# HG changeset patch # User devteam # Date 1392613342 18000 # Node ID 2bfb9ce28275a49d39f7c8133e8d2ce4d8a76ea4 # Parent d8d22fa853d6b9430cd4d57003bdb693b9c9ba23 Uploaded diff -r d8d22fa853d6 -r 2bfb9ce28275 test-data/AsMetrics --- /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 + + diff -r d8d22fa853d6 -r 2bfb9ce28275 test-data/bfast_out1.sam --- /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 diff -r d8d22fa853d6 -r 2bfb9ce28275 test-data/bwa_wrapper_in2.fastqsanger --- /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$5+.(9II +@seq22/1 +AATCAAACTTACCAAGGG ++ +IIIIIIIIIIIIIIIIII +@seq23/1 +TGTGCTTCCCCAACTTGA ++ +IIIIIIIIIIIIIIIIII +@seq24/1 +TTTCTCAATCCCCAATGC ++ +IIIIIIIIIIIIIIIIII +@seq25/1 +TTGCTACTGACCGCTCTT ++ +IIIIIIIIIIIIIIIIII +@seq26/1 +CCGCGTGAAATTTCTATG ++ +IIIIIIIIIIIIIIIIII +@seq27/1 +CGCTAATCAAGTTGTTTC ++ +IIIIIIIIIIIIIIIIII +@seq28/1 +AAAGAGATTATTTGTCGG ++ +IIIIIIIIIIIIIIIIII +@seq29/1 +CAAATTAATGCGCGCTTC ++ +IIIIIIIIIIIIIIIIII +@seq30/1 +ATCCCCTATGCTTGGCTT ++ +IIIIIIIIIIIIIIIIII diff -r d8d22fa853d6 -r 2bfb9ce28275 test-data/bwa_wrapper_in3.fastqsanger --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bwa_wrapper_in3.fastqsanger Mon Feb 17 00:02:22 2014 -0500 @@ -0,0 +1,120 @@ +@seq1/2 +ACGCTCCTTTAAAATATC ++ +IIIII$%*$G$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 diff -r d8d22fa853d6 -r 2bfb9ce28275 test-data/bwa_wrapper_out3.sam --- /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 diff -r d8d22fa853d6 -r 2bfb9ce28275 test-data/phiX.fasta --- /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 + diff -r d8d22fa853d6 -r 2bfb9ce28275 test-data/picard_ARRG_input1.bam Binary file test-data/picard_ARRG_input1.bam has changed diff -r d8d22fa853d6 -r 2bfb9ce28275 test-data/picard_ARRG_input1.sam --- /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 diff -r d8d22fa853d6 -r 2bfb9ce28275 test-data/picard_ARRG_input2.sam --- /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 diff -r d8d22fa853d6 -r 2bfb9ce28275 test-data/picard_ARRG_output1.sam --- /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 diff -r d8d22fa853d6 -r 2bfb9ce28275 test-data/picard_ARRG_output2.bam Binary file test-data/picard_ARRG_output2.bam has changed diff -r d8d22fa853d6 -r 2bfb9ce28275 test-data/picard_ARRG_output2.sam --- /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 diff -r d8d22fa853d6 -r 2bfb9ce28275 test-data/picard_ARRG_output3.bam Binary file test-data/picard_ARRG_output3.bam has changed diff -r d8d22fa853d6 -r 2bfb9ce28275 test-data/picard_ARRG_output3.bam.bai Binary file test-data/picard_ARRG_output3.bam.bai has changed diff -r d8d22fa853d6 -r 2bfb9ce28275 test-data/picard_ARRG_output3.sam --- /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 diff -r d8d22fa853d6 -r 2bfb9ce28275 test-data/picard_BIS_input1.bam Binary file test-data/picard_BIS_input1.bam has changed diff -r d8d22fa853d6 -r 2bfb9ce28275 test-data/picard_BIS_input1.sam --- /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 diff -r d8d22fa853d6 -r 2bfb9ce28275 test-data/picard_BIS_output1.txt --- /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 @@ + + + + + + + + + + +
+Galaxy tool BamIndexStats run at 12/05/2011 14:18:06
The following output files were created (click the filename to view/download a copy):
+ + +
BamIndexStats.log
BamIndexStats.metrics.txt

