Mercurial > repos > evan > bwa_wrappers
diff bwa_wrapper.py @ 2:3a001705dc94 draft default tip
Uploaded
| author | evan |
|---|---|
| date | Fri, 06 Jun 2014 12:55:09 -0400 |
| parents | 8d92246f41bb |
| children |
line wrap: on
line diff
--- a/bwa_wrapper.py Fri Jun 06 12:39:56 2014 -0400 +++ b/bwa_wrapper.py Fri Jun 06 12:55:09 2014 -0400 @@ -76,6 +76,7 @@ parser.add_option( '-X', '--do_not_build_index', dest='do_not_build_index', action='store_true', help="Don't build index" ) parser.add_option( '-H', '--suppressHeader', dest='suppressHeader', help='Suppress header' ) parser.add_option( '-I', '--illumina1.3', dest='illumina13qual', help='Input FASTQ files have Illuina 1.3 quality scores' ) + parser.add_option( '', '--meta_tsv', dest='metadata_tsv', help='Meta data for filling things like sequencing center' ) (options, args) = parser.parse_args() # output version # of tool @@ -204,7 +205,7 @@ if options.metadata_tsv: f = open(options.metadata_tsv, 'r') cols = f.readline().split('\t') - readGroup = '@RG\tID:1\tDS:%s\tPU:%s\tLB:%s\tCN:BMGC\tDT:%s\tFR:%s\tRR:%s\tPL:ILLUMINA' % ( cols[4], cols[16], cols[14], cols[1], cols[19], cols[20] ) + readGroup = '@RG\tID:%s\tDS:%s\tPU:%s\tLB:%s\tCN:BMGC\tDT:%s\tFR:%s\tRR:%s\tPL:ILLUMINA\tSM:%s' % ( cols[0], cols[4], cols[16], cols[14], cols[1], cols[19], cols[20], cols[18] ) gen_alignment_cmds += ' -r "%s"' % readGroup print readGroup if options.rgid: