 phiX2 597 255 50M * 0 0 GCGCTCTAATCTCTGGGCATCTGGCTATGATGTTGATGGAACTGACCAAA IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1599:330/1 0 phiX1 803 255 50M * 0 0 AGAAGAAAACGTGCGTCAAAAATTACGTGCAGAAGGAGTGATGTAATGTC IIIIIII""IIIIIIIIIIIIIIIIIII<III@II"IIIIIII000IIII XA:i:0 MD:Z:30G19 NM:i:1 +HWI-EAS91_1_30788AAXX:1:1:1749:466/1 0 phiX2 1081 255 50M * 0 0 TTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTTATCGCAATCT IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1572:324/1 4 * 0 0 * * 0 0 AAGGTGCTTAAATTCGTGGGTCCTGAGCTGGCGACCCTGTTTTGTATGGC IIIIIII""IIIIIIIIIIIIIIIIIIII+7I05I"IIIIIII000IIII XM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1763:587/1 0 phiX3 191 255 50M * 0 0 AAGCTACATCGTCAACGTTATATTTTGATAGTTTGACGGTTAATGCTGGT IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1616:363/1 0 phiX3 408 255 50M * 0 0 TGTTTATCCTTTGAATGGTCGCCATGATGGTGGTTATTATACCGTCAAGG IIIIIII""IIIIIIIIIIIIIIIIIIIIIIDIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1652:270/1 4 * 0 0 * * 0 0 AGCGTAAAGGCGCTCGTCTTTGGTATGTAGGACTTTGCATTGTTTAATTG IIIIIII""IIIIIIIIIIIIIIIIIIIIIII6II"IIIIIII000IIII XM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1768:715/1 0 phiX3 808 255 50M * 0 0 ACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTGGTGCTATGGCTAAAGCT IIIIIII""IIIIIIIIIIIIIDIIIIIIIIIIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1572:270/1 0 phiX3 1208 255 50M * 0 0 TGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTA IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1629:446/1 4 * 0 0 * * 0 0 AGGTTATAACGCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGT IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII XM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1673:514/1 0 phiX4 378 255 50M * 0 0 ATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTATTGAGGCT IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIII1"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1785:1272/1 0 phiX4 178 255 50M * 0 0 TATTTTTCATGGTATTGATAAAGCTGTTGCCGATACTTGGAACAATTTCT III""""""IIIIIIIII""FI"IIII""II+ICI"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1634:330/1 0 phiX4 778 255 50M * 0 0 GGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATG IIIIIII""IIIIIIIIIIIIIIIIIIIIIII8II"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/picard_RS_input4.fasta Mon Feb 17 00:02:22 2014 -0500 @@ -0,0 +1,82 @@ +>phiX1 length=1120 +GAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAAAAATTATCTT +GATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGGAAAATGAGAAA +ATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATCAACTAACGATTCTG +TCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTA +GATATGAGTCACATTTTGTTCATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATC +TGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTT +TCCAGACCGCTTTGGCCTCTATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTT +CGATTTTCTGACGAGTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCT +TGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCCG +TCATTGCTTATTATGTTCATCCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAATTTAC +GGAAAACATTATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCTTGCGTGTA +CGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAAATTACGTGCGGAAGGAG +TGATGTAATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACT +AAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAATTGCAGGGGCTTCGGC +CCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCCA +TCTTGGCTTCCTTGCTGGTCAGATTGGTCGTCTTATTACCATTTCAACTACTCCGGTTATCGCTGGCGAC +>phiX2 length=1190 +TCCTTCGAGATGGACGCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTA +CTGTAGACATTTTTACTTTTTATGTCCCTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAA +GGATGGTGTTAATGCCACTCCTCTCCCGACTGTTAACACTACTGGTTATATTGACCATGCCGCTTTTCTT +GGCACGATTAACCCTGATACCAATAAAATCCCTAAGCATTTGTTTCAGGGTTATTTGAATATCTATAACA +ACTATTTTAAAGCGCCGTGGATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATCAAGATGATGC +TCGTTATGGTTTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGCTTCCTCCTGAGACTGAGCTT +TCTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGC +ATACTGACCAAGAACGTGATTACTTCATGCAGCGTTACCATGATGTTATTTCTTCATTTGGAGGTAAAAC +CTCTTATGACGCTGACAACCGTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTT +GATGGAACTGACCAAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGC +CGCGTTTCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGAC +TAAAGAGATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTG +TATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGTCTAAGAAGT +TTAAGATTGCTGAGGGTCAGTGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGA +AGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGAT +TATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTT +ATCGCAATCTGCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTGAGGTTATAAC +>phiX3 length=1330 +GCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACCAAGCGAAGCGCGGTAGGTTTTCTGC +TTAGGAGTTTAATCATGTTTCAGACTTTTATTTCTCGCCATAATTCAAACTTTTTTTCTGATAAGCTGGT +TCTCACTTCTGTTACTCCAGCTTCTTCGGCACCTGTTTTACAGACACCTAAAGCTACATCGTCAACGTTA +TATTTTGATAGTTTGACGGTTAATGCTGGTAATGGTGGTTTTCTTCATTGCATTCAGATGGATACATCTG +TCAACGCCGCTAATCAGGTTGTTTCTGTTGGTGCTGATATTGCTTTTGATGCCGACCCTAAATTTTTTGC +CTGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTCCCGACTGCCTATGATGTTTATCCTTTG +AATGGTCGCCATGATGGTGGTTATTATACCGTCAAGGACTGTGTGACTATTGACGTCCTTCCCCGTACGC +CGGGCAATAACGTTTATGTTGGTTTCATGGTTTGGTCTAACTTTACCGCTACTAAATGCCGCGGATTGGT +TTCGCTGAATCAGGTTATTAAAGAGATTATTTGTCTCCAGCCACTTAAGTGAGGTGATTTATGTTTGGTG +CTATTGCTGGCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAA +AGCCGCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCT +GGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTG +GTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGA +TAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTGATTAT +CTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCTCTGCTGGTATGG +TTGACGCCGGATTTGAGAATCAAAAAGAGCTTACTAAAATGCAACTGGACAATCAGAAAGAGATTGCCGA +GATGCAAAATGAGACTCAAAAAGAGATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGAC +CAGGTATATGCACAAAATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTA +TGGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAAGCTCA +>phiX4 length=910 +AACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGAC +TTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTTCTCATATTGGCGCTACTGCAAAGGATATTT +CTAATGTCGTCACTGATGCTGCTTCTGGTGTGGTTGATATTTTTCATGGTATTGATAAAGCTGTTGCCGA +TACTTGGAACAATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAACCG +TCAGGATTGACACCCTCCCAATTGTATGTTTTCATGCCTCCAAATCTTGGAGGCTTTTTTATGGTTCGTT +CTTATTACCCTTCTGAATGTCACGCTGATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTAT +TGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATGGATAACCGC +ATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATATGTATG +TTGACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGA +ATTGGCACAATGCTACAATGTGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGG +GACGAAAAATGGTTTTTAGAGAACGAGAAGACGGTTACGCAGTTTTGCCGCAAGCTGGCTGCTGAACGCC +CTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATGAGTGTTCAAGATT +GCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTGCTATTCAGCGTTTGATGAATGCAATGCGACAG +>phiX5 length=828 +GCTCATGCTGATGGTTGGTTTATCGTTTTTGACACTCTCACGTTGGCTGACGACCGATTAGAGGCGTTTT +ATGATAATCCCAATGCTTTGCGTGACTATTTTCGTGATATTGGTCGTATGGTTCTTGCTGCCGAGGGTCG +CAAGGCTAATGATTCACACGCCGACTGCTATCAGTATTTTTGTGTGCCTGAGTATGGTACAGCTAATGGC +CGTCTTCATTTCCATGCGGTGCACTTTATGCGGACACTTCCTACAGGTAGCGTTGACCCTAATTTTGGTC +GTCGGGTACGCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGTGGCCTTATGGTTACAGTATGCCCAT +CGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAG +CCGCTTAAAGCTACCAGTTATATGGCTGTTGGTTTCTATGTGGCTAAATACGTTAACAAAAAGTCAGATA +TGGACCTTGCTGCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACT +TCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAATGACAAATCTG +TCCACGGAGTGCTTAATCCAACTTACCAAGCTGGGTTACGACGCGACGCCGTTCAACCAGATATTGAAGC +AGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTAGCCGACGTTTTGGCGGCGCAACC +TGTGACGACAAATCTGCTCAAATTTATGCGCGCTTCGATAAAAATGATTGGCGTATCC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/picard_RS_output2.sam Mon Feb 17 00:02:22 2014 -0500 @@ -0,0 +1,22 @@ +@HD VN:1.0 SO:unsorted +@SQ SN:phiX174 LN:5386 UR:file:/afs/bx.psu.edu/user/kpvincent/working/phiX.fa M5:f479307bca04825e98008f37e4f6251a +@PG ID:Bowtie VN:0.12.7 CL:"bowtie -q -p 4 -S --phred33-quals /genome/phiX/bowtie_index/phiX dataset_437.dat" +HWI-EAS91_1_30788AAXX:1:1:1761:343/1 0 phiX174 5 255 50M * 0 0 TTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGA IIIIIII""IIIIIIIIIII?I0IIIIHIIIGIIIII0II?I""IIIIII XA:i:0 MD:Z:50 NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1647:512/1 0 phiX174 401 255 50M * 0 0 TACTGAACAATCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAAGCTCA IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1578:331/1 0 phiX174 209 255 50M * 0 0 TGTCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGC IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1746:351/1 0 phiX174 1218 255 50M * 0 0 CTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAAGGATGGT IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1582:633/1 0 phiX174 1517 255 50M * 0 0 CCGCTTCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGACTTCTACCAC IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1599:330/1 0 phiX174 803 255 50M * 0 0 AGAAGAAAACGTGCGTCAAAAATTACGTGCAGAAGGAGTGATGTAATGTC IIIIIII""IIIIIIIIIIIIIIIIIII<III@II"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1598:534/1 0 phiX174 1717 255 50M * 0 0 GCGCTCTAATCTCTGGGCATCTGGCTATGATGTTGATGGAACTGACCAAA IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1749:466/1 0 phiX174 2201 255 50M * 0 0 TTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTTATCGCAATCT IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1570:620/1 4 * 0 0 * * 0 0 GAGTAACAAAGTAAAGTTTGGACCGTTTTTGTCTCGTGCTCGTCGCTGCG IIIIIII""IIIIIIIIIIIIIBIIIIIIIIIIII"IIIIIII000IIII XM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1629:446/1 0 phiX174 2301 255 50M * 0 0 AGGTTATAACGCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGT IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1763:587/1 0 phiX174 2501 255 50M * 0 0 AAGCTACATCGTCAACGTTATATTTTGATAGTTTGACGGTTAATGCTGGT IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1616:363/1 0 phiX174 2718 255 50M * 0 0 TGTTTATCCTTTGAATGGTCGCCATGATGGTGGTTATTATACCGTCAAGG IIIIIII""IIIIIIIIIIIIIIIIIIIIIIDIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1572:270/1 0 phiX174 3518 255 50M * 0 0 TGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTA IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1768:715/1 0 phiX174 3118 255 50M * 0 0 ACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTGGTGCTATGGCTAAAGCT IIIIIII""IIIIIIIIIIIIIDIIIIIIIIIIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1785:1272/1 0 phiX174 3818 255 50M * 0 0 TATTTTTCATGGTATTGATAAAGCTGTTGCCGATACTTGGAACAATTTCT III""""""IIIIIIIII""FI"IIII""II+ICI"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1673:514/1 0 phiX174 4018 255 50M * 0 0 ATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTATTGAGGCT IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIII1"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1652:270/1 4 * 0 0 * * 0 0 AGCGTAAAGGCGCTCGTCTTTGGTATGTAGGACTTTGCATTGTTTAATTG IIIIIII""IIIIIIIIIIIIIIIIIIIIIII6II"IIIIIII000IIII XM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1572:324/1 4 * 0 0 * * 0 0 AAGGTGCTTAAATTCGTGGGTCCTGAGCTGGCGACCCTGTTTTGTATGGC IIIIIII""IIIIIIIIIIIIIIIIIIII+7I05I"IIIIIII000IIII XM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1634:330/1 0 phiX174 4418 255 50M * 0 0 GGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATG IIIIIII""IIIIIIIIIIIIIIIIIIIIIII8II"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/picard_RS_output3.sam Mon Feb 17 00:02:22 2014 -0500 @@ -0,0 +1,26 @@ +@HD VN:1.0 SO:unsorted +@SQ SN:phiX1 LN:1120 UR:picard_RS_input4.fasta AS:phiX_buildBlah1.1 M5:40156fecb557ec9a4e0e7d0d5379d346 SP:phiX174 +@SQ SN:phiX2 LN:1190 UR:picard_RS_input4.fasta AS:phiX_buildBlah1.1 M5:3ecdb3921cbd184296cefdc675595fc1 SP:phiX174 +@SQ SN:phiX3 LN:1330 UR:picard_RS_input4.fasta AS:phiX_buildBlah1.1 M5:60435b7625ee8862e4af3e839b195198 SP:phiX174 +@SQ SN:phiX4 LN:910 UR:picard_RS_input4.fasta AS:phiX_buildBlah1.1 M5:ae8509d7b91ed64a44dd718513b1fd06 SP:phiX174 +@SQ SN:phiX5 LN:828 UR:picard_RS_input4.fasta AS:phiX_buildBlah1.1 M5:459c70115963cbce5021cac2bc9dfbd1 SP:phiX174 +@PG ID:Bowtie VN:0.12.7 CL:"bowtie -q -p 4 -S --phred33-quals /tmp/tmp1E6jpl/tmpDg42o9 dataset_437.dat" +HWI-EAS91_1_30788AAXX:1:1:1570:620/1 4 * 0 0 * * 0 0 GAGTAACAAAGTAAAGTTTGGACCGTTTTTGTCTCGTGCTCGTCGCTGCG IIIIIII""IIIIIIIIIIIIIBIIIIIIIIIIII"IIIIIII000IIII XM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1572:270/1 0 phiX3 1208 255 50M * 0 0 TGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTA IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1572:324/1 4 * 0 0 * * 0 0 AAGGTGCTTAAATTCGTGGGTCCTGAGCTGGCGACCCTGTTTTGTATGGC IIIIIII""IIIIIIIIIIIIIIIIIIII+7I05I"IIIIIII000IIII XM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1578:331/1 0 phiX1 209 255 50M * 0 0 TGTCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGC IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1582:633/1 0 phiX2 397 255 50M * 0 0 CCGCTTCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGACTTCTACCAC IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1598:534/1 0 phiX2 597 255 50M * 0 0 GCGCTCTAATCTCTGGGCATCTGGCTATGATGTTGATGGAACTGACCAAA IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1599:330/1 0 phiX1 803 255 50M * 0 0 AGAAGAAAACGTGCGTCAAAAATTACGTGCAGAAGGAGTGATGTAATGTC IIIIIII""IIIIIIIIIIIIIIIIIII<III@II"IIIIIII000IIII XA:i:0 MD:Z:30G19 NM:i:1 +HWI-EAS91_1_30788AAXX:1:1:1616:363/1 0 phiX3 408 255 50M * 0 0 TGTTTATCCTTTGAATGGTCGCCATGATGGTGGTTATTATACCGTCAAGG IIIIIII""IIIIIIIIIIIIIIIIIIIIIIDIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1629:446/1 4 * 0 0 * * 0 0 AGGTTATAACGCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGT IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII XM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1634:330/1 0 phiX4 778 255 50M * 0 0 GGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATG IIIIIII""IIIIIIIIIIIIIIIIIIIIIII8II"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1647:512/1 0 phiX1 401 255 50M * 0 0 TACTGAACAATCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAAGCTCA IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1652:270/1 4 * 0 0 * * 0 0 AGCGTAAAGGCGCTCGTCTTTGGTATGTAGGACTTTGCATTGTTTAATTG IIIIIII""IIIIIIIIIIIIIIIIIIIIIII6II"IIIIIII000IIII XM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1673:514/1 0 phiX4 378 255 50M * 0 0 ATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTATTGAGGCT IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIII1"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1746:351/1 0 phiX2 98 255 50M * 0 0 CTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAAGGATGGT IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1749:466/1 0 phiX2 1081 255 50M * 0 0 TTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTTATCGCAATCT IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1761:343/1 0 phiX1 5 255 50M * 0 0 TTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGA IIIIIII""IIIIIIIIIII?I0IIIIHIIIGIIIII0II?I""IIIIII XA:i:0 MD:Z:50 NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1763:587/1 0 phiX3 191 255 50M * 0 0 AAGCTACATCGTCAACGTTATATTTTGATAGTTTGACGGTTAATGCTGGT IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1768:715/1 0 phiX3 808 255 50M * 0 0 ACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTGGTGCTATGGCTAAAGCT IIIIIII""IIIIIIIIIIIIIDIIIIIIIIIIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1785:1272/1 0 phiX4 178 255 50M * 0 0 TATTTTTCATGGTATTGATAAAGCTGTTGCCGATACTTGGAACAATTTCT III""""""IIIIIIIII""FI"IIII""II+ICI"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/picard_input_bait.bed Mon Feb 17 00:02:22 2014 -0500 @@ -0,0 +1,8 @@ +chr1 1 300 - CCDS635.1_cds_0_0_chr1_67052401_r +chr2 1 300 - CCDS635.1_cds_1_0_chr1_67060632_r +chr3 1 300 - CCDS635.1_cds_2_0_chr1_67065091_r +chr4 1 300 - CCDS635.1_cds_3_0_chr1_67066083_r +chr5 1 300 - CCDS635.1_cds_4_0_chr1_67071856_r +chr6 1 300 - CCDS635.1_cds_5_0_chr1_67072262_r +chr7 1 300 - CCDS635.1_cds_6_0_chr1_67073897_r +chr8 1 300 - CCDS635.1_cds_7_0_chr1_67075981_r
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/picard_input_hg18.trimmed.fasta Mon Feb 17 00:02:22 2014 -0500 @@ -0,0 +1,302 @@ +>chrM +GATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTT +CGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTC +GCAGTATCTGTCTTTGATTCCTGCCTCATTCTATTATTTATCGCACCTACGTTCAATATT +ACAGGCGAACATACCTACTAAAGTGTGTTAATTAATTAATGCTTGTAGGACATAATAATA +ACAATTGAATGTCTGCACAGCCGCTTTCCACACAGACATCATAACAAAAAATTTCCACCA +AACCCCCCCCTCCCCCCGCTTCTGGCCACAGCACTTAAACACATCTCTGCCAAACCCCAA +AAACAAAGAACCCTAACACCAGCCTAACCAGATTTCAAATTTTATCTTTAGGCGGTATGC +ACTTTTAACAGTCACCCCCCAACTAACACATTATTTTCCCCTCCCACTCCCATACTACTA +ATCTCATCAATACAACCCCCGCCCATCCTACCCAGCACACACACACCGCTGCTAACCCCA +TACCCCGAACCAACCAAACCCCAAAGACACCCCCCACAGTTTATGTAGCTTACCTCCTCA +AAGCAATACACTGAAAATGTTTAGACGGGCTCACATCACCCCATAAACAAATAGGTTTGG +TCCTAGCCTTTCTATTAGCTCTTAGTAAGATTACACATGCAAGCATCCCCGTTCCAGTGA +GTTCACCCTCTAAATCACCACGATCAAAAGGGACAAGCATCAAGCACGCAGCAATGCAGC +TCAAAACGCTTAGCCTAGCCACACCCCCACGGGAAACAGCAGTGATTAACCTTTAGCAAT +>chr1 +AAACGAAAGTTTAACTAAGCTATACTAACCCCAGGGTTGGTCAATTTCGTGCCAGCCACC +GCGGTCACACGATTAACCCAAGTCAATAGAAGCCGGCGTAAAGAGTGTTTTAGATCACCC +CCTCCCCAATAAAGCTAAAACTCACCTGAGTTGTAAAAAACTCCAGTTGACACAAAATAG +ACTACGAAAGTGGCTTTAACATATCTGAACACACAATAGCTAAGACCCAAACTGGGATTA +GATACCCCACTATGCTTAGCCCTAAACCTCAACAGTTAAATCAACAAAACTGCTCGCCAG +AACACTACGAGCCACAGCTTAAAACTCAAAGGACCTGGCGGTGCTTCATATCCCTCTAGA +GGAGCCTGTTCTGTAATCGATAAACCCCGATCAACCTCACCACCTCTTGCTCAGCCTATA +TACCGCCATCTTCAGCAAACCCTGATGAAGGCTACAAAGTAAGCGCAAGTACCCACGTAA +AGACGTTAGGTCAAGGTGTAGCCCATGAGGTGGCAAGAAATGGGCTACATTTTCTACCCC +AGAAAACTACGATAGCCCTTATGAAACTTAAGGGTCGAAGGTGGATTTAGCAGTAAACTG +AGAGTAGAGTGCTTAGTTGAACAGGGCCCTGAAGCGCGTACACACCGCCCGTCACCCTCC +>chr2 +TCAAGTATACTTCAAAGGACATTTAACTAAAACCCCTACGCATTTATATAGAGGAGACAA +GTCGTAACATGGTAAGTGTACTGGAAAGTGCACTTGGACGAACCAGAGTGTAGCTTAACA +CAAAGCACCCAACTTACACTTAGGAGATTTCAACTTAACTTGACCGCTCTGAGCTAAACC +TAGCCCCAAACCCACTCCACCTTACTACCAGACAACCTTAGCCAAACCATTTACCCAAAT +AAAGTATAGGCGATAGAAATTGAAACCTGGCGCAATAGATATAGTACCGCAAGGGAAAGA +TGAAAAATTATAACCAAGCATAATATAGCAAGGACTAACCCCTATACCTTCTGCATAATG +AATTAACTAGAAATAACTTTGCAAGGAGAGCCAAAGCTAAGACCCCCGAAACCAGACGAG +CTACCTAAGAACAGCTAAAAGAGCACACCCGTCTATGTAGCAAAATAGTGGGAAGATTTA +TAGGTAGAGGCGACAAACCTACCGAGCCTGGTGATAGCTGGTTGTCCAAGATAGAATCTT +>chr3 +AGTTCAACTTTAAATTTGCCCACAGAACCCTCTAAATCCCCTTGTAAATTTAACTGTTAG +TCCAAAGAGGAACAGCTCTTTGGACACTAGGAAAAAACCTTGTAGAGAGAGTAAAAAATT +TAACACCCATAGTAGGCCTAAAAGCAGCCACCAATTAAGAAAGCGTTCAAGCTCAACACC +CACTACCTAAAAAATCCCAAACATATAACTGAACTCCTCACACCCAATTGGACCAATCTA +TCACCCTATAGAAGAACTAATGTTAGTATAAGTAACATGAAAACATTCTCCTCCGCATAA +GCCTGCGTCAGATCAAAACACTGAACTGACAATTAACAGCCCAATATCTACAATCAACCA +ACAAGTCATTATTACCCTCACTGTCAACCCAACACAGGCATGCTCATAAGGAAAGGTTAA +AAAAAGTAAAAGGAACTCGGCAAACCTTACCCCGCCTGTTTACCAAAAACATCACCTCTA +GCATCACCAGTATTAGAGGCACCGCCTGCCCAGTGACACATGTTTAACGGCCGCGGTACC +CTAACCGTGCAaaggtagcataatcacttgttccttaaatagggacctgtatgaatggct +ccacgagggttcagctgtctcttacttttaaccagtgaaattgacctgcccgtgaagagg +cgggcatgacacagcaagacgagaagaccctatggagctttaatttaTTAATGCAAACAG +TACCTAACAAACCCACAGGTCCTAAACTACCAAACCTGCATTAAAAATTTCGGTTGGGGC +GACCTCGGAGCAGAACCCAACCTCCGAGCAGTACATGCTAAGACTTCACCAGTCAAAGCG +AACTACTATACTCAATTGATCCAATAACTTGACCAACGGAACAAGTTACCCTAGGGATAA +CAGCGCAATCCTATTCTAGAGTCCATATCAACAATAGGGTTTACGACCTCGATGTTGGAT +CAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCT +ACGTGATCTGAGTTCAGACCGGAGTAATCCAGGTCGGTTTCTATCTACTTCAAATTCCTC +CCTGTACGAAAGGACAAGAGAAATAAGGCCTACTTCACAAAGCGCCTTCCCCCGTAAATG +ATATCATCTCAACTTAGTATTATACCCACACCCACCCAAGAACAGGGTTTgttaagatgg +cagagcccggtaatcgcataaaacttaaaactttacagtcagaggttcaattcctcttct +taacaacaTACCCATGGCCAACCTCCTACTCCTCATTGTACCCATTCTAATCGCAATGGC +ATTCCTAATGCTTACCGAACGAAAAATTCTAGGCTATATACAACTACGCAAAGGCCCCAA +CGTTGTAGGCCCCTACGGGCTACTACAACCCTTCGCTGACGCCATAAAACTCTTCACCAA +AGAGCCCCTAAAACCCGCCACATCTACCATCACCCTCTACATCACCGCCCCGACCTTAGC +TCTCACCATCGCTCTTCTACTATGAACCCCCCTCCCCATACCCAACCCCCTGGTCAACCT +CAACCTAGGCCTCCTATTTATTCTAGCCACCTCTAGCCTAGCCGTTTACTCAATCCTCTG +>chr4 +ATCAGGGTGAGCATCAAACTCAAACTACGCCCTGATCGGCGCACTGCGAGCAGTAGCCCA +AACAATCTCATATGAAGTCACCCTAGCCATCATTCTACTATCAACATTACTAATAAGTGG +CTCCTTTAACCTCTCCACCCTTATCACAACACAAGAACACCTCTGATTACTCCTGCCATC +ATGACCCTTGGCCATAATATGATTTATCTCCACACTAGCAGAGACCAACCGAACCCCCTT +CGACCTTGCCGAAGGGGAGTCCGAACTAGTCTCAGGCTTCAACATCGAATACGCCGCAGG +CCCCTTCGCCCTATTCTTCATAGCCGAATACACAAACATTATTATAATAAACACCCTCAC +CACTACAATCTTCCTAGGAACAACATATGACGCACTCTCCCCTGAACTCTACACAACATA +TTTTGTCACCAAGACCCTACTTCTAACCTCCCTGTTCTTATGAATTCGAACAGCATACCC +CCGATTCCGCTACGACCAACTCATACACCTCCTATGAAAAAACTTCCTACCACTCACCCT +AGCATTACTTATATGATATGTCTCCATACCCATTACAATCTCCAGCATTCCCCCTCAAAC +CTAAGAAATATGTCTGATAAAAGAGTTACTTTGATAGAGTAAATAATAGGAGCTTAAACC +CCCTTATTTctaggactatgagaatcgaacccatccctgagaatccaaaattctccgtgc +cacctatcacaccccatcctaAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCC +GAAAATGTTGGTTATACCCTTCCCGTACTAATTAATCCCCTGGCCCAACCCGTCATCTAC +TCTACCATCTTTGCAGGCACACTCATCACAGCGCTAAGCTCGCACTGATTTTTTACCTGA +GTAGGCCTAGAAATAAACATGCTAGCTTTTATTCCAGTTCTAACCAAAAAAATAAACCCT +CGTTCCACAGAAGCTGCCATCAAGTATTTCCTCACGCAAGCAACCGCATCCATAATCCTT +CTAATAGCTATCCTCTTCAACAATATACTCTCCGGACAATGAACCATAACCAATACTACC +AATCAATACTCATCATTAATAATCATAATGGCTATAGCAATAAAACTAGGAATAGCCCCC +TTTCACTTCTGAGTCCCAGAGGTTACCCAAGGCACCCCTCTGACATCCGGCCTGCTTCTT +CTCACATGACAAAAACTAGCCCCCATCTCAATCATATACCAAATCTCTCCCTCACTAAAC +GTAAGCCTTCTCCTCACTCTCTCAATCTTATCCATCATAGCAGGCAGTTGAGGTGGATTA +AACCAAACCCAGCTACGCAAAATCTTAGCATACTCCTCAATTACCCACATAGGATGAATA +ATAGCAGTTCTACCGTACAACCCTAACATAACCATTCTTAATTTAACTATTTATATTATC +CTAACTACTACCGCATTCCTACTACTCAACTTAAACTCCAGCACCACGACCCTACTACTA +TCTCGCACCTGAAACAAGCTAACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCC +CTAGGAGGCCTGCCCCCGCTAACCGGCTTTTTGCCCAAATGGGCCATTATCGAAGAATTC +ACAAAAAACAATAGCCTCATCATCCCCACCATCATAGCCACCATCACCCTCCTTAACCTC +TACTTCTACCTACGCCTAATCTACTCCACCTCAATCACACTACTCCCCATATCTAACAAC +>chr5 +GTAAAAATAAAATGACAGTTTGAACATACAAAACCCACCCCATTCCTCCCCACACTCATC +GCCCTTACCACGCTACTCCTACCTATCTCCCCTTTTATACTAATAATCTTATAGAAATTT +AGGTTAAATACAGACCAAGAGCCTTCAAAGCCCTCAGTAAGTTGCAATACTTAATTTCTG +CAACAGCTAAGGACTGCAAAACCCCACTCTGCATCAACTGAACGCAAATCAGCCACTTTA +ATTAAGCTAAGCCCTTACTAGACCAATGGGACTTAAACCCACAAACACTTAGTTAACAGC +TAAGCACCCTAATCAACTGGCTTCAATCTACTTCTCCCGCCGCCGGGAAAAAAGGCGGGA +GAAGCCCCGGCAGGTTTGAAGCTGCTTCTTCGAATTTGCAATTCAATATGAAAATCACCT +CGGAGCTGGTAAAAAGAGGCCTAACCCCTGTCTTTAGATTTACAGTCCAATGCTTCACTC +AGCCATTTTACCTCACCCCCACTGATGTTCGCCGACCGTTGACTATTCTCTACAAACCAC +AAAGACATTGGAACACTATACCTATTATTCGGCGCATGAGCTGGAGTCCTAGGCACAGCT +CTAAGCCTCCTTATTCGAGCCGAGCTGGGCCAGCCAGGCAACCTTCTAGGTAACGACCAC +ATCTACAACGTTATCGTCACAGCCCATGCATTTGTAATAATCTTCTTCATAGTAATACCC +ATCATAATCGGAGGCTTTGGCAACTGACTAGTTCCCCTAATAATCGGTGCCCCCGATATG +GCGTTTCCCCGCATAAACAACATAAGCTTCTGACTCTTACCTCCCTCTCTCCTACTCCTG +CTCGCATCTGCTATAGTGGAGGCCGGAGCAGGAACAGGTTGAACAGTCTACCCTCCCTTA +GCAGGGAACTACTCCCACCCTGGAGCCTCCGTAGACCTAACCATCTTCTCCTTACACCTA +GCAGGTGTCTCCTCTATCTTAGGGGCCATCAATTTCATCACAACAATTATCAATATAAAA +CCCCCTGCCATAACCCAATACCAAACGCCCCTCTTCGTCTGATCCGTCCTAATCACAGCA +GTCCTACTTCTCCTATCTCTCCCAGTCCTAGCTGCTGGCATCACTATACTACTAACAGAC +CGCAACCTCAACACCACCTTCTTCGACCCCGCCGGAGGAGGAGACCCCATTCTATACCAA +CACCTATTCTGATTTTTCGGTCACCCTGAAGTTTATATTCTTATCCTACCAGGCTTCGGA +ATAATCTCCCATATTGTAACTTACTACTCCGGAAAAAAAGAACCATTTGGATACATAGGT +ATGGTCTGAGCTATGATATCAATTGGCTTCCTAGGGTTTATCGTGTGAGCACACCATATA +>chr6 +TTTACAGTAGGAATAGACGTAGACACACGAGCATATTTCACCTCCGCTACCATAATCATC +GCTATCCCCACCGGCGTCAAAGTATTTAGCTGACTCGCCACACTCCACGGAAGCAATATG +AAATGATCTGCTGCAGTGCTCTGAGCCCTAGGATTCATCTTTCTTTTCACCGTAGGTGGC +CTGACTGGCATTGTATTAGCAAACTCATCACTAGACATCGTACTACACGACACGTACTAC +GTTGTAGCTCACTTCCACTATGTCCTATCAATAGGAGCTGTATTTGCCATCATAGGAGGC +TTCATTCACTGATTTCCCCTATTCTCAGGCTACACCCTAGACCAAACCTACGCCAAAATC +CATTTCACTATCATATTCATCGGCGTAAATCTAACTTTCTTCCCACAACACTTTCTCGGC +CTATCCGGAATGCCCCGACGTTACTCGGACTACCCCGATGCATACACCACATGAAACATC +CTATCATCTGTAGGCTCATTCATTTCTCTAACAGCAGTAATATTAATAATTTTCATGATT +TGAGAAGCCTTCGCTTCGAAGCGAAAAGTCCTAATAGTAGAAGAACCCTCCATAAACCTG +GAGTGACTATATGGATGCCCCCCACCCTACCACACATTCGAAGAACCCGTATACATAAAA +TCTAGACAaaaaaggaaggaatcgaaccccccaaagctggtttcaagccaaccccatggc +ctccatgactttttcAAAAAGGTATTAGAAAAACCATTTCATAACTTTGTCAAAGTTAAA +TTATAGGCTAAATCCTATATATCTTAATGGCACATGCAGCGCAAGTAGGTCTACAAGACG +CTACTTCCCCTATCATAGAAGAGCTTATCACCTTTCATGATCACGCCCTCATAATCATTT +TCCTTATCTGCTTCCTAGTCCTGTATGCCCTTTTCCTAACACTCACAACAAAACTAACTA +ATACTAACATCTCAGACGCTCAGGAAATAGAAACCGTCTGAACTATCCTGCCCGCCATCA +TCCTAGTCCTCATCGCCCTCCCATCCCTACGCATCCTTTACATAACAGACGAGGTCAACG +ATCCCTCCCTTACCATCAAATCAATTGGCCACCAATGGTACTGAACCTACGAGTACACCG +ACTACGGCGGACTAATCTTCAACTCCTACATACTTCCCCCATTATTCCTAGAACCAGGCG +>chr7 +ACCTGCGACTCCTTGACGTTGACAATCGAGTAGTACTCCCGATTGAAGCCCCCATTCGTA +TAATAATTACATCACAAGACGTCTTGCACTCATGAGCTGTCCCCACATTAGGCTTAAAAA +CAGATGCAATTCCCGGACGTCTAAACCAAACCACTTTCACCGCTACACGACCGGGGGTAT +ACTACGGTCAATGCTCTGAAATCTGTGGAGCAAACCACAGTTTCATGCCCATCGTCCTAG +AATTAATTCCCCTAAAAATCTTTGAAATAGGGCCCGTATTTACCCTATAGCACCCCCTCT +ACCCCCTCTAGAGCCCACTGTAAAGCTAACTTAGCATTAACCTTTTAAGTTAAAGATTAA +GAGAACCAACACCTCTTTACAGTGAAATGCCCCAACTAAATACTACCGTATGGCCCACCA +TAATTACCCCCATACTCCTTACACTATTCCTCATCACCCAACTAAAAATATTAAACACAA +ACTACCACCTACCTCCCTCACCAAAGCCCATAAAAATAAAAAATTATAACAAACCCTGAG +AACCAAAATGAACGAAAATCTGTTCGCTTCATTCATTGCCCCCACAATCCTAGGCCTACC +CGCCGCAGTACTGATCATTCTATTTCCCCCTCTATTGATCCCCACCTCCAAATATCTCAT +>chr8 +CAACAACCGACTAATCACCACCCAACAATGACTAATCAAACTAACCTCAAAACAAATGAT +AGCCATACACAACACTAAAGGACGAACCTGATCTCTTATACTAGTATCCTTAATCATTTT +TATTGCCACAACTAACCTCCTCGGACTCCTGCCTCACTCATTTACACCAACCACCCAACT +ATCTATAAACCTAGCCATGGCCATCCCCTTATGAGCGGGCGCAGTGATTATAGGCTTTCG +CTCTAAGATTAAAAATGCCCTAGCCCACTTCTTACCACAAGGCACACCTACACCCCTTAT +CCCCATACTAGTTATTATCGAAACCATCAGCCTACTCATTCAACCAATAGCCCTGGCCGT +ACGCCTAACCGCTAACATTACTGCAGGCCACCTACTCATGCACCTAATTGGAAGCGCCAC +CCTAGCAATATCAACCATTAACCTTCCCTCTACACTTATCATCTTCACAATTCTAATTCT +ACTGACTATCCTAGAAATCGCTGTCGCCTTAATCCAAGCCTACGTTTTCACACTTCTAGT +AAGCCTCTACCTGCACGACAACACATAATGACCCACCAATCACATGCCTATCATATAGTA +AAACCCAGCCCATGACCCCTAACAGGGGCCCTCTCAGCCCTCCTAATGACCTCCGGCCTA +GCCATGTGATTTCACTTCCACTCCATAACGCTCCTCATACTAGGCCTACTAACCAACACA +CTAACCATATACCAATGGTGGCGCGATGTAACACGAGAAAGCACATACCAAGGCCACCAC +ACACCACCTGTCCAAAAAGGCCTTCGATACGGGATAATCCTATTTATTACCTCAGAAGTT +TTTTTCTTCGCAGGATTTTTCTGAGCCTTTTACCACTCCAGCCTAGCCCCTACCCCCCAA +CTAGGAGGGCACTGGCCCCCAACAGGCATCACCCCGCTAAATCCCCTAGAAGTCCCACTC +CTAAACACATCCGTATTACTCGCATCAGGAGTATCAATCACCTGAGCTCACCATAGTCTA +ATAGAAAACAACCGAAACCAAATAATTCAAGCACTGCTTATTACAATTTTACTGGGTCTC +TATTTTACCCTCCTACAAGCCTCAGAGTACTTCGAGTCTCCCTTCACCATTTCCGACGGC +>chr9 +ATCTACGGCTCAACATTTTTTGTAGCCACAGGCTTCCACGGACTTCACGTCATTATTGGC +TCAACTTTCCTCACTATCTGCTTCATCCGCCAACTAATATTTCACTTTACATCCAAACAT +CACTTTGGCTTCGAAGCCGCCGCCTGATACTGGCATTTTGTAGATGTGGTTTGACTATTT +CTGTATGTCTCCATCTATTGATGAGGGTCTTACTCTTTTAGTATAAATAGTACCGTTAAC +TTCCAATTAACTAGTTTTGACAACATTCAAAAAAGAGTAATAAACTTCGCCTTAATTTTA +ATAATCAACACCCTCCTAGCCTTACTACTAATAATTATTACATTTTGACTACCACAACTC +AACGGCTACATAGAAAAATCCACCCCTTACGAGTGCGGCTTCGACCCTATATCCCCCGCC +CGCGTCCCTTTCTCCATAAAATTCTTCTTAGTAGCTATTACCTTCTTATTATTTGATCTA +GAAATTGCCCTCCTTTTACCCCTACCATGAGCCCTACAAACAACTAACCTGCCACTAATA +GTTATGTCATCCCTCTTATTAATCATCATCCTAGCCCTAAGTCTGGCCTATGAGTGACTA +CAAAAAGGATTAGACTGAGCCGAATTGGTATATAGTTTAAACAAAACGAATGATTTCGAC +TCATTAAATTATGATAATCATATTTACCAAATGCCCCTCATTTACATAAATATTATACTA +GCATTTACCATCTCACTTCTAGGAATACTAGTATATCGCTCACACCTCATATCCTCCCTA +CTATGCCTAGAAGGAATAATACTATCGCTGTTCATTATAGCTACTCTCATAACCCTCAAC +ACCCACTCCCTCTTAGCCAATATTGTGCCTATTGCCATACTAGTCTTTGCCGCCTGCGAA +GCAGCGGTGGGCCTAGCCCTACTAGTCTCAATCTCCAACACATATGGCCTAGACTACGTA +CATAACCTAAACCTACTCCAATGCTAAAACTAATCGTCCCAACAATTATATTACTACCAC +TGACATGACTTTCCAAAAAGCACATAATTTGAATCAACACAACCACCCACAGCCTAATTA +>chr10 +TTAGCATCATCCCCCTACTATTTTTTAACCAAATCAACAACAACCTATTTAGCTGTTCCC +CAACCTTTTCCTCCGACCCCCTAACAACCCCCCTCCTAATACTAACTACCTGACTCCTAC +CCCTCACAATCATGGCAAGCCAACGCCACTTATCCAGCGAACCACTATCACGAAAAAAAC +TCTACCTCTCTATACTAATCTCCCTACAAATCTCCTTAATTATAACATTCACAGCCACAG +AACTAATCATATTTTATATCTTCTTCGAAACCACACTTATCCCCACCTTGGCTATCATCA +CCCGATGAGGCAACCAGCCAGAACGCCTGAACGCAGGCACATACTTCCTATTCTACACCC +TAGTAGGCTCCCTTCCCCTACTCATCGCACTAATTTACACTCACAACACCCTAGGCTCAC +TAAACATTCTACTACTCACTCTCACTGCCCAAGAACTATCAAACTCCTGAGCCAACAACT +TAATATGACTAGCTTACACAATAGCTTTTATAGTAAAGATACCTCTTTACGGACTCCACT +TATGACTCCCTAAAGCCCATGTCGAAGCCCCCATCGCTGGGTCAATAGTACTTGCCGCAG +TACTCTTAAAACTAGGCGGCTATGGTATAATACGCCTCACACTCATTCTCAACCCCCTGA +CAAAACACATAGCCTACCCCTTCCTTGTACTATCCCTATGAGGCATAATTATAACAAGCT +CCATCTGCCTACGACAAACAGACCTAAAATCGCTCATTGCATACTCTTCAATCAGCCACA +TAGCCCTCGTAGTAACAGCCATTCTCATCCAAACCCCCTGAAGCTTCACCGGCGCAGTCA +TTCTCATAATCGCCCACGGACTCACATCCTCATTACTATTCTGCCTAGCAAACTCAAACT +ACGAACGCACTCACAGTCGCATCATAATCCTCTCTCAAGGACTTCAAACTCTACTCCCAC +TAATAGCTTTTTGATGACTTCTAGCAAGCCTCGCTAACCTCGCCTTACCCCCCACTATTA +ACCTACTGGGAGAACTCTCTGTGCTAGTAACCACGTTCTCCTGATCAAATATCACTCTCC +TACTTACAGGACTCAACATACTAGTCACAGCCCTATACTCCCTCTACATATTTACCACAA +CACAATGGGGCTCACTCACCCACCACATTAACAACATAAAACCCTCATTCACACGAGAAA +ACACCCTCATGTTCATACACCTATCCCCCATTCTCCTCCTATCCCTCAACCCCGACATCA +TTACCGGGTTTTCCTCTTGTAAATATAGTTTAACCAAAACATCAGATTGTGAATCTGACA +ACAGAGGCTTACGACCCCTTATTTACCGAGAAAGCTCACAAGAACTGCTAACTCATGCCC +CCATGTCTAACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGTCTTA +GGCCCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAACCATGCACACTACTATAAC +CACCCTAACCCTGACTTCCCTAATTCCCCCCATCCTTACCACCCTCGTTAACCCTAACAA +AAAAAACTCATACCCCCATTATGTAAAATCCATTGTCGCATCCACCTTTATTATCAGTCT +CTTCCCCACAACAATATTCATGTGCCTAGACCAAGAAGTTATTATCTCGAACTGACACTG +AGCCACAACCCAAACAACCCAGCTCTCCCTAAGCTTCAAACTAGACTACTTCTCCATAAT +ATTCATCCCTGTAGCATTGTTCGTTACATGGTCCATCATAGAATTCTCACTGTGATATAT +AAACTCAGACCCAAACATTAATCAGTTCTTCAAATATCTACTCATTTTCCTAATTACCAT +>chr11 +ACTAATCTTAGTTACCGCTAACAACCTATTCCAACTGTTCATCGGCTGAGAGGGCGTAGG +AATTATATCCTTCTTGCTCATCAGTTGATGATACGCCCGAGCAGATGCCAACACAGCAGC +CATTCAAGCAGTCCTATACAACCGTATCGGCGATATCGGTTTCATCCTCGCCTTAGCATG +ATTTATCCTACACTCCAACTCATGAGACCCACAACAAATAGCCCTTCTAAACGCTAATCC +AAGCCTCACCCCACTACTAGGCCTCCTCCTAGCAGCAGCAGGCAAATCAGCCCAATTAGG +TCTCCACCCCTGACTCCCCTCAGCCATAGAAGGCCCCACCCCAGTCTCAGCCCTACTCCA +CTCAAGCACTATAGTTGTAGCAGGAATCTTCTTACTCATCCGCTTCCACCCCCTAGCAGA +AAATAGCCCACTAATCCAAACTCTAACACTATGCTTAGGCGCTATCACCACTCTGTTCGC +AGCAGTCTGCGCCCTTACACAAAATGACATCAAAAAAATCGTAGCCTTCTCCACTTCAAG +TCAACTAGGACTCATAATAGTTACAATCGGCATCAACCAACCACACCTAGCATTCCTGCA +CATCTGTACCCACGCCTTCTTCAAAGCCATACTATTTATGTGCTCCGGGTCCATCATCCA +CAACCTTAACAATGAACAAGATATTCGAAAAATAGGAGGACTACTCAAAACCATACCTCT +CACTTCAACCTCCCTCACCATTGGCAGCCTAGCATTAGCAGGAATACCTTTCCTCACAGG +TTTCTACTCCAAAGACCACATCATCGAAACCGCAAACATATCATACACAAACGCCTGAGC +CCTATCTATTACTCTCATCGCTACCTCCCTGACAAGCGCCTATAGCACTCGAATAATTCT +TCTCACCCTAACAGGTCAACCTCGCTTCCCCACCCTTACTAACATTAACGAAAATAACCC +CACCCTACTAAACCCCATTAAACGCCTGGCAGCCGGAAGCCTATTCGCAGGATTTCTCAT +TACTAACAACATTTCCCCCGCATCCCCCTTCCAAACAACAATCCCCCTCTACCTAAAACT +>chr12 +CACAGCCCTCGCTGTCACTTTCCTAGGACTTCTAACAGCCCTAGACCTCAACTACCTAAC +CAACAAACTTAAAATAAAATCCCCACTATGCACATTTTATTTCTCCAACATACTCGGATT +CTACCCTAGCATCACACACCGCACAATCCCCTATCTAGGCCTTCTTACGAGCCAAAACCT +GCCCCTACTCCTCCTAGACCTAACCTGACTAGAAAAGCTATTACCTAAAACAATTTCACA +GCACCAAATCTCCACCTCCATCATCACCTCAACCCAAAAAGGCATAATTAAACTTTACTT +CCTCTCTTTCTTCTTCCCACTCATCCTAACCCTACTCCTAATCACATAACCTATTCCCCC +GAGCAATCTCAATTACAATATATACACCAACAAACAATGTTCAACCAGTAACCACTACTA +ATCAACGCCCATAATCATACAAAGCCCCCGCACCAATAGGATCCTCCCGAATCAACCCTG +ACCCCTCTCCTTCATAAATTATTCAGCTTCCTACACTATTAAAGTTTACCACAACCACCA +CCCCATCATACTCTTTCACCCACAGCACCAATCCTACCTCCATCGCTAACCCCACTAAAA +CACTCACCAAGACCTCAACCCCTGACCCCCATGCCTCAGGATACTCCTCAATAGCCATCG +CTGTAGTATATCCAAAGACAACCATCATTCCCCCTAAATAAATTAAAAAAACTATTAAAC +CCATATAACCTCCCCCAAAATTCAGAATAATAACACACCCGACCACACCGCTAACAATCA +GTACTAAACCCCCATAAATAGGAGAAGGCTTAGAAGAAAACCCCACAAACCCCATTACTA +AACCCACACTCAACAGAAACAAAGCATACATCATTATTCTCGCACGGACTACAACCACGA +CCAATGATATGAAAAACCATCGTTGTATTTCAACTACAAGAACACCAATGACCCCAATAC +GCAAAATTAACCCCCTAATAAAATTAATTAACCACTCATTCATCGACCTCCCCACCCCAT +CCAACATCTCCGCATGATGAAACTTCGGCTCACTCCTTGGCGCCTGCCTGATCCTCCAAA +TCACCACAGGACTATTCCTAGCCATACACTACTCACCAGACGCCTCAACCGCCTTTTCAT +CAATCGCCCACATCACTCGAGACGTAAATTATGGCTGAATCATCCGCTACCTTCACGCCA +ATGGCGCCTCAATATTCTTTATCTGCCTCTTCCTACACATCGGGCGAGGCCTATATTACG +GATCATTTCTCTACTCAGAAACCTGAAACATCGGCATTATCCTCCTGCTTGCAACTATAG +CAACAGCCTTCATAGGCTATGTCCTCCCGTGAGGCCAAATATCATTCTGAGGGGCCACAG +TAATTACAAACTTACTATCCGCCATCCCATACATTGGGACAGACCTAGTTCAATGAATCT +GAGGAGGCTACTCAGTAGACAGTCCCACCCTCACACGATTCTTTACCTTTCACTTCATCT +TACCCTTCATTATTGCAGCCCTAGCAGCACTCCACCTCCTATTCTTGCACGAAACGGGAT +CAAACAACCCCCTAGGAATCACCTCCCATTCCGATAAAATCACCTTCCACCCTTACTACA +CAATCAAAGACGCCCTCGGCTTACTTCTCTTCCTTCTCTCCTTAATGACATTAACACTAT +TCTCACCAGACCTCCTAGGCGACCCAGACAATTATACCCTAGCCAACCCCTTAAACACCC +CTCCCCACATCAAGCCCGAATGATATTTCCTATTCGCCTACACAATTCTCCGATCCGTCC +CTAACAAACTAGGAGGCGTCCTTGCCCTATTACTATCCATCCTCATCCTAGCAATAATCC +CCATCCTCCATATATCCAAACAACAAAGCATAATATTTCGCCCACTAAGCCAATCACTTT +ATTGACTCCTAGCCGCAGACCTCCTCATTCTAACCTGAATCGGAGGACAACCAGTAAGCT +>chr13 +ACCCTTTTACCATCATTGGACAAGTAGCATCCGTACTATACTTCACAACAATCCTAATCC +TAATACCAACTATCTCCCTAATTGAAAACAAAATACTCAAATGGGCCTGTCCTTGTAGTA +TAAACTAATACACCAGTCTTGTAAACCGGAGACGAAAACCTTTTTCCAAGGACAAATCAG +AGAAAAAGTCTTTAACTCCACCATTAGCACCCAAAGCTAAGATTCTAATTTAAACTATTC +TCTGTTCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAAC +AACCGCTATGTATTTCGTACATTACTGCCAGCCACCATGAATATTGTACGGTACCATAAA +TACTTGACCACCTGTAGTACATAAAAACCCAACCCACATCAAACCCCCCCCCCCCATGCT +TACAAGCAAGTACAGCAATCAACCTTCAACTATCACACATCAACTGCAACTCCAAAGCCA +CCCCTCACCCACTAGGATACCAACAAACCTACCCACCCTTAACAGTACATAGTACATAAA +GTCATTTACCGTACATAGCACATTACAGTCAAATCCCTTCTCGTCCCCATGGATGACCCC +CCTCAGATAGGGGTCCCTTGACCACCATCCTCCGTGAAATCAATATCCCGCACAAGAGTG +CTACTCTCCTCGCTCCGGGCCCATAACACTTGGGGGTAGCTAAAGTGAACTGTATCCGAC +ATCTGGTTCCTACTTCAGGGCCATAAAGCCTAAATAGCCCACACGTTCCCCTTAAATAAG +ACATCACGATG +>chr20 +NNNNNNNNNNNNNNNNNNNNGATCCAgaggtggaagaggaaggaagcttggaaccctata +gagttgctgagtgccaggaccagatcctggccctaaacaggtggtaaggaaggagagagt +gaaggaactgccaggtgacacactcccaccatggacctctgggatcctagctttaagaga +tcccatcacccacatgaacgtttgaattgacagggggagctgcctggagagtaggcagat +gcagagctcaagcctgtgcagagcccaggttttgtgagtgggacagttgcagcaaaacac +aaccataggtgcccatccaccaaggcaggctctccatcttgctcagagtggctctagccc +ttgctgactgctgggcagggagagagcagagctaacttcctcatgggacctgggtgtgtc +tgatctgtgcacaccactatccaaccgatcccgaggctccaccctggccactcttgtgtg +cacacagcacagcctctactgctacacctgagtactttgccagtggcctggaagcacttt +gtcccccctggcacaaatggtgctggaccacgaggggccagagaacaaagccttgggcgt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/picard_input_sorted_pair.bam Mon Feb 17 00:02:22 2014 -0500 @@ -0,0 +1,10 @@ +bar:record:1 77 chr1 10 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg1 +bar:record:1 141 chr1 20 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1 +bar:record:2 77 chr2 10 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg1 +bar:record:2 141 chr2 30 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1 +bar:record:3 77 chr1 10 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg1 +bar:record:3 141 chr3 20 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1 +bar:record:4 77 chr1 1 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg1 +bar:record:4 141 chr1 40 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1 +bar:record:5 77 chr1 40 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg1 +bar:record:5 141 chr3 40 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/picard_input_sorted_pair.sam Mon Feb 17 00:02:22 2014 -0500 @@ -0,0 +1,15 @@ +@HD VN:1.0 SO:coordinate +@SQ SN:chr1 LN:10001 +@SQ SN:chr2 LN:10001 +@SQ SN:chr3 LN:10001 +@RG ID:rg1 SM:Z +bar:record:1 77 chr1 10 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg1 +bar:record:1 141 chr1 20 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1 +bar:record:2 77 chr1 40 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg1 +bar:record:2 141 chr1 50 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1 +bar:record:3 77 chr2 10 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg1 +bar:record:3 141 chr2 20 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1 +bar:record:4 77 chr2 50 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg1 +bar:record:4 141 chr2 60 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1 +bar:record:5 77 chr3 40 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg1 +bar:record:5 141 chr3 50 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/picard_input_summary_alignment_stats.sam Mon Feb 17 00:02:22 2014 -0500 @@ -0,0 +1,28 @@ +@HD VN:1.0 SO:coordinate +@SQ SN:chr1 LN:255 +@SQ SN:chr2 LN:255 +@SQ SN:chr3 LN:255 +@SQ SN:chr4 LN:255 +@SQ SN:chr5 LN:255 +@SQ SN:chr6 LN:255 +@SQ SN:chr7 LN:255 +@SQ SN:chr8 LN:255 +@RG ID:0 SM:Hi,Mom! +SL-XAV:1:1:0:764#0/1 89 chr1 1 255 101M * 0 0 TTCATGCTGANGCNCTCTTACGATCGTACAGATGCAAATATTAACANNCNTTNAAGNNCANNNNNNNNNCAATACAATANTAGAGTACGTNAACACTCCAN &/,&-.1/6/&&)&).)/,&0768)&/.,/874,&.4137572)&/&&,&1-&.0/&&*,&&&&&&&&&&18775799,&16:8775-56256/69::;0& RG:Z:0 XN:i:1 +SL-XAV:1:1:0:1668#0/2 153 chr2 1 255 101M * 0 0 CATCTCTACANGCGCGTCCTACCAGACGCGCTTCCGATCTGAGAGCATACTTTTCATTGGATTCCAGCACAACTCCATTTTTGATCCACTNGACACCTTTN (/,'-/'0////(1'&&1&&&&'2''-6/,/3-33653.6:1'.86/-++32.-4864653/5/583/346423203+28888644446688456/4880& RG:Z:0 XN:i:1 +SL-XAV:1:1:0:1914#0/2 153 chr3 1 255 101M * 0 0 CGTATGCGCTNTTTATGTCGCCCACAGTGCCTAGTATAGCCCCTGCTAATAAAAAGAGATGAATACGTTTACTTAAAAAACTGAAACTAGNAATGTGCAAN (0,7&&*/*0*,)10/).-*&.&*/6669.&-337599;3,&,6/.,5::999987893+387020775777547999::668997448:::9;999::0& RG:Z:0 +SL-XAV:1:1:0:1639#0/2 153 chr4 1 255 101M * 0 0 CGTGATACCANCTCATGTTCACAGCCAAAGCCTGAAGCTGTCTATTATATTTCTCAACCATAAACTTTTGCCTCAGGCATCCGCAGAATGNTTTGCAGCCN '.&.&&'.0+01'2(1'(''-)','+0041/.+032;:867115/5267-.0/)-5.&-26200224,,0+0/0275/5605688::646875568882*& RG:Z:0 +SL-XAV:1:1:0:68#0/2 137 chr5 1 255 101M * 0 0 NTCTCATTTANAAATGGTTATAAAAACATTTATGCTGAAAAGGTGAAGTTCATTAATGAACAGGCTGACTGTCTCACTATCGCGTTCGCANGACGTTATCT &1<<999;;;;<<<87579:556972789977444.'.023.&,7621/54.49.)/53055-22--''+(.'-))6-168/(3&&0(<).))*&&&&&'0 RG:Z:0 +SL-XAV:1:1:0:700#0/2 137 chr6 1 255 101M * 0 0 NAATTGTTCTNAGTTTCTCGGTTTATGTGCTCTTCCAGGTGGGTAACACAATAATGGCCTTCCAGATCGTAAGAGCGACGTGTGTTGCACNAGTGTCGATC &0::887::::6/646::838388811/679:87640&./2+/-4/28:3,536/4''&&.78/(/554/./02*)*',-(57()&.6(6:(0601'/(,* RG:Z:0 +SL-XAV:1:1:0:1721#0/1 83 chr7 1 255 101M = 102 40 CAACAGAAGGNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCGAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 +SL-XAV:1:1:0:1721#0/2 163 chr7 102 255 101M = 1 -40 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTCACTATGGTACATCTTGTCGTGCGGCNAGAGCATACA &/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1 RG:Z:0 +SL-XAV:1:1:0:105#0/2 147 chr8 1 255 101M = 102 79 CACATCGTGANTCTTACAATCTGCGGTTTCAGATGTGGAGCGATGTGTGAGAGATTGAGCAACTGATCTGAAAAGCAGACACAGCTATTCNTAAGATGACN /))3--/&*()&)&&+'++.'-&,(.))'4,)&'&&,')8,&&*'.&*0'225/&)3-8//)*,5-*).7851453583.3568526:863688:::85.& RG:Z:0 +SL-XAV:1:1:0:105#0/1 99 chr8 102 255 101M = 1 -79 NCAGGTTCAANTGTGCAGCCCNTTTTGAGAGATNNNNNNNNTGNNCTGNAANANNGACACAGCTATTCCTAAGATGACAAGATCAGANAANAAGTCAAGCA &06665578::41.*/7577/&/77403-324.&&&&&&&&/.&&..&&.0&&&&',:9:/-/(55002020+3'12+2/&.2-&//&),&*&&&&&&&51 RG:Z:0 +SL-XAV:1:1:0:1300#0/1 77 * 0 0 * * 0 0 NAAACACAAGNNANAGTCTTANCNGCTATTCCNNNNNNNNNCTNNNCTNAGNANNACATACAACAGTATCCACACAAGTGTACTCGTNCANACATGTGAAC &*5535)*-,,&.&.*-1)*,&'&)&1&&.,)&&&&&&&&&)0&&&0'&&&&.&&*2'/4''0/**&)&,'-&*,&,&&&.0.&)&&&**&,.&&&')&&) RG:Z:0 +SL-XAV:1:1:0:1300#0/2 141 * 0 0 * * 0 0 NGATCATGGANGACTCTCCCCATCCCCCGCTCCAGCGCTCAGTTATATGCCTAGCCTCGGACACGTCACCAACATCTCACGCACTCTGCANAGTCTCTCAC &&'+''3*&-/)/1'26/*-2-/542-*&-&/'/*/&-'&)-')&.'-/&&2+122*'&+,(/-&)((,/-,,.'2(2'+)/&/&-66-&&/16&)&*&'3 RG:Z:0 +SL-XAV:1:1:0:1639#0/1 101 * 0 0 * chr1 1 0 NCCCTCTCAGNNTNTCTGCCANANCCTTAAGCNNNNNNNNNTANNNCTNAANCNNAAACTTTTGCCTCAGGCATCCGCAGAATGTTTNTCNGCCTATATCG &1::::::64/&/&0:3.280&/&087881,/&&&&&&&&&..&&&..&,,&-&&,265341-)/5680&-.5552-25/322/42/&)&&).421&-&-/ RG:Z:0 +SL-XAV:1:1:0:1668#0/1 101 * 0 0 * chr2 1 0 NATAGCATACNNTNCATTGGANTNCAGCACAANNNNNNNNNTGNNNCANTNNANNCCTTTGAGATCGGAAGAGCGGTTCAGCAGGAANNCNCAGACCGATC &1988998890&0&.8863//&.&.0-2875.&&&&&&&&&.)&&&..&.&&.&&.5782-2+262)&-0-0510*.332-2.-,0*&&*&'.&-2-)0., RG:Z:0 +SL-XAV:1:1:0:1914#0/1 101 * 0 0 * chr3 1 0 NTTTTTCTCCNNCNGTGCCTANTNTAGCCCCTNNNNNNNNNAANNNATNANNANNTTTACTTAAAAAACTGAAACTAGTAATGTGCANNANATCGNAAGAG &0::::<<;90&/&.244760&,&.414798/&&&&&&&&&00&&&0.&/&&-&&.4475687363504.&.557/.*)65.&/*./&&.&.+*)&..).& RG:Z:0 +SL-XAV:1:1:0:68#0/1 581 * 0 0 * chr4 1 0 NAATATTCATNNGNTCAGCCTNTNCATTAATTNNNNNNNNNTTNNNATNATNANNTTTTTTATAACCATTTATAAATGAGAGAGATCNTANCACAATATCA &0<<:::::</&&&.73'290&.&0;:::90&&&&&&&&&&..&&&0)&0-&0&&&.743799995253348597921.,.'050.*&.0&)*)&&&&*). RG:Z:0 +SL-XAV:1:1:0:700#0/1 581 * 0 0 * chr5 1 0 NGAAGCCCATNNTNGTGTTACNCNCCTGGAAGNNNNNNNNNACNNNGANACNTNNAACAATTCAGATCGGAAGAGCGGTTCAGCAGANNTNCCGAGACCGA &.88888:88/&0&,03189.&/&.8/))12/&&&&&&&&&./&&&&.&1.&)&&/35962/6432-3&),0&/2+0,),61&-6,&&&'&/,.0&...)0 RG:Z:0 +SL-XAV:1:1:0:764#0/2 165 * 0 0 * chr6 1 0 NACAGATGCANATATTAACAGGCTTTAAAGGACAGATGGACTGCAATACAATAATAGAGTACGTCAACACTCCACAGATCGCTAGAGCATNACATCGGTGT &/:5358::9999::99998255::7275,,/5567-'+387537857:54-4.51'31059547320;73/720+22.4(6.;((.;(;8()(''&&2&& RG:Z:0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/picard_input_tiny.sam Mon Feb 17 00:02:22 2014 -0500 @@ -0,0 +1,14 @@ +@HD VN:1.0 SO:queryname +@SQ SN:chr1 LN:101 +@SQ SN:chr7 LN:404 +@SQ SN:chr8 LN:202 +@RG ID:0 SM:Hi,Mom! +@PG ID:1 PN:Hey! VN:2.0 +both_reads_align_clip_adapter 99 chr7 21 255 101M = 16 96 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 +both_reads_align_clip_adapter 147 chr7 16 255 101M = 21 -96 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 +both_reads_align_clip_marked 83 chr7 1 255 101M = 302 201 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 +both_reads_align_clip_marked 163 chr7 302 255 101M = 1 -201 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA &/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1 RG:Z:0 +both_reads_present_only_first_aligns 89 chr7 1 255 101M * 0 0 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 +both_reads_present_only_first_aligns 165 * 0 0 * chr7 1 0 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA &/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1 RG:Z:0 +read_2_too_many_gaps 83 chr7 1 255 101M = 302 201 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 +read_2_too_many_gaps 163 chr7 302 255 10M1D10M5I76M = 1 -201 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA &/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1 RG:Z:0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/picard_input_tiny_coord.sam Mon Feb 17 00:02:22 2014 -0500 @@ -0,0 +1,14 @@ +@HD VN:1.0 SO:coordinate +@SQ SN:chr1 LN:101 +@SQ SN:chr7 LN:404 +@SQ SN:chr8 LN:202 +@RG ID:0 SM:Hi,Mom! +@PG ID:1 PN:Hey! VN:2.0 +both_reads_align_clip_marked 83 chr7 1 255 101M = 302 201 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 +both_reads_present_only_first_aligns 89 chr7 1 255 101M * 0 0 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 +read_2_too_many_gaps 83 chr7 1 255 101M = 302 201 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 +both_reads_align_clip_adapter 147 chr7 16 255 101M = 21 -96 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 +both_reads_align_clip_adapter 99 chr7 21 255 101M = 16 96 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 +both_reads_align_clip_marked 163 chr7 302 255 101M = 1 -201 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA &/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1 RG:Z:0 +read_2_too_many_gaps 163 chr7 302 255 10M1D10M5I76M = 1 -201 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA &/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1 RG:Z:0 +both_reads_present_only_first_aligns 165 * 0 0 * chr7 1 0 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA &/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1 RG:Z:0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/picard_output_AsMetrics_indexed_hg18_sorted_pair.html Mon Feb 17 00:02:22 2014 -0500 @@ -0,0 +1,57 @@ +<style type="text/css"> + tr.d0 td {background-color: oldlace; color: black;} + tr.d1 td {background-color: aliceblue; color: black;} + </style><?xml version="1.0" encoding="utf-8" ?