1Setup: 2 3 $ TOOLS_BIN="@PacBioBAM_BinDir@" && export TOOLS_BIN 4 $ PBMERGE="$TOOLS_BIN/pbmerge" && export PBMERGE 5 $ BAM2SAM="$TOOLS_BIN/bam2sam" && export BAM2SAM 6 7 $ DATADIR="@PacBioBAM_TestsDir@/data" && export DATADIR 8 $ INPUT_FOFN="$DATADIR/merge.fofn" && export INPUT_FOFN 9 $ INPUT_1="$DATADIR/aligned.bam" && export INPUT_1 10 $ INPUT_2="$DATADIR/aligned2.bam" && export INPUT_2 11 12 $ MERGED_BAM="@GeneratedTestDataDir@/aligned_ordering_merged.bam" && export MERGED_BAM 13 $ MERGED_BAM_PBI="@GeneratedTestDataDir@/aligned_ordering_merged.bam.pbi" && export MERGED_BAM_PBI 14 15Sanity Check: 16 17 $ $BAM2SAM --header-only $INPUT_1 18 @HD\tVN:1.3.1\tSO:coordinate\tpb:3.0.3 (esc) 19 @SQ\tSN:lambda_NEB3011\tLN:48502\tM5:a1319ff90e994c8190a4fe6569d0822a (esc) 20 @RG\tID:0d7b28fa\tPL:PACBIO\tDS:READTYPE=SUBREAD;BINDINGKIT=100-619-300;SEQUENCINGKIT=100-619-400;BASECALLERVERSION=3.0;FRAMERATEHZ=100\tPU:singleInsertion\tPM:SEQUEL (esc) 21 @PG\tID:bwa\tPN:bwa\tVN:0.7.10-r1017-dirty\tCL:bwa mem lambdaNEB.fa singleInsertion.fasta (esc) 22 23 $ $BAM2SAM --no-header $INPUT_1 | cut -f 1,3,4 | head -n 10 24 singleInsertion/100/0_49\tlambda_NEB3011\t5211 (esc) 25 singleInsertion/200/0_49\tlambda_NEB3011\t5211 (esc) 26 singleInsertion/100/0_111\tlambda_NEB3011\t9378 (esc) 27 singleInsertion/100/0_111\tlambda_NEB3011\t9378 (esc) 28 29 $ $BAM2SAM --header-only $INPUT_2 30 @HD\tVN:1.3.1\tSO:coordinate\tpb:3.0.3 (esc) 31 @SQ\tSN:lambda_NEB3011\tLN:48502\tM5:a1319ff90e994c8190a4fe6569d0822a (esc) 32 @RG\tID:b89a4406\tDS:READTYPE=SUBREAD;BINDINGKIT=100356300;SEQUENCINGKIT=100356200;BASECALLERVERSION=2.3;FRAMERATEHZ=100;InsertionQV=iq;DeletionQV=dq;SubstitutionQV=sq;MergeQV=mq;SubstitutionTag=st;DeletionTag=dt\tPL:PACBIO\tPU:m140905_042212_sidney_c100564852550000001823085912221377_s1_X0\tSM:c100564852550000001823085912221377\tPM:SEQUEL (esc) 33 @PG\tID:BLASR\tVN:1.3.1.141565\tCL:/home/UNIXHOME/yli/for_the_people/blasr_bam_out/blasr m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.1.bax.h5 lambdaNEB.fa -out tmp.bam -bam -bestn 10 -minMatch 12 -nproc 8 -minSubreadLength 50 -minReadLength 50 -randomSeed 1 -clipping subread (esc) 34 35 $ $BAM2SAM --no-header $INPUT_2 | cut -f 1,3,4 | head -n 10 36 m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/49050/48_1132\tlambda_NEB3011\t1 (esc) 37 m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/32328/387_1134\tlambda_NEB3011\t303 (esc) 38 m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/32328/0_344\tlambda_NEB3011\t676 (esc) 39 m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/6469/9936_10187\tlambda_NEB3011\t2171 (esc) 40 m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/6469/10232_10394\tlambda_NEB3011\t2204 (esc) 41 m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/30983/7468_8906\tlambda_NEB3011\t3573 (esc) 42 m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/13473/5557_7235\tlambda_NEB3011\t4507 (esc) 43 m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/13473/7285_8657\tlambda_NEB3011\t4508 (esc) 44 m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/19915/426_1045\tlambda_NEB3011\t4593 (esc) 45 m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/30983/7064_7421\tlambda_NEB3011\t4670 (esc) 46 47Normal Merge from FOFN: 48 49 $ $PBMERGE -o $MERGED_BAM $INPUT_FOFN 50 51 $ [ -f $MERGED_BAM ] && echo "Found" || echo "Not found" 52 Found 53 54 $ [ -f $MERGED_BAM_PBI ] && echo "Found" || echo "Not found" 55 Found 56 57 $ $BAM2SAM --header-only $MERGED_BAM 58 @HD\tVN:1.3.1\tSO:coordinate\tpb:3.0.3 (esc) 59 @SQ\tSN:lambda_NEB3011\tLN:48502\tM5:a1319ff90e994c8190a4fe6569d0822a (esc) 60 @RG\tID:0d7b28fa\tPL:PACBIO\tDS:READTYPE=SUBREAD;BINDINGKIT=100-619-300;SEQUENCINGKIT=100-619-400;BASECALLERVERSION=3.0;FRAMERATEHZ=100\tPU:singleInsertion\tPM:SEQUEL (esc) 61 @RG\tID:b89a4406\tPL:PACBIO\tDS:READTYPE=SUBREAD;DeletionQV=dq;DeletionTag=dt;InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;SubstitutionTag=st;BINDINGKIT=100356300;SEQUENCINGKIT=100356200;BASECALLERVERSION=2.3;FRAMERATEHZ=100\tPU:m140905_042212_sidney_c100564852550000001823085912221377_s1_X0\tSM:c100564852550000001823085912221377\tPM:SEQUEL (esc) 62 @PG\tID:BLASR\tVN:1.3.1.141565\tCL:/home/UNIXHOME/yli/for_the_people/blasr_bam_out/blasr m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.1.bax.h5 lambdaNEB.fa -out tmp.bam -bam -bestn 10 -minMatch 12 -nproc 8 -minSubreadLength 50 -minReadLength 50 -randomSeed 1 -clipping subread (esc) 63 @PG\tID:bwa\tPN:bwa\tVN:0.7.10-r1017-dirty\tCL:bwa mem lambdaNEB.fa singleInsertion.fasta (esc) 64 @PG\tID:pbmerge-@PacBioBAM_VERSION@\tPN:pbmerge\tVN:@PacBioBAM_VERSION@ (esc) 65 66 $ $BAM2SAM --no-header $MERGED_BAM | cut -f 1,3,4 | head -n 20 67 m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/49050/48_1132\tlambda_NEB3011\t1 (esc) 68 m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/32328/387_1134\tlambda_NEB3011\t303 (esc) 69 m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/32328/0_344\tlambda_NEB3011\t676 (esc) 70 m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/6469/9936_10187\tlambda_NEB3011\t2171 (esc) 71 m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/6469/10232_10394\tlambda_NEB3011\t2204 (esc) 72 m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/30983/7468_8906\tlambda_NEB3011\t3573 (esc) 73 m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/13473/5557_7235\tlambda_NEB3011\t4507 (esc) 74 m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/13473/7285_8657\tlambda_NEB3011\t4508 (esc) 75 m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/19915/426_1045\tlambda_NEB3011\t4593 (esc) 76 m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/30983/7064_7421\tlambda_NEB3011\t4670 (esc) 77 singleInsertion/100/0_49\tlambda_NEB3011\t5211 (esc) 78 singleInsertion/200/0_49\tlambda_NEB3011\t5211 (esc) 79 singleInsertion/100/0_111\tlambda_NEB3011\t9378 (esc) 80 singleInsertion/100/0_111\tlambda_NEB3011\t9378 (esc) 81 82 $ rm $MERGED_BAM 83 $ rm $MERGED_BAM_PBI 84 85Normal Merge from FOFN (disabled PBI): 86 87 $ $PBMERGE --no-pbi -o $MERGED_BAM $INPUT_FOFN 88 89 $ [ -f $MERGED_BAM ] && echo "Found" || echo "Not found" 90 Found 91 92 $ [ -f $MERGED_BAM_PBI ] && echo "Found" || echo "Not found" 93 Not found 94 95 $ $BAM2SAM --header-only $MERGED_BAM 96 @HD\tVN:1.3.1\tSO:coordinate\tpb:3.0.3 (esc) 97 @SQ\tSN:lambda_NEB3011\tLN:48502\tM5:a1319ff90e994c8190a4fe6569d0822a (esc) 98 @RG\tID:0d7b28fa\tPL:PACBIO\tDS:READTYPE=SUBREAD;BINDINGKIT=100-619-300;SEQUENCINGKIT=100-619-400;BASECALLERVERSION=3.0;FRAMERATEHZ=100\tPU:singleInsertion\tPM:SEQUEL (esc) 99 @RG\tID:b89a4406\tPL:PACBIO\tDS:READTYPE=SUBREAD;DeletionQV=dq;DeletionTag=dt;InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;SubstitutionTag=st;BINDINGKIT=100356300;SEQUENCINGKIT=100356200;BASECALLERVERSION=2.3;FRAMERATEHZ=100\tPU:m140905_042212_sidney_c100564852550000001823085912221377_s1_X0\tSM:c100564852550000001823085912221377\tPM:SEQUEL (esc) 100 @PG\tID:BLASR\tVN:1.3.1.141565\tCL:/home/UNIXHOME/yli/for_the_people/blasr_bam_out/blasr m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.1.bax.h5 lambdaNEB.fa -out tmp.bam -bam -bestn 10 -minMatch 12 -nproc 8 -minSubreadLength 50 -minReadLength 50 -randomSeed 1 -clipping subread (esc) 101 @PG\tID:bwa\tPN:bwa\tVN:0.7.10-r1017-dirty\tCL:bwa mem lambdaNEB.fa singleInsertion.fasta (esc) 102 @PG\tID:pbmerge-@PacBioBAM_VERSION@\tPN:pbmerge\tVN:@PacBioBAM_VERSION@ (esc) 103 104 $ $BAM2SAM --no-header $MERGED_BAM | cut -f 1,3,4 | head -n 20 105 m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/49050/48_1132\tlambda_NEB3011\t1 (esc) 106 m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/32328/387_1134\tlambda_NEB3011\t303 (esc) 107 m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/32328/0_344\tlambda_NEB3011\t676 (esc) 108 m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/6469/9936_10187\tlambda_NEB3011\t2171 (esc) 109 m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/6469/10232_10394\tlambda_NEB3011\t2204 (esc) 110 m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/30983/7468_8906\tlambda_NEB3011\t3573 (esc) 111 m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/13473/5557_7235\tlambda_NEB3011\t4507 (esc) 112 m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/13473/7285_8657\tlambda_NEB3011\t4508 (esc) 113 m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/19915/426_1045\tlambda_NEB3011\t4593 (esc) 114 m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/30983/7064_7421\tlambda_NEB3011\t4670 (esc) 115 singleInsertion/100/0_49\tlambda_NEB3011\t5211 (esc) 116 singleInsertion/200/0_49\tlambda_NEB3011\t5211 (esc) 117 singleInsertion/100/0_111\tlambda_NEB3011\t9378 (esc) 118 singleInsertion/100/0_111\tlambda_NEB3011\t9378 (esc) 119 120 $ rm $MERGED_BAM 121