+Picard on line resources

+Picard output
+ + + + + +
chr1 length= 101 Aligned= 0 Unaligned= 0
chr7 length= 404 Aligned= 7 Unaligned= 0
chr8 length= 202 Aligned= 0 Unaligned= 0
NoCoordinateCount= 1
+Picard Tool Run Log
+
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
+
+
+
The freely available Picard software +generated all outputs reported here running as a Galaxy tool
+ diff -r d8d22fa853d6 -r 2bfb9ce28275 test-data/picard_BIS_output2.txt --- /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 @@ + + + + + + + + + + +
+Galaxy tool BamIndexStats run at 12/05/2011 14:18:22
The following output files were created (click the filename to view/download a copy):
+ + +
BamIndexStats.log
BamIndexStats.metrics.txt

+Picard on line resources

+Picard output
+ + + + + + + +
chr1 length= 101 Aligned= 0 Unaligned= 0
chr7 length= 404 Aligned= 7 Unaligned= 0
chr8 length= 202 Aligned= 0 Unaligned= 0
chr10 length= 303 Aligned= 0 Unaligned= 0
chr14 length= 505 Aligned= 0 Unaligned= 0
NoCoordinateCount= 1
+Picard Tool Run Log
+
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
+
+
+
The freely available Picard software +generated all outputs reported here running as a Galaxy tool
+ diff -r d8d22fa853d6 -r 2bfb9ce28275 test-data/picard_MD_output1.txt --- /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 + diff -r d8d22fa853d6 -r 2bfb9ce28275 test-data/picard_MD_output2.bam Binary file test-data/picard_MD_output2.bam has changed diff -r d8d22fa853d6 -r 2bfb9ce28275 test-data/picard_MD_output3.txt --- /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 + diff -r d8d22fa853d6 -r 2bfb9ce28275 test-data/picard_MD_output4.sam --- /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 diff -r d8d22fa853d6 -r 2bfb9ce28275 test-data/picard_RSH_input1.bam Binary file test-data/picard_RSH_input1.bam has changed diff -r d8d22fa853d6 -r 2bfb9ce28275 test-data/picard_RSH_input1.sam --- /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 diff -r d8d22fa853d6 -r 2bfb9ce28275 test-data/picard_RSH_output1.sam --- /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 diff -r d8d22fa853d6 -r 2bfb9ce28275 test-data/picard_RSH_output2.bam Binary file test-data/picard_RSH_output2.bam has changed diff -r d8d22fa853d6 -r 2bfb9ce28275 test-data/picard_RSH_output2.sam --- /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 diff -r d8d22fa853d6 -r 2bfb9ce28275 test-data/picard_RS_input1.bam Binary file test-data/picard_RS_input1.bam has changed diff -r d8d22fa853d6 -r 2bfb9ce28275 test-data/picard_RS_input2.sam --- /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""IIIIIIIIIIIIIIIIIIIphiX1 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 diff -r d8d22fa853d6 -r 2bfb9ce28275 test-data/picard_RS_output1.bam Binary file test-data/picard_RS_output1.bam has changed diff -r d8d22fa853d6 -r 2bfb9ce28275 test-data/picard_RS_output2.sam --- /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""IIIIIIIIIIIIIIIIIIIchrM +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 diff -r d8d22fa853d6 -r 2bfb9ce28275 test-data/picard_input_sorted_pair.bam --- /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 diff -r d8d22fa853d6 -r 2bfb9ce28275 test-data/picard_input_sorted_pair.sam --- /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 diff -r d8d22fa853d6 -r 2bfb9ce28275 test-data/picard_input_summary_alignment_stats.sam --- /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<<::::: + tr.d0 td {background-color: oldlace; color: black;} + tr.d1 td {background-color: aliceblue; color: black;} + + + + + + + + + + +
+Galaxy tool CollectAlignmentSummaryMetrics run at 11/11/2011 08:07:27
The following output files were created (click the filename to view/download a copy):
+ + +
CollectAlignmentSummaryMetrics.log
CollectAlignmentSummaryMetrics.metrics.txt

+Picard on line resources

+Picard output (transposed to make it easier to see)
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
## net.sf.picard.metrics.StringHeader
# 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
## net.sf.picard.metrics.StringHeader
# Started on: Fri Nov 11 08:07:22 EST 2011
## METRICS CLASS net.sf.picard.analysis.AlignmentSummaryMetrics
CATEGORYFIRST_OF_PAIR 
TOTAL_READS5 
PF_READS5 
PCT_PF_READS1 
PF_NOISE_READS0 
PF_READS_ALIGNED0 
PCT_PF_READS_ALIGNED0 
PF_ALIGNED_BASES0 
PF_HQ_ALIGNED_READS0 
PF_HQ_ALIGNED_BASES0 
PF_HQ_ALIGNED_Q20_BASES0 
PF_HQ_MEDIAN_MISMATCHES0 
PF_MISMATCH_RATE0 
PF_HQ_ERROR_RATE0 
PF_INDEL_RATE0 
MEAN_READ_LENGTH13 
READS_ALIGNED_IN_PAIRS0 
PCT_READS_ALIGNED_IN_PAIRS0 
BAD_CYCLES0 
STRAND_BALANCE0 
PCT_CHIMERAS0 
PCT_ADAPTER0 
SAMPLE 
LIBRARY 
READ_GROUP + + 
+Picard Tool Run Log
+
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
+
+
The freely available Picard software +generated all outputs reported here running as a Galaxy tool
+ diff -r d8d22fa853d6 -r 2bfb9ce28275 test-data/picard_output_GcBias_uploaded_hg18_summary_alignment_stats.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<<::::: + tr.d0 td {background-color: oldlace; color: black;} + tr.d1 td {background-color: aliceblue; color: black;} + + + + + + + + + + +
+Galaxy tool CollectAlignmentSummaryMetrics run at 11/11/2011 08:07:10
The following output files were created (click the filename to view/download a copy):
+ + +
CollectAlignmentSummaryMetrics.log
CollectAlignmentSummaryMetrics.metrics.txt

+Picard on line resources

+Picard output (transposed to make it easier to see)
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
## net.sf.picard.metrics.StringHeader
# 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
## net.sf.picard.metrics.StringHeader
# Started on: Fri Nov 11 08:07:10 EST 2011
## METRICS CLASS net.sf.picard.analysis.AlignmentSummaryMetrics
CATEGORYFIRST_OF_PAIR 
TOTAL_READS4 
PF_READS4 
PCT_PF_READS1 
PF_NOISE_READS0 
PF_READS_ALIGNED4 
PCT_PF_READS_ALIGNED1 
PF_ALIGNED_BASES404 
PF_HQ_ALIGNED_READS4 
PF_HQ_ALIGNED_BASES404 
PF_HQ_ALIGNED_Q20_BASES28 
PF_HQ_MEDIAN_MISMATCHES78 
PF_MISMATCH_RATE0.777228 
PF_HQ_ERROR_RATE0.777228 
PF_INDEL_RATE0 
MEAN_READ_LENGTH101 
READS_ALIGNED_IN_PAIRS3 
PCT_READS_ALIGNED_IN_PAIRS0.75 
BAD_CYCLES63 
STRAND_BALANCE0.25 
PCT_CHIMERAS0 
PCT_ADAPTER0 
SAMPLE 
LIBRARY 
READ_GROUP + + 
+Picard Tool Run Log
+
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
+
+
The freely available Picard software +generated all outputs reported here running as a Galaxy tool
+ diff -r d8d22fa853d6 -r 2bfb9ce28275 test-data/picard_output_collect_AS_sorted_pair.txt --- /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 + + diff -r d8d22fa853d6 -r 2bfb9ce28275 test-data/picard_output_estlibcomplexity_tinysam.html --- /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 @@ + + + + + + + + + + +
+Galaxy Rgenetics tool output rgEstLibComplexity.py run at 10/04/2011 14:52:24Your job produced the following output files.
+ + +
estlibcompout.txt