> +<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> +<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"> +<head> +<meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> +<meta name="generator" content="Galaxy picard_wrapper tool output - see http://getgalaxy.org/" /> +<title></title> +<link rel="stylesheet" href="/static/style/base.css" type="text/css" /> +</head> +<body> +<div class="document"> +Galaxy tool CollectAlignmentSummaryMetrics run at 11/11/2011 08:07:27</b><br/><b>The following output files were created (click the filename to view/download a copy):</b><hr/><table> +<tr><td><a href="CollectAlignmentSummaryMetrics.log">CollectAlignmentSummaryMetrics.log</a></td></tr> +<tr><td><a href="CollectAlignmentSummaryMetrics.metrics.txt">CollectAlignmentSummaryMetrics.metrics.txt</a></td></tr> +</table><p/> +<b>Picard on line resources</b><ul> +<li><a href="http://picard.sourceforge.net/index.shtml">Click here for Picard Documentation</a></li> +<li><a href="http://picard.sourceforge.net/picard-metric-definitions.shtml">Click here for Picard Metrics definitions</a></li></ul><hr/> +<b>Picard output (transposed to make it easier to see)</b><hr/> +<table cellpadding="3" > +<tr class="d0"><td colspan="2">## net.sf.picard.metrics.StringHeader</td></tr><tr class="d1"><td colspan="2"># net.sf.picard.analysis.CollectAlignmentSummaryMetrics MAX_INSERT_SIZE=100000 ADAPTER_SEQUENCE=[AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, IS_BISULFITE_SEQUENCED=false] INPUT=/data/tmp/tmpLLcl1w/database/files/000/dataset_4.dat OUTPUT=/data/home/rlazarus/galaxy/database/job_working_directory/5/dataset_5_files/CollectAlignmentSummaryMetrics.metrics.txt REFERENCE_SEQUENCE=/data/home/rlazarus/galaxy/database/job_working_directory/5/dataset_5_files/hg19.fa_fake.fasta ASSUME_SORTED=true TMP_DIR=[/tmp] VALIDATION_STRINGENCY=LENIENT METRIC_ACCUMULATION_LEVEL=[ALL_READS] IS_BISULFITE_SEQUENCED=false STOP_AFTER=0 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false</td></tr><tr class="d0"><td colspan="2">## net.sf.picard.metrics.StringHeader</td></tr><tr class="d1"><td colspan="2"># Started on: Fri Nov 11 08:07:22 EST 2011</td></tr><tr class="d0"><td colspan="2">## METRICS CLASS net.sf.picard.analysis.AlignmentSummaryMetrics</td></tr><tr class="d0"><td>CATEGORY</td><td>FIRST_OF_PAIR </td></tr> +<tr class="d1"><td>TOTAL_READS</td><td>5 </td></tr> +<tr class="d0"><td>PF_READS</td><td>5 </td></tr> +<tr class="d1"><td>PCT_PF_READS</td><td>1 </td></tr> +<tr class="d0"><td>PF_NOISE_READS</td><td>0 </td></tr> +<tr class="d1"><td>PF_READS_ALIGNED</td><td>0 </td></tr> +<tr class="d0"><td>PCT_PF_READS_ALIGNED</td><td>0 </td></tr> +<tr class="d1"><td>PF_ALIGNED_BASES</td><td>0 </td></tr> +<tr class="d0"><td>PF_HQ_ALIGNED_READS</td><td>0 </td></tr> +<tr class="d1"><td>PF_HQ_ALIGNED_BASES</td><td>0 </td></tr> +<tr class="d0"><td>PF_HQ_ALIGNED_Q20_BASES</td><td>0 </td></tr> +<tr class="d1"><td>PF_HQ_MEDIAN_MISMATCHES</td><td>0 </td></tr> +<tr class="d0"><td>PF_MISMATCH_RATE</td><td>0 </td></tr> +<tr class="d1"><td>PF_HQ_ERROR_RATE</td><td>0 </td></tr> +<tr class="d0"><td>PF_INDEL_RATE</td><td>0 </td></tr> +<tr class="d1"><td>MEAN_READ_LENGTH</td><td>13 </td></tr> +<tr class="d0"><td>READS_ALIGNED_IN_PAIRS</td><td>0 </td></tr> +<tr class="d1"><td>PCT_READS_ALIGNED_IN_PAIRS</td><td>0 </td></tr> +<tr class="d0"><td>BAD_CYCLES</td><td>0 </td></tr> +<tr class="d1"><td>STRAND_BALANCE</td><td>0 </td></tr> +<tr class="d0"><td>PCT_CHIMERAS</td><td>0 </td></tr> +<tr class="d1"><td>PCT_ADAPTER</td><td>0 </td></tr> +<tr class="d0"><td>SAMPLE</td><td> </td></tr> +<tr class="d1"><td>LIBRARY</td><td> </td></tr> +<tr class="d0"><td>READ_GROUP +</td><td> + </td></tr> +</table> +<b>Picard Tool Run Log</b><hr/> +<pre>INFO:root:## executing java -Xmx4g -jar /data/home/rlazarus/galaxy/tool-data/shared/jars/picard/CollectAlignmentSummaryMetrics.jar VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true ADAPTER_SEQUENCE= IS_BISULFITE_SEQUENCED=false MAX_INSERT_SIZE=100000 OUTPUT=/data/home/rlazarus/galaxy/database/job_working_directory/5/dataset_5_files/CollectAlignmentSummaryMetrics.metrics.txt R=/data/home/rlazarus/galaxy/database/job_working_directory/5/dataset_5_files/hg19.fa_fake.fasta TMP_DIR=/tmp INPUT=/data/tmp/tmpLLcl1w/database/files/000/dataset_4.dat returned status 0 and nothing on stderr + +</pre><hr/>The freely available <a href="http://picard.sourceforge.net/command-line-overview.shtml">Picard software</a> +generated all outputs reported here running as a <a href="http://getgalaxy.org">Galaxy</a> tool</div></body></html> +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/picard_output_GcBias_uploaded_hg18_summary_alignment_stats.html Mon Feb 17 00:02:22 2014 -0500 @@ -0,0 +1,28 @@ +@HD VN:1.0 SO:coordinate +@SQ SN:chr1 LN:255 +@SQ SN:chr2 LN:255 +@SQ SN:chr3 LN:255 +@SQ SN:chr4 LN:255 +@SQ SN:chr5 LN:255 +@SQ SN:chr6 LN:255 +@SQ SN:chr7 LN:255 +@SQ SN:chr8 LN:255 +@RG ID:0 SM:Hi,Mom! +SL-XAV:1:1:0:764#0/1 89 chr1 1 255 101M * 0 0 TTCATGCTGANGCNCTCTTACGATCGTACAGATGCAAATATTAACANNCNTTNAAGNNCANNNNNNNNNCAATACAATANTAGAGTACGTNAACACTCCAN &/,&-.1/6/&&)&).)/,&0768)&/.,/874,&.4137572)&/&&,&1-&.0/&&*,&&&&&&&&&&18775799,&16:8775-56256/69::;0& RG:Z:0 XN:i:1 +SL-XAV:1:1:0:1668#0/2 153 chr2 1 255 101M * 0 0 CATCTCTACANGCGCGTCCTACCAGACGCGCTTCCGATCTGAGAGCATACTTTTCATTGGATTCCAGCACAACTCCATTTTTGATCCACTNGACACCTTTN (/,'-/'0////(1'&&1&&&&'2''-6/,/3-33653.6:1'.86/-++32.-4864653/5/583/346423203+28888644446688456/4880& RG:Z:0 XN:i:1 +SL-XAV:1:1:0:1914#0/2 153 chr3 1 255 101M * 0 0 CGTATGCGCTNTTTATGTCGCCCACAGTGCCTAGTATAGCCCCTGCTAATAAAAAGAGATGAATACGTTTACTTAAAAAACTGAAACTAGNAATGTGCAAN (0,7&&*/*0*,)10/).-*&.&*/6669.&-337599;3,&,6/.,5::999987893+387020775777547999::668997448:::9;999::0& RG:Z:0 +SL-XAV:1:1:0:1639#0/2 153 chr4 1 255 101M * 0 0 CGTGATACCANCTCATGTTCACAGCCAAAGCCTGAAGCTGTCTATTATATTTCTCAACCATAAACTTTTGCCTCAGGCATCCGCAGAATGNTTTGCAGCCN '.&.&&'.0+01'2(1'(''-)','+0041/.+032;:867115/5267-.0/)-5.&-26200224,,0+0/0275/5605688::646875568882*& RG:Z:0 +SL-XAV:1:1:0:68#0/2 137 chr5 1 255 101M * 0 0 NTCTCATTTANAAATGGTTATAAAAACATTTATGCTGAAAAGGTGAAGTTCATTAATGAACAGGCTGACTGTCTCACTATCGCGTTCGCANGACGTTATCT &1<<999;;;;<<<87579:556972789977444.'.023.&,7621/54.49.)/53055-22--''+(.'-))6-168/(3&&0(<).))*&&&&&'0 RG:Z:0 +SL-XAV:1:1:0:700#0/2 137 chr6 1 255 101M * 0 0 NAATTGTTCTNAGTTTCTCGGTTTATGTGCTCTTCCAGGTGGGTAACACAATAATGGCCTTCCAGATCGTAAGAGCGACGTGTGTTGCACNAGTGTCGATC &0::887::::6/646::838388811/679:87640&./2+/-4/28:3,536/4''&&.78/(/554/./02*)*',-(57()&.6(6:(0601'/(,* RG:Z:0 +SL-XAV:1:1:0:1721#0/1 83 chr7 1 255 101M = 102 40 CAACAGAAGGNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCGAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 +SL-XAV:1:1:0:1721#0/2 163 chr7 102 255 101M = 1 -40 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTCACTATGGTACATCTTGTCGTGCGGCNAGAGCATACA &/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1 RG:Z:0 +SL-XAV:1:1:0:105#0/2 147 chr8 1 255 101M = 102 79 CACATCGTGANTCTTACAATCTGCGGTTTCAGATGTGGAGCGATGTGTGAGAGATTGAGCAACTGATCTGAAAAGCAGACACAGCTATTCNTAAGATGACN /))3--/&*()&)&&+'++.'-&,(.))'4,)&'&&,')8,&&*'.&*0'225/&)3-8//)*,5-*).7851453583.3568526:863688:::85.& RG:Z:0 +SL-XAV:1:1:0:105#0/1 99 chr8 102 255 101M = 1 -79 NCAGGTTCAANTGTGCAGCCCNTTTTGAGAGATNNNNNNNNTGNNCTGNAANANNGACACAGCTATTCCTAAGATGACAAGATCAGANAANAAGTCAAGCA &06665578::41.*/7577/&/77403-324.&&&&&&&&/.&&..&&.0&&&&',:9:/-/(55002020+3'12+2/&.2-&//&),&*&&&&&&&51 RG:Z:0 +SL-XAV:1:1:0:1300#0/1 77 * 0 0 * * 0 0 NAAACACAAGNNANAGTCTTANCNGCTATTCCNNNNNNNNNCTNNNCTNAGNANNACATACAACAGTATCCACACAAGTGTACTCGTNCANACATGTGAAC &*5535)*-,,&.&.*-1)*,&'&)&1&&.,)&&&&&&&&&)0&&&0'&&&&.&&*2'/4''0/**&)&,'-&*,&,&&&.0.&)&&&**&,.&&&')&&) RG:Z:0 +SL-XAV:1:1:0:1300#0/2 141 * 0 0 * * 0 0 NGATCATGGANGACTCTCCCCATCCCCCGCTCCAGCGCTCAGTTATATGCCTAGCCTCGGACACGTCACCAACATCTCACGCACTCTGCANAGTCTCTCAC &&'+''3*&-/)/1'26/*-2-/542-*&-&/'/*/&-'&)-')&.'-/&&2+122*'&+,(/-&)((,/-,,.'2(2'+)/&/&-66-&&/16&)&*&'3 RG:Z:0 +SL-XAV:1:1:0:1639#0/1 101 * 0 0 * chr1 1 0 NCCCTCTCAGNNTNTCTGCCANANCCTTAAGCNNNNNNNNNTANNNCTNAANCNNAAACTTTTGCCTCAGGCATCCGCAGAATGTTTNTCNGCCTATATCG &1::::::64/&/&0:3.280&/&087881,/&&&&&&&&&..&&&..&,,&-&&,265341-)/5680&-.5552-25/322/42/&)&&).421&-&-/ RG:Z:0 +SL-XAV:1:1:0:1668#0/1 101 * 0 0 * chr2 1 0 NATAGCATACNNTNCATTGGANTNCAGCACAANNNNNNNNNTGNNNCANTNNANNCCTTTGAGATCGGAAGAGCGGTTCAGCAGGAANNCNCAGACCGATC &1988998890&0&.8863//&.&.0-2875.&&&&&&&&&.)&&&..&.&&.&&.5782-2+262)&-0-0510*.332-2.-,0*&&*&'.&-2-)0., RG:Z:0 +SL-XAV:1:1:0:1914#0/1 101 * 0 0 * chr3 1 0 NTTTTTCTCCNNCNGTGCCTANTNTAGCCCCTNNNNNNNNNAANNNATNANNANNTTTACTTAAAAAACTGAAACTAGTAATGTGCANNANATCGNAAGAG &0::::<<;90&/&.244760&,&.414798/&&&&&&&&&00&&&0.&/&&-&&.4475687363504.&.557/.*)65.&/*./&&.&.+*)&..).& RG:Z:0 +SL-XAV:1:1:0:68#0/1 581 * 0 0 * chr4 1 0 NAATATTCATNNGNTCAGCCTNTNCATTAATTNNNNNNNNNTTNNNATNATNANNTTTTTTATAACCATTTATAAATGAGAGAGATCNTANCACAATATCA &0<<:::::</&&&.73'290&.&0;:::90&&&&&&&&&&..&&&0)&0-&0&&&.743799995253348597921.,.'050.*&.0&)*)&&&&*). RG:Z:0 +SL-XAV:1:1:0:700#0/1 581 * 0 0 * chr5 1 0 NGAAGCCCATNNTNGTGTTACNCNCCTGGAAGNNNNNNNNNACNNNGANACNTNNAACAATTCAGATCGGAAGAGCGGTTCAGCAGANNTNCCGAGACCGA &.88888:88/&0&,03189.&/&.8/))12/&&&&&&&&&./&&&&.&1.&)&&/35962/6432-3&),0&/2+0,),61&-6,&&&'&/,.0&...)0 RG:Z:0 +SL-XAV:1:1:0:764#0/2 165 * 0 0 * chr6 1 0 NACAGATGCANATATTAACAGGCTTTAAAGGACAGATGGACTGCAATACAATAATAGAGTACGTCAACACTCCACAGATCGCTAGAGCATNACATCGGTGT &/:5358::9999::99998255::7275,,/5567-'+387537857:54-4.51'31059547320;73/720+22.4(6.;((.;(;8()(''&&2&& RG:Z:0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/picard_output_alignment_summary_metrics.html Mon Feb 17 00:02:22 2014 -0500 @@ -0,0 +1,59 @@ +<style type="text/css"> + tr.d0 td {background-color: oldlace; color: black;} + tr.d1 td {background-color: aliceblue; color: black;} + </style><?xml version="1.0" encoding="utf-8" ?> +<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> +<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"> +<head> +<meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> +<meta name="generator" content="Galaxy picard_wrapper tool output - see http://getgalaxy.org/" /> +<title></title> +<link rel="stylesheet" href="/static/style/base.css" type="text/css" /> +</head> +<body> +<div class="document"> +Galaxy tool CollectAlignmentSummaryMetrics run at 11/11/2011 08:07:10</b><br/><b>The following output files were created (click the filename to view/download a copy):</b><hr/><table> +<tr><td><a href="CollectAlignmentSummaryMetrics.log">CollectAlignmentSummaryMetrics.log</a></td></tr> +<tr><td><a href="CollectAlignmentSummaryMetrics.metrics.txt">CollectAlignmentSummaryMetrics.metrics.txt</a></td></tr> +</table><p/> +<b>Picard on line resources</b><ul> +<li><a href="http://picard.sourceforge.net/index.shtml">Click here for Picard Documentation</a></li> +<li><a href="http://picard.sourceforge.net/picard-metric-definitions.shtml">Click here for Picard Metrics definitions</a></li></ul><hr/> +<b>Picard output (transposed to make it easier to see)</b><hr/> +<table cellpadding="3" > +<tr class="d0"><td colspan="2">## net.sf.picard.metrics.StringHeader</td></tr><tr class="d1"><td colspan="2"># net.sf.picard.analysis.CollectAlignmentSummaryMetrics MAX_INSERT_SIZE=100000 ADAPTER_SEQUENCE=[AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, IS_BISULFITE_SEQUENCED=false] INPUT=/data/tmp/tmpLLcl1w/database/files/000/dataset_2.dat OUTPUT=/data/home/rlazarus/galaxy/database/job_working_directory/3/dataset_3_files/CollectAlignmentSummaryMetrics.metrics.txt REFERENCE_SEQUENCE=/data/home/rlazarus/galaxy/database/job_working_directory/3/dataset_3_files/CollectAlignmentSummaryMetricsfq2hit.fasta_fake.fasta ASSUME_SORTED=true TMP_DIR=[/tmp] VALIDATION_STRINGENCY=LENIENT METRIC_ACCUMULATION_LEVEL=[ALL_READS] IS_BISULFITE_SEQUENCED=false STOP_AFTER=0 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false</td></tr><tr class="d0"><td colspan="2">## net.sf.picard.metrics.StringHeader</td></tr><tr class="d1"><td colspan="2"># Started on: Fri Nov 11 08:07:10 EST 2011</td></tr><tr class="d0"><td colspan="2">## METRICS CLASS net.sf.picard.analysis.AlignmentSummaryMetrics</td></tr><tr class="d0"><td>CATEGORY</td><td>FIRST_OF_PAIR </td></tr> +<tr class="d1"><td>TOTAL_READS</td><td>4 </td></tr> +<tr class="d0"><td>PF_READS</td><td>4 </td></tr> +<tr class="d1"><td>PCT_PF_READS</td><td>1 </td></tr> +<tr class="d0"><td>PF_NOISE_READS</td><td>0 </td></tr> +<tr class="d1"><td>PF_READS_ALIGNED</td><td>4 </td></tr> +<tr class="d0"><td>PCT_PF_READS_ALIGNED</td><td>1 </td></tr> +<tr class="d1"><td>PF_ALIGNED_BASES</td><td>404 </td></tr> +<tr class="d0"><td>PF_HQ_ALIGNED_READS</td><td>4 </td></tr> +<tr