Commit 11dc0b2e authored by Aflitos, Saulo Alves's avatar Aflitos, Saulo Alves
Browse files

fixed bug in run.py

parent 6efceef6
......@@ -441,14 +441,14 @@ def run_bwa(data):
# F 4 (NOT qry is unmapped), F 8 (NOT mate is unpaired),
# F 512 (NOT failed QC), F 1024 (NOT PCR duplicate) = 4+8+512+1024= 1548
# bam format
CMD_FILTER = '%(samtools_exe)s view -f 1 -F 1548 -b -o %(bamrnd2)s %(bam)s' % bam_data
#CMD_FIX = '%(samtools_exe)s fixmate ' + '%(filter)s %(fix)s' % bam_data
#CMD_DEDUP = '%(samtools_exe)s rmdup -S ' + '%(filter)s %(dedup)s' % bam_data
CMD_FINDEX = '%(samtools_exe)s index ' + '%(filter)s' % bam_data
CMD_FCOV = '%(samtools_exe)s depth ' + '%(filter)s > %(fcov)s' % bam_data
CMD_FSTAT = '%(samtools_exe)s idxstats ' + '%(filter)s > %(fstat)s' % bam_data
CMD_FFLAG = '%(samtools_exe)s flagstat ' + '%(filter)s > %(fflag)s' % bam_data
CMD_FILTER = '%(samtools_exe)s view -f 1 -F 1548 -b -o %(bamrnd2)s %(bam)s' % bam_data
#CMD_FIX = '%(samtools_exe)s fixmate %(filter)s %(fix)s' % bam_data
#CMD_DEDUP = '%(samtools_exe)s rmdup -S %(filter)s %(dedup)s' % bam_data
CMD_FINDEX = '%(samtools_exe)s index %(filter)s' % bam_data
CMD_FCOV = '%(samtools_exe)s depth %(filter)s > %(fcov)s' % bam_data
CMD_FSTAT = '%(samtools_exe)s idxstats %(filter)s > %(fstat)s' % bam_data
CMD_FFLAG = '%(samtools_exe)s flagstat %(filter)s > %(fflag)s' % bam_data
......
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