+Picard on line resources

+Picard output (transposed to make it easier to see)
+ +
## net.sf.picard.metrics.StringHeader
# 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
## net.sf.picard.metrics.StringHeader
# Started on: Sun Apr 10 14:52:24 EDT 2011
+Picard log
+
## 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
+
+
+
The freely available Picard software +generated all outputs reported here, using this command line:
+
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
+
+ diff -r d8d22fa853d6 -r 2bfb9ce28275 test-data/picard_output_fixmate_sorted_pair.bam Binary file test-data/picard_output_fixmate_sorted_pair.bam has changed diff -r d8d22fa853d6 -r 2bfb9ce28275 test-data/picard_output_fixmate_sorted_pair.sam --- /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 diff -r d8d22fa853d6 -r 2bfb9ce28275 test-data/picard_output_fixmate_tiny.bam Binary file test-data/picard_output_fixmate_tiny.bam has changed diff -r d8d22fa853d6 -r 2bfb9ce28275 test-data/picard_output_gc_summary_alignment_stats.pdf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/picard_output_gc_summary_alignment_stats.pdf Mon Feb 17 00:02:22 2014 -0500 @@ -0,0 +1,829 @@ +%PDF-1.4 +%âãÏÓ\r +1 0 obj +<< +/CreationDate (D:20101026135453) +/ModDate (D:20101026135453) +/Title (R Graphics Output) +/Producer (R 2.10.1) +/Creator (R) +>> +endobj +2 0 obj +<< +/Type /Catalog +/Pages 3 0 R +>> +endobj +5 0 obj +<< +/Type /Page +/Parent 3 0 R +/Contents 6 0 R +/Resources 4 0 R +>> +endobj +6 0 obj +<< +/Length 7 0 R +>> +stream +q +Q q 57.60 72.00 388.80 374.40 re W n +0.255 0.412 0.882 RG +0.75 w 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+/Encoding 8 0 R +>> endobj +xref +0 12 +0000000000 65535 f +0000000021 00000 n +0000000164 00000 n +0000016896 00000 n +0000016979 00000 n +0000000213 00000 n +0000000293 00000 n +0000016875 00000 n +0000017083 00000 n +0000017340 00000 n +0000017423 00000 n +0000017520 00000 n +trailer +<< +/Size 12 +/Info 1 0 R +/Root 2 0 R +>> +startxref +17622 +%%EOF diff -r d8d22fa853d6 -r 2bfb9ce28275 test-data/picard_output_gc_summary_alignment_stats.txt --- /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 + + diff -r d8d22fa853d6 -r 2bfb9ce28275 test-data/picard_output_hs_transposed_summary_alignment_stats.html --- /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 @@ + + + + + + + + + + +
+Galaxy tool wrapper run picard_wrapper at 07/05/2011 00:15:30
The following output files were created (click the filename to view/download a copy):
+ + + +
tempSamHead.txt
rgPicardHsMetrics.bait
CalculateHsMetrics.metrics.txt