class="d1"><td>PF_HQ_ALIGNED_BASES</td><td>404 </td></tr> +<tr class="d0"><td>PF_HQ_ALIGNED_Q20_BASES</td><td>28 </td></tr> +<tr class="d1"><td>PF_HQ_MEDIAN_MISMATCHES</td><td>78 </td></tr> +<tr class="d0"><td>PF_MISMATCH_RATE</td><td>0.777228 </td></tr> +<tr class="d1"><td>PF_HQ_ERROR_RATE</td><td>0.777228 </td></tr> +<tr class="d0"><td>PF_INDEL_RATE</td><td>0 </td></tr> +<tr class="d1"><td>MEAN_READ_LENGTH</td><td>101 </td></tr> +<tr class="d0"><td>READS_ALIGNED_IN_PAIRS</td><td>3 </td></tr> +<tr class="d1"><td>PCT_READS_ALIGNED_IN_PAIRS</td><td>0.75 </td></tr> +<tr class="d0"><td>BAD_CYCLES</td><td>63 </td></tr> +<tr class="d1"><td>STRAND_BALANCE</td><td>0.25 </td></tr> +<tr class="d0"><td>PCT_CHIMERAS</td><td>0 </td></tr> +<tr class="d1"><td>PCT_ADAPTER</td><td>0 </td></tr> +<tr class="d0"><td>SAMPLE</td><td> </td></tr> +<tr class="d1"><td>LIBRARY</td><td> </td></tr> +<tr class="d0"><td>READ_GROUP +</td><td> + </td></tr> +</table> +<b>Picard Tool Run Log</b><hr/> +<pre>INFO:root:## executing java -Xmx4g -jar /data/home/rlazarus/galaxy/tool-data/shared/jars/picard/CreateSequenceDictionary.jar REFERENCE=/tmp/CollectAlignmentSummaryMetricsfq2hit.fasta OUTPUT=/tmp/CollectAlignmentSummaryMetricsfq2hit.dict URI=dataset_1.dat TRUNCATE_NAMES_AT_WHITESPACE=None returned status 0 and nothing on stderr + +INFO:root:## executing java -Xmx4g -jar /data/home/rlazarus/galaxy/tool-data/shared/jars/picard/CollectAlignmentSummaryMetrics.jar VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true ADAPTER_SEQUENCE= IS_BISULFITE_SEQUENCED=false MAX_INSERT_SIZE=100000 OUTPUT=/data/home/rlazarus/galaxy/database/job_working_directory/3/dataset_3_files/CollectAlignmentSummaryMetrics.metrics.txt R=/data/home/rlazarus/galaxy/database/job_working_directory/3/dataset_3_files/CollectAlignmentSummaryMetricsfq2hit.fasta_fake.fasta TMP_DIR=/tmp INPUT=/data/tmp/tmpLLcl1w/database/files/000/dataset_2.dat returned status 0 and nothing on stderr + +</pre><hr/>The freely available <a href="http://picard.sourceforge.net/command-line-overview.shtml">Picard software</a> +generated all outputs reported here running as a <a href="http://getgalaxy.org">Galaxy</a> tool</div></body></html> +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/picard_output_collect_AS_sorted_pair.txt Mon Feb 17 00:02:22 2014 -0500 @@ -0,0 +1,12 @@ +## net.sf.picard.metrics.StringHeader +# net.sf.picard.analysis.CollectAlignmentSummaryMetrics INPUT=testdata/picard/sam/bam2fastq/paired/ok/sorted-pair.sam OUTPUT=output_test_as/test_as_sorted-pair.txt REFERENCE_SEQUENCE=testdata/picard/reference/Homo_sapiens_assembly18.trimmed.fasta ASSUME_SORTED=true MAX_INSERT_SIZE=100000 ADAPTER_SEQUENCE=[AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG] IS_BISULFITE_SEQUENCED=false TMP_DIR=/tmp/raphael VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false +## net.sf.picard.metrics.StringHeader +# Started on: Tue Oct 26 14:06:32 EDT 2010 + +## METRICS CLASS net.sf.picard.analysis.AlignmentSummaryMetrics +CATEGORY TOTAL_READS PF_READS PCT_PF_READS PF_NOISE_READS PF_READS_ALIGNED PCT_PF_READS_ALIGNED PF_HQ_ALIGNED_READS PF_HQ_ALIGNED_BASES PF_HQ_ALIGNED_Q20_BASES PF_HQ_MEDIAN_MISMATCHES PF_HQ_ERROR_RATE MEAN_READ_LENGTH READS_ALIGNED_IN_PAIRS PCT_READS_ALIGNED_IN_PAIRS BAD_CYCLES STRAND_BALANCE PCT_CHIMERAS PCT_ADAPTER +FIRST_OF_PAIR 5 5 1 0 0 0 0 0 0 0 ? 13 0 ? 0 ? ? 0 +SECOND_OF_PAIR 5 5 1 0 0 0 0 0 0 0 ? 13 0 ? 0 ? ? 0 +PAIR 10 10 1 0 0 0 0 0 0 0 ? 13 0 ? 0 ? ? 0 + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/picard_output_estlibcomplexity_tinysam.html Mon Feb 17 00:02:22 2014 -0500 @@ -0,0 +1,38 @@ +<style type="text/css"> + tr.d0 td {background-color: oldlace; color: black;} + tr.d1 td {background-color: aliceblue; color: black;} + </style><?xml version="1.0" encoding="utf-8" ?> +<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> +<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"> +<head> +<meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> +<meta name="generator" content="Galaxy rgEstLibComplexity.py tool output - see http://g2.trac.bx.psu.edu/" /> +<title></title> +<link rel="stylesheet" href="/static/style/base.css" type="text/css" /> +</head> +<body> +<div class="document"> +<b><a href="http://rgenetics.org">Galaxy Rgenetics</a> tool output rgEstLibComplexity.py run at 10/04/2011 14:52:24</b><b>Your job produced the following output files.</b><hr/> +<table> +<tr><td><a href="estlibcompout.txt">estlibcompout.txt</a></td></tr> +</table><p/> +<b>Picard on line resources</b><ul> +<li><a href="http://picard.sourceforge.net/index.shtml">Click here for Picard Documentation</a></li> +<li><a href="http://picard.sourceforge.net/picard-metric-definitions.shtml">Click here for Picard Metrics definitions</a></li></ul><hr/> +<b>Picard output (transposed to make it easier to see)</b><hr/> +<table cellpadding="3" > +<tr class="d0"><td>## net.sf.picard.metrics.StringHeader</td></tr><tr class="d1"><td># net.sf.picard.sam.EstimateLibraryComplexity INPUT=[/export/tmp/tmpBfU1Um/database/files/000/dataset_111.dat] OUTPUT=estlibcompout.txt MIN_IDENTICAL_BASES=5 MAX_DIFF_RATE=0.03 MIN_MEAN_QUALITY=20 READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).* OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VALIDATION_STRINGENCY=LENIENT TMP_DIR=/tmp/rerla VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false</td></tr><tr class="d0"><td>## net.sf.picard.metrics.StringHeader</td></tr><tr class="d1"><td># Started on: Sun Apr 10 14:52:24 EDT 2011</td></tr></table> +<b>Picard log</b><hr/> +<pre>## executing java -Xmx2g -jar /udd/rerla/rgalaxy/tool-data/shared/jars/EstimateLibraryComplexity.jar MIN_IDENTICAL_BASES=5 O=estlibcompout.txt VALIDATION_STRINGENCY=LENIENT MIN_MEAN_QUALITY=20 READ_NAME_REGEX="[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*" OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 I=/export/tmp/tmpBfU1Um/database/files/000/dataset_111.dat MAX_DIFF_RATE=0.03 returned status 0 and log (stdout/stderr) records: +[Sun Apr 10 14:52:24 EDT 2011] net.sf.picard.sam.EstimateLibraryComplexity INPUT=[/export/tmp/tmpBfU1Um/database/files/000/dataset_111.dat] OUTPUT=estlibcompout.txt MIN_IDENTICAL_BASES=5 MAX_DIFF_RATE=0.03 MIN_MEAN_QUALITY=20 READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).* OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VALIDATION_STRINGENCY=LENIENT TMP_DIR=/tmp/rerla VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false +INFO 2011-04-10 14:52:24 EstimateLibraryComplexity Will store 3098916 read pairs in memory before sorting. +INFO 2011-04-10 14:52:24 EstimateLibraryComplexity Finished reading - moving on to scanning for duplicates. +[Sun Apr 10 14:52:24 EDT 2011] net.sf.picard.sam.EstimateLibraryComplexity done. +Runtime.totalMemory()=33947648 + + +</pre><hr/>The freely available <a href="http://picard.sourceforge.net/command-line-overview.shtml">Picard software</a> +generated all outputs reported here, using this command line:<br/> +<pre>java -Xmx2g -jar /udd/rerla/rgalaxy/tool-data/shared/jars/EstimateLibraryComplexity.jar MIN_IDENTICAL_BASES=5 O=estlibcompout.txt VALIDATION_STRINGENCY=LENIENT MIN_MEAN_QUALITY=20 READ_NAME_REGEX="[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*" OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 I=/export/tmp/tmpBfU1Um/database/files/000/dataset_111.dat MAX_DIFF_RATE=0.03</pre> +</div></body></html> +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/picard_output_fixmate_sorted_pair.sam Mon Feb 17 00:02:22 2014 -0500 @@ -0,0 +1,15 @@ +@HD VN:1.0 SO:coordinate +@SQ SN:chr1 LN:10001 +@SQ SN:chr2 LN:10001 +@SQ SN:chr3 LN:10001 +@RG ID:rg1 SM:Z +bar:record:1 77 * 0 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg1 +bar:record:1 141 * 0 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1 +bar:record:2 77 * 0 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg1 +bar:record:2 141 * 0 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1 +bar:record:3 77 * 0 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg1 +bar:record:3 141 * 0 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1 +bar:record:4 77 * 0 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg1 +bar:record:4 141 * 0 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1 +bar:record:5 77 * 0 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg1 +bar:record:5 141 * 0 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/picard_output_gc_summary_alignment_stats.txt Mon Feb 17 00:02:22 2014 -0500 @@ -0,0 +1,102 @@ +## net.sf.picard.metrics.StringHeader +# net.sf.picard.analysis.CollectGcBiasMetrics REFERENCE_SEQUENCE=testdata/picard/reference/Homo_sapiens_assembly18.trimmed.nodict.fasta INPUT=testdata/picard/sam/summary_alignment_stats_test.sam OUTPUT=output_test_gc_nodict/test_nodic_ref_gc_summary_alignment_stats_test.txt CHART_OUTPUT=output_test_gc_nodict/test_nodic_ref_gc_summary_alignment_stats_test.pdf WINDOW_SIZE=100 MINIMUM_GENOME_FRACTION=1.0E-5 TMP_DIR=/tmp/raphael VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false +## net.sf.picard.metrics.StringHeader +# Started on: Tue Oct 26 13:54:53 EDT 2010 + +## METRICS CLASS net.sf.picard.analysis.GcBiasDetailMetrics +GC WINDOWS READ_STARTS MEAN_BASE_QUALITY NORMALIZED_COVERAGE ERROR_BAR_WIDTH +6 3 0 0 0 0 +7 7 0 0 0 0 +8 6 0 0 0 0 +9 45 0 0 0 0 +10 54 0 0 0 0 +11 83 0 0 0 0 +12 110 0 0 0 0 +13 83 0 0 0 0 +14 130 0 0 0 0 +15 178 0 0 0 0 +16 276 0 0 0 0 +17 352 0 0 0 0 +18 519 0 0 0 0 +19 658 0 0 0 0 +20 1073 0 0 0 0 +21 1543 0 0 0 0 +22 2024 0 0 0 0 +23 2631 0 0 0 0 +24 3758 0 0 0 0 +25 5087 0 0 0 0 +26 6543 0 0 0 0 +27 8020 0 0 0 0 +28 10251 0 0 0 0 +29 12241 0 0 0 0 +30 14189 0 0 0 0 +31 16295 0 0 0 0 +32 17995 0 0 0 0 +33 20131 0 0 0 0 +34 22194 0 0 0 0 +35 23848 0 0 0 0 +36 25355 0 0 0 0 +37 27310 0 0 0 0 +38 28274 0 0 0 0 +39 28818 0 0 0 0 +40 28806 0 0 0 0 +41 29651 0 0 0 0 +42 30773 0 0 0 0 +43 31217 0 0 0 0 +44 31743 0 0 0 0 +45 32727 0 0 0 0 +46 34084 0 0 0 0 +47 35307 0 0 0 0 +48 36752 0 0 0 0 +49 36917 0 0 0 0 +50 36561 0 0 0 0 +51 36399 0 0 0 0 +52 35677 0 0 0 0 +53 34354 1 1 29.352448 29.352448 +54 32401 0 0 0 0 +55 30417 0 0 0 0 +56 28588 0 0 0 0 +57 27083 0 0 0 0 +58 24090 0 0 0 0 +59 20995 0 0 0 0 +60 17702 0 0 0 0 +61 14252 0 0 0 0 +62 11595 0 0 0 0 +63 9077 0 0 0 0 +64 6863 0 0 0 0 +65 5394 0 0 0 0 +66 4304 0 0 0 0 +67 3551 0 0 0 0 +68 2776 0 0 0 0 +69 2321 0 0 0 0 +70 1999 0 0 0 0 +71 1777 0 0 0 0 +72 1444 0 0 0 0 +73 1367 0 0 0 0 +74 1182 0 0 0 0 +75 975 0 0 0 0 +76 807 0 0 0 0 +77 852 0 0 0 0 +78 867 0 0 0 0 +79 925 0 0 0 0 +80 786 0 0 0 0 +81 762 0 0 0 0 +82 578 0 0 0 0 +83 475 0 0 0 0 +84 391 0 0 0 0 +85 219 0 0 0 0 +86 184 0 0 0 0 +87 75 0 0 0 0 +88 36 0 0 0 0 +89 37 0 0 0 0 +90 24 0 0 0 0 +91 40 0 0 0 0 +92 33 0 0 0 0 +93 11 0 0 0 0 +94 24 0 0 0 0 +95 12 0 0 0 0 +96 11 0 0 0 0 +97 11 0 0 0 0 +98 9 0 0 0 0 + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/picard_output_hs_transposed_summary_alignment_stats.html Mon Feb 17 00:02:22 2014 -0500 @@ -0,0 +1,167 @@ +<style type="text/css"> + tr.d0 td {background-color: oldlace; color: black;} + tr.d1 td {background-color: aliceblue; color: black;} + </style><?xml version="1.0" encoding="utf-8" ?> +<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> +<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"> +<head> +<meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> +<meta name="generator" content="Galaxy picard_wrapper tool output - see http://getgalaxy.org/" /> +<title></title> +<link rel="stylesheet" href="/static/style/base.css" type="text/css" /> +</head> +<body> +<div class="document"> +Galaxy tool wrapper run picard_wrapper at 07/05/2011 00:15:30</b><br/><b>The following output files were created (click the filename to view/download a copy):</b><hr/><table> +<tr><td><a href="tempSamHead.txt">tempSamHead.txt</a></td></tr> +<tr><td><a href="rgPicardHsMetrics.bait">rgPicardHsMetrics.bait</a></td></tr> +<tr><td><a href="CalculateHsMetrics.metrics.txt">CalculateHsMetrics.metrics.txt</a></td></tr> +</table><p/> +<b>Picard on line resources - maxrows=100</b><ul> +<li><a href="http://picard.sourceforge.net/index.shtml">Click here for Picard Documentation</a></li> +<li><a href="http://picard.sourceforge.net/picard-metric-definitions.shtml">Click here for Picard Metrics definitions</a></li></ul><hr/> +<b>Picard output (transposed to make it easier to see)</b><hr/> +<table cellpadding="3" > +<tr class="d0"><td>## net.sf.picard.metrics.StringHeader</td></tr><tr class="d1"><td># net.sf.picard.analysis.directed.CalculateHsMetrics BAIT_INTERVALS=/udd/rerla/rgalaxy/database/job_working_directory/95/dataset_97_files/rgPicardHsMetrics.bait TARGET_INTERVALS=/udd/rerla/rgalaxy/database/job_working_directory/95/dataset_97_files/rgPicardHsMetrics.bait INPUT=/tmp/6728811.1.all.q/tmpCsP1vm/database/files/000/dataset_95.dat OUTPUT=/udd/rerla/rgalaxy/database/job_working_directory/95/dataset_97_files/CalculateHsMetrics.metrics.txt TMP_DIR=/tmp/6728811.1.all.q/tmpCsP1vm/database/tmp VALIDATION_STRINGENCY=LENIENT VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false</td></tr><tr class="d0"><td>## net.sf.picard.metrics.StringHeader</td></tr><tr class="d1"><td># Started on: Sat May 07 00:15:15 EDT 2011</td></tr><tr class="d0"><td>## METRICS CLASS net.sf.picard.analysis.directed.HsMetrics</td></tr><tr class="d0"><td>BAIT_SET</td><td>rgPicardHsMetrics</td></tr> +<tr class="d1"><td>GENOME_SIZE</td><td>2040</td></tr> +<tr class="d0"><td>BAIT_TERRITORY</td><td>14601938</td></tr> +<tr class="d1"><td>TARGET_TERRITORY</td><td>14601938</td></tr> +<tr class="d0"><td>BAIT_DESIGN_EFFICIENCY</td><td>1</td></tr> +<tr class="d1"><td>TOTAL_READS</td><td>18</td></tr> +<tr class="d0"><td>PF_READS</td><td>16</td></tr> +<tr class="d1"><td>PF_UNIQUE_READS</td><td>16</td></tr> +<tr class="d0"><td>PCT_PF_READS</td><td>0.888889</td></tr> +<tr class="d1"><td>PCT_PF_UQ_READS</td><td>0.888889</td></tr> +<tr class="d0"><td>PF_UQ_READS_ALIGNED</td><td>10</td></tr> +<tr class="d1"><td>PCT_PF_UQ_READS_ALIGNED</td><td>0.625</td></tr> +<tr class="d0"><td>PF_UQ_BASES_ALIGNED</td><td>1010</td></tr> +<tr class="d1"><td>ON_BAIT_BASES</td><td>0</td></tr> +<tr class="d0"><td>NEAR_BAIT_BASES</td><td>0</td></tr> +<tr class="d1"><td>OFF_BAIT_BASES</td><td>1010</td></tr> +<tr class="d0"><td>ON_TARGET_BASES</td><td>0</td></tr> +<tr class="d1"><td>PCT_SELECTED_BASES</td><td>0</td></tr> +<tr class="d0"><td>PCT_OFF_BAIT</td><td>1</td></tr> +<tr class="d1"><td>ON_BAIT_VS_SELECTED</td><td>?