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@ekg
Created February 4, 2019 11:37
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summarize the softclips in a SAM/BAM file
#!/usr/bin/python
import sys;
import pysam
bamFile = sys.argv[1];
bamFP = pysam.Samfile(bamFile, "rb");
for read in bamFP:
if( not( read.is_unmapped ) ): #if it's mapped
cigarLine=read.cigar;
for (cigarType,cigarLength) in cigarLine:
try:
if cigarType == 4:
print cigarLength
except:
print "Problem";
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