+Picard on line resources - maxrows=100

+Picard output (transposed to make it easier to see)
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
## net.sf.picard.metrics.StringHeader
# 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
## net.sf.picard.metrics.StringHeader
# Started on: Sat May 07 00:15:15 EDT 2011
## METRICS CLASS net.sf.picard.analysis.directed.HsMetrics
BAIT_SETrgPicardHsMetrics
GENOME_SIZE2040
BAIT_TERRITORY14601938
TARGET_TERRITORY14601938
BAIT_DESIGN_EFFICIENCY1
TOTAL_READS18
PF_READS16
PF_UNIQUE_READS16
PCT_PF_READS0.888889
PCT_PF_UQ_READS0.888889
PF_UQ_READS_ALIGNED10
PCT_PF_UQ_READS_ALIGNED0.625
PF_UQ_BASES_ALIGNED1010
ON_BAIT_BASES0
NEAR_BAIT_BASES0
OFF_BAIT_BASES1010
ON_TARGET_BASES0
PCT_SELECTED_BASES0
PCT_OFF_BAIT1
ON_BAIT_VS_SELECTED?
MEAN_BAIT_COVERAGE0
MEAN_TARGET_COVERAGE?
PCT_USABLE_BASES_ON_BAIT0
PCT_USABLE_BASES_ON_TARGET0
FOLD_ENRICHMENT0
ZERO_CVG_TARGETS_PCT0.841776
FOLD_80_BASE_PENALTY?
PCT_TARGET_BASES_2X0
PCT_TARGET_BASES_10X0
PCT_TARGET_BASES_20X0
PCT_TARGET_BASES_30X0
HS_LIBRARY_SIZE
HS_PENALTY_10X0
HS_PENALTY_20X0
HS_PENALTY_30X +0 +
+Picard log
+
## 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
+
+## WARNING - 434559 log lines truncated - CalculateHsMetrics.log contains entire output
The freely available Picard software +generated all outputs reported here running as a Galaxy tool
+ diff -r d8d22fa853d6 -r 2bfb9ce28275 test-data/picard_output_insertsize_tinysam.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 @@ + + + + + + + + + + +
+Galaxy tool CollectInsertSizeMetrics run at 13/05/2011 15:20:46
+ +
+The following output files were created (click the filename to view/download a copy):
+ + + + +
CollectInsertSizeMetrics.metrics.txt
CollectInsertSizeMetrics.log
InsertSizeHist.pdf
InsertSizeHist.jpg

+Picard on line resources

+Picard output (transposed to make it easier to see)
+ + + + + + + +
## net.sf.picard.metrics.StringHeader
# 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
## net.sf.picard.metrics.StringHeader
# Started on: Fri May 13 15:20:45 EDT 2011
## METRICS CLASS net.sf.picard.analysis.InsertSizeMetrics
## HISTOGRAM java.lang.Integer
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
96 96 96 96 ? 1 FR 1 1 1 1 1 1 1 1 1 1
201 201 201 201 ? 1 RF 1 1 1 1 1 1 1 1 1 1
insert_size fr_count rf_count
96 1 0
201 0 1
+Picard Tool Run Log
+
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
+
+
The freely available Picard software +generated all outputs reported here running as a Galaxy tool
+ diff -r d8d22fa853d6 -r 2bfb9ce28275 test-data/picard_output_markdups_remdupes.bam Binary file test-data/picard_output_markdups_remdupes.bam has changed diff -r d8d22fa853d6 -r 2bfb9ce28275 test-data/picard_output_markdups_sortedpairsam.bam Binary file test-data/picard_output_markdups_sortedpairsam.bam has changed diff -r d8d22fa853d6 -r 2bfb9ce28275 test-data/picard_output_markdups_sortedpairsam.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 @@ + + + + + + + + + + +
+Galaxy tool MarkDuplicates run at 12/05/2011 14:34:29
The following output files were created (click the filename to view/download a copy):
+ + +
MarkDuplicates.log
MarkDuplicates.metrics.txt

+Picard on line resources

+Picard output (transposed to make it easier to see)
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
## net.sf.picard.metrics.StringHeader
# 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
## net.sf.picard.metrics.StringHeader
# Started on: Thu May 12 14:34:28 EDT 2011
## METRICS CLASS net.sf.picard.sam.DuplicationMetrics
LIBRARY 
UNPAIRED_READS_EXAMINED1 
READ_PAIRS_EXAMINED3 
UNMAPPED_READS1 
UNPAIRED_READ_DUPLICATES1 
READ_PAIR_DUPLICATES1 
READ_PAIR_OPTICAL_DUPLICATES0 
PERCENT_DUPLICATION0.428571 
ESTIMATED_LIBRARY_SIZE +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
+Picard Tool Run Log
+
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
+
+
+
The freely available Picard software +generated all outputs reported here running as a Galaxy tool
+ diff -r d8d22fa853d6 -r 2bfb9ce28275 test-data/picard_output_markdups_sortedpairsam.sam --- /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 @@ + + + + + + + + + +
+

Rgenetics tool rgPicardMarkDups.py run at 19/11/2010 18:25:23

+ Your job produced the following outputs - check here for a record of what was done and any unexpected events +
+
+ Output files. + + +
rgPicardMarkDups.txt (1.8 KB)
+
+
+
+ Log of activity +
+ ## 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: +
+[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 +
+INFO 2010-11-19 18:25:23 MarkDuplicates Start of doWork freeMemory: 8645600; totalMemory: 9109504; maxMemory: 1908932608 +
+INFO 2010-11-19 18:25:23 MarkDuplicates Reading input file and constructing read end information. +
+INFO 2010-11-19 18:25:23 MarkDuplicates Will retain up to 7575129 data points before spilling to disk. +
+[Fri Nov 19 18:25:23 EST 2010] net.sf.picard.sam.MarkDuplicates done. +
+Runtime.totalMemory()=130351104 +
+Exception in thread "main" net.sf.picard.PicardException: /share/shared/relul.galaxy/database/files/000/dataset_57.dat is not coordinate sorted. +
+ at net.sf.picard.sam.MarkDuplicates.buildSortedReadEndLists(MarkDuplicates.java:248) +
+ at net.sf.picard.sam.MarkDuplicates.doWork(MarkDuplicates.java:109) +
+ at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:165) +
+ at net.sf.picard.sam.MarkDuplicates.main(MarkDuplicates.java:93) +
+ +
+ +
+ +
+

Note: The freely available + Picard software + 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: +

+
+
/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
+
+ + diff -r d8d22fa853d6 -r 2bfb9ce28275 test-data/picard_output_validate_tiny_sam.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 @@ + + + + + + + + + + +
+Galaxy Rgenetics tool output rgPicardValidate.py run at 19/04/2011 11:19:17
Running this Galaxy tool produced the following output files (click the filename to view/download a copy).
+ +
rgPicardValidate.out

+Picard on line resources

+Picard output
+ + + + + + + + + + +
['WARNING: Record 1, Read name both_reads_align_clip_marked, NM tag (nucleotide differences) is missing\n']
['WARNING: Record 2, Read name both_reads_present_only_first_aligns, NM tag (nucleotide differences) is missing\n']
['WARNING: Record 3, Read name read_2_too_many_gaps, NM tag (nucleotide differences) is missing\n']
['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']
['WARNING: Record 4, Read name both_reads_align_clip_adapter, NM tag (nucleotide differences) is missing\n']
['WARNING: Record 5, Read name both_reads_align_clip_adapter, NM tag (nucleotide differences) is missing\n']
['WARNING: Record 6, Read name both_reads_align_clip_marked, NM tag (nucleotide differences) is missing\n']
['WARNING: Record 7, Read name read_2_too_many_gaps, NM tag (nucleotide differences) is missing\n']
['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']
+Picard log
+
## 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
+
+
+
The freely available Picard software +generated all outputs reported here, using this command line:
+
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
+
+ diff -r d8d22fa853d6 -r 2bfb9ce28275 test-data/picard_summary_alignment_stats.sam --- /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<<:::::