</td></tr> +<tr class="d0"><td>MEAN_BAIT_COVERAGE</td><td>0</td></tr> +<tr class="d1"><td>MEAN_TARGET_COVERAGE</td><td>?</td></tr> +<tr class="d0"><td>PCT_USABLE_BASES_ON_BAIT</td><td>0</td></tr> +<tr class="d1"><td>PCT_USABLE_BASES_ON_TARGET</td><td>0</td></tr> +<tr class="d0"><td>FOLD_ENRICHMENT</td><td>0</td></tr> +<tr class="d1"><td>ZERO_CVG_TARGETS_PCT</td><td>0.841776</td></tr> +<tr class="d0"><td>FOLD_80_BASE_PENALTY</td><td>?</td></tr> +<tr class="d1"><td>PCT_TARGET_BASES_2X</td><td>0</td></tr> +<tr class="d0"><td>PCT_TARGET_BASES_10X</td><td>0</td></tr> +<tr class="d1"><td>PCT_TARGET_BASES_20X</td><td>0</td></tr> +<tr class="d0"><td>PCT_TARGET_BASES_30X</td><td>0</td></tr> +<tr class="d1"><td>HS_LIBRARY_SIZE</td><td></td></tr> +<tr class="d0"><td>HS_PENALTY_10X</td><td>0</td></tr> +<tr class="d1"><td>HS_PENALTY_20X</td><td>0</td></tr> +<tr class="d0"><td>HS_PENALTY_30X +</td><td>0 +</td></tr> +</table> +<b>Picard log</b><hr/> +<pre>## got 10 rows of header +## executing java -Xmx8G -jar /udd/rerla/rgalaxy/tool-data/shared/jars/CalculateHsMetrics.jar VALIDATION_STRINGENCY=LENIENT BAIT_INTERVALS=/udd/rerla/rgalaxy/database/job_working_directory/95/dataset_97_files/rgPicardHsMetrics.bait TARGET_INTERVALS=/udd/rerla/rgalaxy/database/job_working_directory/95/dataset_97_files/rgPicardHsMetrics.bait INPUT=/tmp/6728811.1.all.q/tmpCsP1vm/database/files/000/dataset_95.dat OUTPUT=/udd/rerla/rgalaxy/database/job_working_directory/95/dataset_97_files/CalculateHsMetrics.metrics.txt TMP_DIR=/tmp/6728811.1.all.q/tmpCsP1vm/database/tmp returned status 0 and stderr: +[Sat May 07 00:15:15 EDT 2011] net.sf.picard.analysis.directed.CalculateHsMetrics BAIT_INTERVALS=/udd/rerla/rgalaxy/database/job_working_directory/95/dataset_97_files/rgPicardHsMetrics.bait TARGET_INTERVALS=/udd/rerla/rgalaxy/database/job_working_directory/95/dataset_97_files/rgPicardHsMetrics.bait INPUT=/tmp/6728811.1.all.q/tmpCsP1vm/database/files/000/dataset_95.dat OUTPUT=/udd/rerla/rgalaxy/database/job_working_directory/95/dataset_97_files/CalculateHsMetrics.metrics.txt TMP_DIR=/tmp/6728811.1.all.q/tmpCsP1vm/database/tmp VALIDATION_STRINGENCY=LENIENT VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false +WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8307873-8307942 +WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8309830-8309966 +WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8321581-8321736 +WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8328921-8329047 +WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8330342-8330469 +WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8331089-8331268 +WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8331692-8331978 +WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8365935-8366090 +WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8366606-8366726 +WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8379231-8379407 +WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8394536-8394660 +WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8426591-8426689 +WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8439724-8439837 +WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8450410-8450571 +WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8455465-8455675 +WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8460994-8461085 +WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8474118-8474378 +WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8475226-8475324 +WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8475761-8476349 +WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8482861-8482979 +WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8487241-8487268 +WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8489646-8489840 +WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8490753-8491059 +WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8494260-8494405 +WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8497300-8497434 +WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8507847-8508429 +WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8511276-8511546 +WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8513512-8513524 +WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8514924-8515035 +WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8516626-8516644 +WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8517344-8517353 +WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8518590-8518779 +WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8623316-8623458 +WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8626698-8626844 +WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8723779-8723843 +WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8307873-8307942 +WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8309830-8309966 +WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8321581-8321736 +WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8328921-8329047 +WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8330342-8330469 +WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8331089-8331268 +WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8331692-8331978 +WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8365935-8366090 +WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8366606-8366726 +WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8379231-8379407 +WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8394536-8394660 +WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8426591-8426689 +WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8439724-8439837 +WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8450410-8450571 +WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8455465-8455675 +WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8460994-8461085 +WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8474118-8474378 +WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8475226-8475324 +WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8475761-8476349 +WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8482861-8482979 +WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8487241-8487268 +WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8489646-8489840 +WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8490753-8491059 +WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8494260-8494405 +WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8497300-8497434 +WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8507847-8508429 +WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8511276-8511546 +WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8514924-8515035 +WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8518590-8518779 +WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8623316-8623458 +WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8626698-8626844 +WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8723779-8723843 +WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:16408986-16409647 +WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:16425552-16427522 +WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:16542527-16542763 +WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:16572980-16573083 +WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:16717794-16717995 +WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:16728357-16728483 +WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:16860643-16860646 +WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:125814448-125814568 +WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:125816060-125816263 +WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:125817221-125817625 +WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:125823198-125823404 +WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:125834519-125834807 +WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:2019022-2019247 +WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:2022951-2023081 +WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:2029465-2029900 +WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:2037228-2037484 +WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:2044596-2044723 +WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:2046671-2046845 +WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:2048290-2048464 +WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:2050815-2050986 +WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:2060417-2060471 +WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:2063211-2063342 +WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:2063565-2063623 +WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:2066228-2066329 +WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:2067628-2067776 +WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:2071831-2071995 +WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:2073346-2073413 +WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:2074085-2074196 +WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:2076828-2077071 +WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:2078499-2078613 + +<b>## WARNING - 434559 log lines truncated - CalculateHsMetrics.log contains entire output</pre><hr/>The freely available <a href="http://picard.sourceforge.net/command-line-overview.shtml">Picard software</a> +generated all outputs reported here running as a <a href="http://getgalaxy.org">Galaxy</a> tool</div></body></html> +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/picard_output_insertsize_tinysam.html Mon Feb 17 00:02:22 2014 -0500 @@ -0,0 +1,53 @@ +<style type="text/css"> + tr.d0 td {background-color: oldlace; color: black;} + tr.d1 td {background-color: aliceblue; color: black;} + </style><?xml version="1.0" encoding="utf-8" ?> +<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> +<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"> +<head> +<meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> +<meta name="generator" content="Galaxy picard_wrapper tool output - see http://getgalaxy.org/" /> +<title></title> +<link rel="stylesheet" href="/static/style/base.css" type="text/css" /> +</head> +<body> +<div class="document"> +Galaxy tool CollectInsertSizeMetrics run at 13/05/2011 15:20:46</b><br/><table cellpadding="10"><tr><td> +<a href="InsertSizeHist.pdf"><img src="InsertSizeHist.jpg" title="Click image preview for a print quality PDF version" hspace="10" align="middle"></a> +</tr></td></table> +<b>The following output files were created (click the filename to view/download a copy):</b><hr/><table> +<tr><td><a href="CollectInsertSizeMetrics.metrics.txt">CollectInsertSizeMetrics.metrics.txt</a></td></tr> +<tr><td><a href="CollectInsertSizeMetrics.log">CollectInsertSizeMetrics.log</a></td></tr> +<tr><td><a href="InsertSizeHist.pdf">InsertSizeHist.pdf</a></td></tr> +<tr><td><a href="InsertSizeHist.jpg">InsertSizeHist.jpg</a></td></tr> +</table><p/> +<b>Picard on line resources</b><ul> +<li><a href="http://picard.sourceforge.net/index.shtml">Click here for Picard Documentation</a></li> +<li><a href="http://picard.sourceforge.net/picard-metric-definitions.shtml">Click here for Picard Metrics definitions</a></li></ul><hr/> +<b>Picard output (transposed to make it easier to see)</b><hr/> +<table cellpadding="3" > +<tr class="d0"><td colspan="2">## net.sf.picard.metrics.StringHeader</td></tr><tr class="d1"><td colspan="2"># net.sf.picard.analysis.CollectInsertSizeMetrics HISTOGRAM_FILE=InsertSizeHist.pdf TAIL_LIMIT=10000 MINIMUM_PCT=0.01 INPUT=/dev/shm/tmpHpwBHW/database/files/000/dataset_1.dat OUTPUT=/udd/rerla/rgalaxy/database/job_working_directory/2/dataset_2_files/CollectInsertSizeMetrics.metrics.txt VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true STOP_AFTER=0 TMP_DIR=/tmp/rerla VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false</td></tr><tr class="d0"><td colspan="2">## net.sf.picard.metrics.StringHeader</td></tr><tr class="d1"><td colspan="2"># Started on: Fri May 13 15:20:45 EDT 2011</td></tr><tr class="d0"><td colspan="2">## METRICS CLASS net.sf.picard.analysis.InsertSizeMetrics</td></tr><tr class="d1"><td colspan="2">## HISTOGRAM java.lang.Integer</td></tr><tr class="d0"><td colspan="2">MEDIAN_INSERT_SIZE MIN_INSERT_SIZE MAX_INSERT_SIZE MEAN_INSERT_SIZE STANDARD_DEVIATION READ_PAIRS PAIR_ORIENTATION WIDTH_OF_10_PERCENT WIDTH_OF_20_PERCENT WIDTH_OF_30_PERCENT WIDTH_OF_40_PERCENT WIDTH_OF_50_PERCENT WIDTH_OF_60_PERCENT WIDTH_OF_70_PERCENT WIDTH_OF_80_PERCENT WIDTH_OF_90_PERCENT WIDTH_OF_99_PERCENT</td></tr> +<tr class="d1"><td colspan="2">96 96 96 96 ? 1 FR 1 1 1 1 1 1 1 1 1 1</td></tr> +<tr class="d0"><td colspan="2">201 201 201 201 ? 