SAM.py 文件源码

def __init__(self,inputFile):
        '''constructor. input could be bam or sam'''
        try:
            self.samfile = pysam.Samfile(inputFile,'rb')
            if len(self.samfile.header) ==0:
                print >>sys.stderr, "BAM/SAM file has no header section. Exit!"
                sys.exit(1)
            self.bam_format = True
        except:
            self.samfile = pysam.Samfile(inputFile,'r')
            if len(self.samfile.header) ==0:
                print >>sys.stderr, "BAM/SAM file has no header section. Exit!"
                sys.exit(1)
            self.bam_format = False