1 RF 1 1 1 1 1 1 1 1 1 1</td></tr> +<tr class="d1"><td colspan="2">insert_size fr_count rf_count</td></tr> +<tr class="d0"><td colspan="2">96 1 0</td></tr> +<tr class="d1"><td colspan="2">201 0 1</td></tr> +</table> +<b>Picard Tool Run Log</b><hr/> +<pre>INFO:root:## executing java -Xmx2g -jar /udd/rerla/rgalaxy/tool-data/shared/jars/CollectInsertSizeMetrics.jar VALIDATION_STRINGENCY=LENIENT I=/dev/shm/tmpHpwBHW/database/files/000/dataset_1.dat O=/udd/rerla/rgalaxy/database/job_working_directory/2/dataset_2_files/CollectInsertSizeMetrics.metrics.txt HISTOGRAM_FILE=InsertSizeHist.pdf TAIL_LIMIT=10000 MINIMUM_PCT=0.01 returned status 0 and stderr: +[Fri May 13 15:20:45 EDT 2011] net.sf.picard.analysis.CollectInsertSizeMetrics HISTOGRAM_FILE=InsertSizeHist.pdf TAIL_LIMIT=10000 MINIMUM_PCT=0.01 INPUT=/dev/shm/tmpHpwBHW/database/files/000/dataset_1.dat OUTPUT=/udd/rerla/rgalaxy/database/job_working_directory/2/dataset_2_files/CollectInsertSizeMetrics.metrics.txt VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true STOP_AFTER=0 TMP_DIR=/tmp/rerla VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false +WARNING 2011-05-13 15:20:45 SinglePassSamProgram File reports sort order 'queryname', assuming it's coordinate sorted anyway. +INFO 2011-05-13 15:20:46 ProcessExecutor [1] "FR = red" "RF = blue" +INFO 2011-05-13 15:20:46 ProcessExecutor null device +INFO 2011-05-13 15:20:46 ProcessExecutor 1 +[Fri May 13 15:20:46 EDT 2011] net.sf.picard.analysis.CollectInsertSizeMetrics done. +Runtime.totalMemory()=9109504 + + +INFO:root:## executing mogrify -format jpg -resize x400 /udd/rerla/rgalaxy/database/job_working_directory/2/dataset_2_files/InsertSizeHist.pdf returned status 0 and nothing on stderr + +INFO:root:## executing mogrify -format jpg -resize x400 /udd/rerla/rgalaxy/database/job_working_directory/2/dataset_2_files/InsertSizeHist.pdf returned status 0 and nothing on stderr + +</pre><hr/>The freely available <a href="http://picard.sourceforge.net/command-line-overview.shtml">Picard software</a> +generated all outputs reported here running as a <a href="http://getgalaxy.org">Galaxy</a> tool</div></body></html> +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/picard_output_markdups_sortedpairsam.html Mon Feb 17 00:02:22 2014 -0500 @@ -0,0 +1,160 @@ +<style type="text/css"> + tr.d0 td {background-color: oldlace; color: black;} + tr.d1 td {background-color: aliceblue; color: black;} + </style><?xml version="1.0" encoding="utf-8" ?> +<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> +<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"> +<head> +<meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> +<meta name="generator" content="Galaxy picard_wrapper tool output - see http://getgalaxy.org/" /> +<title></title> +<link rel="stylesheet" href="/static/style/base.css" type="text/css" /> +</head> +<body> +<div class="document"> +Galaxy tool MarkDuplicates run at 12/05/2011 14:34:29</b><br/><b>The following output files were created (click the filename to view/download a copy):</b><hr/><table> +<tr><td><a href="MarkDuplicates.log">MarkDuplicates.log</a></td></tr> +<tr><td><a href="MarkDuplicates.metrics.txt">MarkDuplicates.metrics.txt</a></td></tr> +</table><p/> +<b>Picard on line resources</b><ul> +<li><a href="http://picard.sourceforge.net/index.shtml">Click here for Picard Documentation</a></li> +<li><a href="http://picard.sourceforge.net/picard-metric-definitions.shtml">Click here for Picard Metrics definitions</a></li></ul><hr/> +<b>Picard output (transposed to make it easier to see)</b><hr/> +<table cellpadding="3" > +<tr class="d0"><td colspan="2">## net.sf.picard.metrics.StringHeader</td></tr><tr class="d1"><td colspan="2"># net.sf.picard.sam.MarkDuplicates INPUT=/tmp/6729253.1.all.q/tmpM5wI_h/database/files/001/dataset_1097.dat OUTPUT=/tmp/6729253.1.all.q/tmpM5wI_h/database/files/001/dataset_1098.dat METRICS_FILE=/udd/rerla/galaxy-central/database/job_working_directory/1032/dataset_1099_files/MarkDuplicates.metrics.txt REMOVE_DUPLICATES=true ASSUME_SORTED=true READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).* OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VALIDATION_STRINGENCY=LENIENT MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 TMP_DIR=/tmp/rerla VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false</td></tr><tr class="d0"><td colspan="2">## net.sf.picard.metrics.StringHeader</td></tr><tr class="d1"><td colspan="2"># Started on: Thu May 12 14:34:28 EDT 2011</td></tr><tr class="d0"><td colspan="2">## METRICS CLASS net.sf.picard.sam.DuplicationMetrics</td></tr><tr class="d0"><td>LIBRARY</td><td> </td></tr> +<tr class="d1"><td>UNPAIRED_READS_EXAMINED</td><td>1 </td></tr> +<tr class="d0"><td>READ_PAIRS_EXAMINED</td><td>3 </td></tr> +<tr class="d1"><td>UNMAPPED_READS</td><td>1 </td></tr> +<tr class="d0"><td>UNPAIRED_READ_DUPLICATES</td><td>1 </td></tr> +<tr class="d1"><td>READ_PAIR_DUPLICATES</td><td>1 </td></tr> +<tr class="d0"><td>READ_PAIR_OPTICAL_DUPLICATES</td><td>0 </td></tr> +<tr class="d1"><td>PERCENT_DUPLICATION</td><td>0.428571 </td></tr> +<tr class="d0"><td>ESTIMATED_LIBRARY_SIZE +</td><td>3 + </td></tr> +<tr class="d0"><td colspan="2">## HISTOGRAM java.lang.Double</td></tr><tr class="d0"><td colspan="2">BIN VALUE</td></tr> +<tr class="d1"><td colspan="2">1.0 0.948181</td></tr> +<tr class="d0"><td colspan="2">2.0 1.296997</td></tr> +<tr class="d1"><td colspan="2">3.0 1.425319</td></tr> +<tr class="d0"><td colspan="2">4.0 1.472527</td></tr> +<tr class="d1"><td colspan="2">5.0 1.489893</td></tr> +<tr class="d0"><td colspan="2">6.0 1.496282</td></tr> +<tr class="d1"><td colspan="2">7.0 1.498632</td></tr> +<tr class="d0"><td colspan="2">8.0 1.499497</td></tr> +<tr class="d1"><td colspan="2">9.0 1.499815</td></tr> +<tr class="d0"><td colspan="2">10.0 1.499932</td></tr> +<tr class="d1"><td colspan="2">11.0 1.499975</td></tr> +<tr class="d0"><td colspan="2">12.0 1.499991</td></tr> +<tr class="d1"><td colspan="2">13.0 1.499997</td></tr> +<tr class="d0"><td colspan="2">14.0 1.499999</td></tr> +<tr class="d1"><td colspan="2">15.0 1.5</td></tr> +<tr class="d0"><td colspan="2">16.0 1.5</td></tr> +<tr class="d1"><td colspan="2">17.0 1.5</td></tr> +<tr class="d0"><td colspan="2">18.0 1.5</td></tr> +<tr class="d1"><td colspan="2">19.0 1.5</td></tr> +<tr class="d0"><td colspan="2">20.0 1.5</td></tr> +<tr class="d1"><td colspan="2">21.0 1.5</td></tr> +<tr class="d0"><td colspan="2">22.0 1.5</td></tr> +<tr class="d1"><td colspan="2">23.0 1.5</td></tr> +<tr class="d0"><td colspan="2">24.0 1.5</td></tr> +<tr class="d1"><td colspan="2">25.0 1.5</td></tr> +<tr class="d0"><td colspan="2">26.0 1.5</td></tr> +<tr class="d1"><td colspan="2">27.0 1.5</td></tr> +<tr class="d0"><td colspan="2">28.0 1.5</td></tr> +<tr class="d1"><td colspan="2">29.0 1.5</td></tr> +<tr class="d0"><td colspan="2">30.0 1.5</td></tr> +<tr class="d1"><td colspan="2">31.0 1.5</td></tr> +<tr class="d0"><td colspan="2">32.0 1.5</td></tr> +<tr class="d1"><td colspan="2">33.0 1.5</td></tr> +<tr class="d0"><td colspan="2">34.0 1.5</td></tr> +<tr class="d1"><td colspan="2">35.0 1.5</td></tr> +<tr class="d0"><td colspan="2">36.0 1.5</td></tr> +<tr class="d1"><td colspan="2">37.0 1.5</td></tr> +<tr class="d0"><td colspan="2">38.0 1.5</td></tr> +<tr class="d1"><td colspan="2">39.0 1.5</td></tr> +<tr class="d0"><td colspan="2">40.0 1.5</td></tr> +<tr class="d1"><td colspan="2">41.0 1.5</td></tr> +<tr class="d0"><td colspan="2">42.0 1.5</td></tr> +<tr class="d1"><td colspan="2">43.0 1.5</td></tr> +<tr class="d0"><td colspan="2">44.0 1.5</td></tr> +<tr class="d1"><td colspan="2">45.0 1.5</td></tr> +<tr class="d0"><td colspan="2">46.0 1.5</td></tr> +<tr class="d1"><td colspan="2">47.0 1.5</td></tr> +<tr class="d0"><td colspan="2">48.0 1.5</td></tr> +<tr class="d1"><td colspan="2">49.0 1.5</td></tr> +<tr class="d0"><td colspan="2">50.0 1.5</td></tr> +<tr class="d1"><td colspan="2">51.0 1.5</td></tr> +<tr class="d0"><td colspan="2">52.0 1.5</td></tr> +<tr class="d1"><td colspan="2">53.0 1.5</td></tr> +<tr class="d0"><td colspan="2">54.0 1.5</td></tr> +<tr class="d1"><td colspan="2">55.0 1.5</td></tr> +<tr class="d0"><td colspan="2">56.0 1.5</td></tr> +<tr class="d1"><td colspan="2">57.0 1.5</td></tr> +<tr class="d0"><td colspan="2">58.0 1.5</td></tr> +<tr class="d1"><td colspan="2">59.0 1.5</td></tr> +<tr class="d0"><td colspan="2">60.0 1.5</td></tr> +<tr class="d1"><td colspan="2">61.0 1.5</td></tr> +<tr class="d0"><td colspan="2">62.0 1.5</td></tr> +<tr class="d1"><td colspan="2">63.0 1.5</td></tr> +<tr class="d0"><td colspan="2">64.0 1.5</td></tr> +<tr class="d1"><td colspan="2">65.0 1.5</td></tr> +<tr class="d0"><td colspan="2">66.0 1.5</td></tr> +<tr class="d1"><td colspan="2">67.0 1.5</td></tr> +<tr class="d0"><td colspan="2">68.0 1.5</td></tr> +<tr class="d1"><td colspan="2">69.0 1.5</td></tr> +<tr class="d0"><td colspan="2">70.0 1.5</td></tr> +<tr class="d1"><td colspan="2">71.0 1.5</td></tr> +<tr class="d0"><td colspan="2">72.0 1.5</td></tr> +<tr class="d1"><td colspan="2">73.0 1.5</td></tr> +<tr class="d0"><td colspan="2">74.0 1.5</td></tr> +<tr class="d1"><td colspan="2">75.0 1.5</td></tr> +<tr class="d0"><td colspan="2">76.0 1.5</td></tr> +<tr class="d1"><td colspan="2">77.0 1.5</td></tr> +<tr class="d0"><td colspan="2">78.0 1.5</td></tr> +<tr class="d1"><td colspan="2">79.0 1.5</td></tr> +<tr class="d0"><td colspan="2">80.0 1.5</td></tr> +<tr class="d1"><td colspan="2">81.0 1.5</td></tr> +<tr class="d0"><td colspan="2">82.0 1.5</td></tr> +<tr class="d1"><td colspan="2">83.0 1.5</td></tr> +<tr class="d0"><td colspan="2">84.0 1.5</td></tr> +<tr class="d1"><td colspan="2">85.0 1.5</td></tr> +<tr class="d0"><td colspan="2">86.0 1.5</td></tr> +<tr class="d1"><td colspan="2">87.0 1.5</td></tr> +<tr class="d0"><td colspan="2">88.0 1.5</td></tr> +<tr class="d1"><td colspan="2">89.0 1.5</td></tr> +<tr class="d0"><td colspan="2">90.0 1.5</td></tr> +<tr class="d1"><td colspan="2">91.0 1.5</td></tr> +<tr class="d0"><td colspan="2">92.0 1.5</td></tr> +<tr class="d1"><td colspan="2">93.0 1.5</td></tr> +<tr class="d0"><td colspan="2">94.0 1.5</td></tr> +<tr class="d1"><td colspan="2">95.0 1.5</td></tr> +<tr class="d0"><td colspan="2">96.0 1.5</td></tr> +<tr class="d1"><td colspan="2">97.0 1.5</td></tr> +<tr class="d0"><td colspan="2">98.0 1.5</td></tr> +<tr class="d1"><td colspan="2">99.0 1.5</td></tr> +</table> +<b>Picard Tool Run Log</b><hr/> +<pre>Thu, 12 May 2011 14:34:29 INFO + ## executing java -Xmx2g -jar /udd/rerla/galaxy-central/tool-data/shared/jars/MarkDuplicates.jar VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true INPUT=/tmp/6729253.1.all.q/tmpM5wI_h/database/files/001/dataset_1097.dat OUTPUT=/tmp/6729253.1.all.q/tmpM5wI_h/database/files/001/dataset_1098.dat METRICS_FILE=/udd/rerla/galaxy-central/database/job_working_directory/1032/dataset_1099_files/MarkDuplicates.metrics.txt REMOVE_DUPLICATES=true READ_NAME_REGEX="[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*" OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 returned status 0 and stderr: +[Thu May 12 14:34:28 EDT 2011] net.sf.picard.sam.MarkDuplicates INPUT=/tmp/6729253.1.all.q/tmpM5wI_h/database/files/001/dataset_1097.dat OUTPUT=/tmp/6729253.1.all.q/tmpM5wI_h/database/files/001/dataset_1098.dat METRICS_FILE=/udd/rerla/galaxy-central/database/job_working_directory/1032/dataset_1099_files/MarkDuplicates.metrics.txt REMOVE_DUPLICATES=true ASSUME_SORTED=true READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).* OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VALIDATION_STRINGENCY=LENIENT MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 TMP_DIR=/tmp/rerla VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false +INFO 2011-05-12 14:34:28 MarkDuplicates Start of doWork freeMemory: 8644632; totalMemory: 9109504; maxMemory: 1908932608 +INFO 2011-05-12 14:34:28 MarkDuplicates Reading input file and constructing read end information. +INFO 2011-05-12 14:34:28 MarkDuplicates Will retain up to 7575129 data points before spilling to disk. +INFO 2011-05-12 14:34:28 MarkDuplicates Read 7 records. 0 pairs never matched. +INFO 2011-05-12 14:34:29 MarkDuplicates After buildSortedReadEndLists freeMemory: 8316168; totalMemory: 130351104; maxMemory: 1908932608 +INFO 2011-05-12 14:34:29 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. +INFO 2011-05-12 14:34:29 MarkDuplicates Traversing read pair information and detecting duplicates. +INFO 2011-05-12 14:34:29 MarkDuplicates Traversing fragment information and detecting duplicates. +INFO 2011-05-12 14:34:29 MarkDuplicates Sorting list of duplicate records. +INFO 2011-05-12 14:34:29 MarkDuplicates After generateDuplicateIndexes freeMemory: 129615120; totalMemory: 607649792; maxMemory: 1908932608 +INFO 2011-05-12 14:34:29 MarkDuplicates Marking 3 records as duplicates. +INFO 2011-05-12 14:34:29 MarkDuplicates Found 0 optical duplicate clusters. +INFO 2011-05-12 14:34:29 MarkDuplicates Before output close freeMemory: 128997520; totalMemory: 607649792; maxMemory: 1908932608 +INFO 2011-05-12 14:34:29 MarkDuplicates After output close freeMemory: 128997280; totalMemory: 607649792; maxMemory: 1908932608 +[Thu May 12 14:34:29 EDT 2011] net.sf.picard.sam.MarkDuplicates done. +Runtime.totalMemory()=607649792 + + +</pre><hr/>The freely available <a href="http://picard.sourceforge.net/command-line-overview.shtml">Picard software</a> +generated all outputs reported here running as a <a href="http://getgalaxy.org">Galaxy</a> tool</div></body></html> +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/picard_output_markdups_sortedpairsam.sam Mon Feb 17 00:02:22 2014 -0500 @@ -0,0 +1,63 @@ +<?xml version="1.0" encoding="utf-8" ?> +<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> +<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"> + <head> + <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> + <meta name="generator" content="Galaxy rgPicardMarkDups.py tool output - see http://g2.trac.bx.psu.edu/" /> + <link rel="stylesheet" href="/static/style/base.css" type="text/css" /> + </head> + <body> + <div class="document"> + <h3><a href="http://rgenetics.org">Rgenetics</a> tool rgPicardMarkDups.py run at 19/11/2010 18:25:23</h3> + <b>Your job produced the following outputs - check here for a record of what was done and any unexpected events</b> + <hr /> + <div> + <b>Output files.</b> + <table> + <tr><td><a href="rgPicardMarkDups.txt">rgPicardMarkDups.txt (1.8 KB)</a></td></tr> + </table> + </div> + <hr /> + <div> + <b>Log of activity</b> + <hr/> + ## executing java -Xmx2g -jar /share/shared/relul.galaxy/tool-data/shared/jars/MarkDuplicates.jar I= /share/shared/relul.galaxy/database/files/000/dataset_57.dat O= /share/shared/relul.galaxy/database/files/000/dataset_99.dat M= rgPicardMarkDupsMetrics.txt READ_NAME_REGEX="[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*" OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 returned status 1 and log (stdout/stderr) records: +<BR /> +[Fri Nov 19 18:25:23 EST 2010] net.sf.picard.sam.MarkDuplicates INPUT=/share/shared/relul.galaxy/database/files/000/dataset_57.dat OUTPUT=/share/shared/relul.galaxy/database/files/000/dataset_99.dat METRICS_FILE=rgPicardMarkDupsMetrics.txt READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).* OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 REMOVE_DUPLICATES=false ASSUME_SORTED=false MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 TMP_DIR=/tmp/relul VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false +<BR /> +INFO 2010-11-19 18:25:23 MarkDuplicates Start of doWork freeMemory: 8645600; totalMemory: 9109504; maxMemory: 1908932608 +<BR /> +INFO 2010-11-19 18:25:23 MarkDuplicates Reading input file and constructing read end information. +<BR /> +INFO 2010-11-19 18:25:23 MarkDuplicates Will retain up to 7575129 data points before spilling to disk. +<BR /> +[Fri Nov 19 18:25:23 EST 2010] net.sf.picard.sam.MarkDuplicates done. +<BR /> +Runtime.totalMemory()=130351104 +<BR /> +Exception in thread "main" net.sf.picard.PicardException: /share/shared/relul.galaxy/database/files/000/dataset_57.dat is not coordinate sorted. +<BR /> + at net.sf.picard.sam.MarkDuplicates.buildSortedReadEndLists(MarkDuplicates.java:248) +<BR /> + at net.sf.picard.sam.MarkDuplicates.doWork(MarkDuplicates.java:109) +<BR /> + at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:165) +<BR /> + at net.sf.picard.sam.MarkDuplicates.main(MarkDuplicates.java:93) +<BR /> + +<BR /> + + </div> + + <div> + <p>Note: The freely available + <a href="http://picard.sourceforge.net/command-line-overview.shtml">Picard software</a> + generated all outputs reported here. These third party tools were orchestrated by the Galaxy + rgPicardMarkDups.py wrapper and this command line from the Galaxy form: + </p> + <hr /> + <div>/share/shared/relul.galaxy/tools/development/rgPicardMarkDups.py -i /share/shared/relul.galaxy/database/files/000/dataset_57.dat -n Dupes Marked --tmp_dir /export/tmp/relul -o /share/shared/relul.galaxy/database/files/000/dataset_99.dat --remdups false --assumesorted true --readregex [a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).* --optdupedist 100 -j /share/shared/relul.galaxy/tool-data/shared/jars/MarkDuplicates.jar -d /share/shared/relul.galaxy/database/job_working_directory/81/dataset_98_files -t /share/shared/relul.galaxy/database/files/000/dataset_98.dat</div> + </div> + </body> +</html>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/picard_output_validate_tiny_sam.html Mon Feb 17 00:02:22 2014 -0500 @@ -0,0 +1,46 @@ +<style type="text/css"> + tr.d0 td {background-color: oldlace; color: black;} + tr.d1 td {background-color: aliceblue; color: black;} + </style><?xml version="1.0" encoding="utf-8" ?> +<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> +<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"> +<head> +<meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> +<meta name="generator" content="Galaxy rgPicardValidate.py tool output - see http://g2.trac.bx.psu.edu/" /> +<title></title> +<link rel="stylesheet" href="/static/style/base.css" type="text/css" /> +</head> +<body> +<div class="document"> +<b><a href="http://rgenetics.org">Galaxy Rgenetics</a> tool output rgPicardValidate.py run at 19/04/2011 11:19:17</b><br/><b>Running this Galaxy tool produced the following output files (click the filename to view/download a copy).</b><hr/><table> +<tr><td><a href="rgPicardValidate.out">rgPicardValidate.out</a></td></tr> +</table><p/> +<b>Picard on line resources</b><ul> +<li><a href="http://picard.sourceforge.net/index.shtml">Click here for Picard Documentation</a></li> +<li><a href="http://picard.sourceforge.net/picard-metric-definitions.shtml">Click here for Picard Metrics definitions</a></li></ul><hr/> +<b>Picard output</b><hr/> +<table cellpadding="3" > +<tr class="d0"><td>['WARNING: Record 1, Read name both_reads_align_clip_marked, NM tag (nucleotide differences) is missing\n']</td></tr> +<tr class="d1"><td>['WARNING: Record 2, Read name both_reads_present_only_first_aligns, NM tag (nucleotide differences) is missing\n']</td></tr> +<tr class="d0"><td>['WARNING: Record 3, Read name read_2_too_many_gaps, NM tag (nucleotide differences) is missing\n']</td></tr> +<tr class="d1"><td>['ERROR: Record 4, Read name both_reads_align_clip_adapter, The record is out of [queryname] order, prior read name [read_2_too_many_gaps], prior coodinates [1:1]\n']</td></tr> +<tr class="d0"><td>['WARNING: Record 4, Read name both_reads_align_clip_adapter, NM tag (nucleotide differences) is missing\n']</td></tr> +<tr class="d1"><td>['WARNING: Record 5, Read name both_reads_align_clip_adapter, NM tag (nucleotide differences) is missing\n']</td></tr> +<tr class="d0"><td>['WARNING: Record 6, Read name both_reads_align_clip_marked, NM tag (nucleotide differences) is missing\n']</td></tr> +<tr class="d1"><td>['WARNING: Record 7, Read name read_2_too_many_gaps, NM tag (nucleotide differences) is missing\n']</td></tr> +<tr class="d0"><td>['ERROR: Record 8, Read name both_reads_present_only_first_aligns, The record is out of [queryname] order, prior read name [read_2_too_many_gaps], prior coodinates [1:302]\n']</td></tr> +</table> +<b>Picard log</b><hr/> +<pre>## executing samtools sort /udd/rerla/rgalaxy/database/job_working_directory/98/dataset_100_files/tmpELItj4rgSortBamTemp.bam /udd/rerla/rgalaxy/database/job_working_directory/98/dataset_100_files/rgcleansam.sorted returned status 0. Nothing appeared on stderr/stdout + +rectory/98/dataset_100_files/rgPicardValidate.out IGNORE=INVALID_TAG_NM MAX_OUTPUT=100 TMP_DIR=/tmp returned status 1 and log (stdout/stderr) records: +[Tue Apr 19 11:19:17 EDT 2011] net.sf.picard.sam.ValidateSamFile INPUT=/udd/rerla/rgalaxy/database/job_working_directory/98/dataset_100_files/rgcleansam.sorted.bam OUTPUT=/udd/rerla/rgalaxy/database/job_working_directory/98/dataset_100_files/rgPicardValidate.out IGNORE=[INVALID_TAG_NM] MAX_OUTPUT=100 REFERENCE_SEQUENCE=/share/shared/data/hg18/hg18.fasta TMP_DIR=/tmp MODE=VERBOSE IGNORE_WARNINGS=false VALIDATE_INDEX=true IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false +[Tue Apr 19 11:19:17 EDT 2011] net.sf.picard.sam.ValidateSamFile done. +Runtime.totalMemory()=9109504 + + +</pre><hr/>The freely available <a href="http://picard.sourceforge.net/command-line-overview.shtml">Picard software</a> +generated all outputs reported here, using this command line:<br/> +<pre>java -Xmx8g -jar /udd/rerla/rgalaxy/tool-data/shared/jars/ValidateSamFile.jar I=/udd/rerla/rgalaxy/database/job_working_directory/98/dataset_100_files/rgcleansam.sorted.bam R=/share/shared/data/hg18/hg18.fasta O=/udd/rerla/rgalaxy/database/job_working_directory/98/dataset_100_files/rgPicardValidate.out IGNORE=INVALID_TAG_NM MAX_OUTPUT=100 TMP_DIR=/tmp</pre> +</div></body></html> +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/picard_summary_alignment_stats.sam Mon Feb 17 00:02:22 2014 -0500 @@ -0,0 +1,28 @@ +@HD VN:1.0 SO:coordinate +@SQ SN:chr1 LN:101 +@SQ SN:chr2 LN:101 +@SQ SN:chr3 LN:101 +@SQ SN:chr4 LN:101 +@SQ SN:chr5 LN:101 +@SQ SN:chr6 LN:101 +@SQ SN:chr7 LN:202 +@SQ SN:chr8 LN:202 +@RG ID:0 SM:Hi,Mom! +SL-XAV:1:1:0:764#0/1 89 chr1 1 255 101M * 0 0 TTCATGCTGANGCNCTCTTACGATCGTACAGATGCAAATATTAACANNCNTTNAAGNNCANNNNNNNNNCAATACAATANTAGAGTACGTNAACACTCCAN &/,&-.1/6/&&)&).)/,&0768)&/.,/874,&.4137572)&/&&,&1-&.0/&&*,&&&&&&&&&&18775799,&16:8775-56256/69::;0& RG:Z:0 XN:i:1 +SL-XAV:1:1:0:1668#0/2 153 chr2 1 255 101M * 0 0 CATCTCTACANGCGCGTCCTACCAGACGCGCTTCCGATCTGAGAGCATACTTTTCATTGGATTCCAGCACAACTCCATTTTTGATCCACTNGACACCTTTN (/,'-/'0////(1'&&1&&&&'2''-6/,/3-33653.6:1'.86/-++32.-4864653/5/583/346423203+28888644446688456/4880& RG:Z:0 XN:i:1 +SL-XAV:1:1:0:1914#0/2 153 chr3 1 255 101M * 0 0 CGTATGCGCTNTTTATGTCGCCCACAGTGCCTAGTATAGCCCCTGCTAATAAAAAGAGATGAATACGTTTACTTAAAAAACTGAAACTAGNAATGTGCAAN (0,7&&*/*0*,)10/).-*&.&*/6669.&-337599;3,&,6/.,5::999987893+387020775777547999::668997448:::9;999::0& RG:Z:0 +SL-XAV:1:1:0:1639#0/2 153 chr4 1 255 101M * 0 0 CGTGATACCANCTCATGTTCACAGCCAAAGCCTGAAGCTGTCTATTATATTTCTCAACCATAAACTTTTGCCTCAGGCATCCGCAGAATGNTTTGCAGCCN '.&.&&'.0+01'2(1'(''-)','+0041/.+032;:867115/5267-.0/)-5.&-26200224,,0+0/0275/5605688::646875568882*& RG:Z:0 +SL-XAV:1:1:0:68#0/2 137 chr5 1 255 101M * 0 0 NTCTCATTTANAAATGGTTATAAAAACATTTATGCTGAAAAGGTGAAGTTCATTAATGAACAGGCTGACTGTCTCACTATCGCGTTCGCANGACGTTATCT &1<<999;;;;<<<87579:556972789977444.'.023.&,7621/54.49.)/53055-22--''+(.'-))6-168/(3&&0(<).))*&&&&&'0 RG:Z:0 +SL-XAV:1:1:0:700#0/2 137 chr6 1 255 101M * 0 0 NAATTGTTCTNAGTTTCTCGGTTTATGTGCTCTTCCAGGTGGGTAACACAATAATGGCCTTCCAGATCGTAAGAGCGACGTGTGTTGCACNAGTGTCGATC &0::887::::6/646::838388811/679:87640&./2+/-4/28:3,536/4''&&.78/(/554/./02*)*',-(57()&.6(6:(0601'/(,* RG:Z:0 +SL-XAV:1:1:0:1721#0/1 83 chr7 1 255 101M = 102 40 CAACAGAAGGNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCGAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 +SL-XAV:1:1:0:1721#0/2 163 chr7 102 255 101M = 1 -40 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTCACTATGGTACATCTTGTCGTGCGGCNAGAGCATACA &/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1 RG:Z:0 +SL-XAV:1:1:0:105#0/2 147 chr8 1 255 101M = 102 79 CACATCGTGANTCTTACAATCTGCGGTTTCAGATGTGGAGCGATGTGTGAGAGATTGAGCAACTGATCTGAAAAGCAGACACAGCTATTCNTAAGATGACN /))3--/&*()&)&&+'++.'-&,(.))'4,)&'&&,')8,&&*'.&*0'225/&)3-8//)*,5-*).7851453583.3568526:863688:::85.& RG:Z:0 +SL-XAV:1:1:0:105#0/1 99 chr8 102 255 101M = 1 -79 NCAGGTTCAANTGTGCAGCCCNTTTTGAGAGATNNNNNNNNTGNNCTGNAANANNGACACAGCTATTCCTAAGATGACAAGATCAGANAANAAGTCAAGCA &06665578::41.*/7577/&/77403-324.&&&&&&&&/.&&..&&.0&&&&',:9:/-/(55002020+3'12+2/&.2-&//&),&*&&&&&&&51 RG:Z:0 +SL-XAV:1:1:0:1300#0/1 77 * 0 0 * * 0 0 NAAACACAAGNNANAGTCTTANCNGCTATTCCNNNNNNNNNCTNNNCTNAGNANNACATACAACAGTATCCACACAAGTGTACTCGTNCANACATGTGAAC &*5535)*-,,&.&.*-1)*,&'&)&1&&.,)&&&&&&&&&)0&&&0'&&&&.&&*2'/4''0/**&)&,'-&*,&,&&&.0.&)&&&**&,.&&&')&&) RG:Z:0 +SL-XAV:1:1:0:1300#0/2 141 * 0 0 * * 0 0 NGATCATGGANGACTCTCCCCATCCCCCGCTCCAGCGCTCAGTTATATGCCTAGCCTCGGACACGTCACCAACATCTCACGCACTCTGCANAGTCTCTCAC &&'+''3*&-/)/1'26/*-2-/542-*&-&/'/*/&-'&)-')&.'-/&&2+122*'&+,(/-&)((,/-,,.'2(2'+)/&/&-66-&&/16&)&*&'3 RG:Z:0 +SL-XAV:1:1:0:1639#0/1 101 * 0 0 * chr1 1 0 NCCCTCTCAGNNTNTCTGCCANANCCTTAAGCNNNNNNNNNTANNNCTNAANCNNAAACTTTTGCCTCAGGCATCCGCAGAATGTTTNTCNGCCTATATCG &1::::::64/&/&0:3.280&/&087881,/&&&&&&&&&..&&&..&,,&-&&,265341-)/5680&-.5552-25/322/42/&)&&).421&-&-/ RG:Z:0 +SL-XAV:1:1:0:1668#0/1 101 * 0 0 * chr2 1 0 NATAGCATACNNTNCATTGGANTNCAGCACAANNNNNNNNNTGNNNCANTNNANNCCTTTGAGATCGGAAGAGCGGTTCAGCAGGAANNCNCAGACCGATC &1988998890&0&.8863//&.&.0-2875.&&&&&&&&&.)&&&..&.&&.&&.5782-2+262)&-0-0510*.332-2.-,0*&&*&'.&-2-)0., RG:Z:0 +SL-XAV:1:1:0:1914#0/1 101 * 0 0 * chr3 1 0 NTTTTTCTCCNNCNGTGCCTANTNTAGCCCCTNNNNNNNNNAANNNATNANNANNTTTACTTAAAAAACTGAAACTAGTAATGTGCANNANATCGNAAGAG &0::::<<;90&/&.244760&,&.414798/&&&&&&&&&00&&&0.&/&&-&&.4475687363504.&.557/.*)65.&/*./&&.&.+*)&..).& RG:Z:0 +SL-XAV:1:1:0:68#0/1 581 * 0 0 * chr4 1 0 NAATATTCATNNGNTCAGCCTNTNCATTAATTNNNNNNNNNTTNNNATNATNANNTTTTTTATAACCATTTATAAATGAGAGAGATCNTANCACAATATCA &0<<:::::</&&&.73'290&.&0;:::90&&&&&&&&&&..&&&0)&0-&0&&&.743799995253348597921.,.'050.*&.0&)*)&&&&*). RG:Z:0 +SL-XAV:1:1:0:700#0/1 581 * 0 0 * chr5 1 0 NGAAGCCCATNNTNGTGTTACNCNCCTGGAAGNNNNNNNNNACNNNGANACNTNNAACAATTCAGATCGGAAGAGCGGTTCAGCAGANNTNCCGAGACCGA &.88888:88/&0&,03189.&/&.8/))12/&&&&&&&&&./&&&&.&1.&)&&/35962/6432-3&),0&/2+0,),61&-6,&&&'&/,.0&...)0 RG:Z:0 +SL-XAV:1:1:0:764#0/2 165 * 0 0 * chr6 1 0 NACAGATGCANATATTAACAGGCTTTAAAGGACAGATGGACTGCAATACAATAATAGAGTACGTCAACACTCCACAGATCGCTAGAGCATNACATCGGTGT &/:5358::9999::99998255::7275,,/5567-'+387537857:54-4.51'31059547320;73/720+22.4(6.;((.;(;8()(''&&2&& RG:Z:0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/random_phiX_1.fastqsanger Mon Feb 17 00:02:22 2014 -0500 @@ -0,0 +1,80 @@ +@random_phiX_region_0 +TTGAGGCTTGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTT ++ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +@random_phiX_region_1 +GTTAGTGCTGAGGTTGACTTAGTTCATCAGCAAACGCAGAATCAGCGGTA ++ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +@random_phiX_region_2 +AATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTTTCCA ++ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +@random_phiX_region_3 +GGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTC ++ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +@random_phiX_region_4 +ACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTAGCCGAC ++ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +@random_phiX_region_5 +AGCTAAAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACTTCCCA ++ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +@random_phiX_region_6 +CACGTTTATGGTGAACAGTGGATTAAGTTCATGAAGGATGGTGTTAATGC ++ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +@random_phiX_region_7 +AACTACTCCGGTTATCGCTGGCGACTCCTTCGAGATGGACGCCGTTGGCG ++ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +@random_phiX_region_8 +CTCGTGCTCGTCGCTGCGTTGAGGCTTGCGTTTATGGTACGCTGGACTTT ++ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +@random_phiX_region_9 +CAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGACTTAGTTCA ++ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +@random_phiX_region_10 +TACAGTATGCCCATCGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTC ++ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +@random_phiX_region_11 +TATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGACTAAAGAGA ++ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +@random_phiX_region_12 +AGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATA ++ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +@random_phiX_region_13 +TTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGACTAAAGAGATTCA ++ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +@random_phiX_region_14 +CCGGGCAATAACGTTTATGTTGGTTTCATGGTTTGGTCTAACTTTACCGC ++ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +@random_phiX_region_15 +AACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTT ++ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +@random_phiX_region_16 +GCCGGATTTGAGAATCAAAAAGAGCTTACTAAAATGCAACTGGACAATCA ++ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +@random_phiX_region_17 +CATGATTATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAG ++ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +@random_phiX_region_18 +TGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGA ++ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +@random_phiX_region_19 +GCTGTCGCTACTTCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACT ++ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~