explain_sam_flags.py

#!/usr/bin/env python

# The MIT License
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# Copyright (c) $today.year The Broad Institute
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# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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# $Header$

"""usage %prog decimal-flag [decimal-flag...]

Explain each flag on the command line in plain English
"""

from __future__ import division
import sys

lstFlags = [
    ("read paired", 0x1),
    ("read mapped in proper pair", 0x2),
    ("read unmapped", 0x4),
    ("mate unmapped", 0x8),
    ("read reverse strand", 0x10),
    ("mate reverse strand", 0x20),
    ("first in pair", 0x40),
    ("second in pair", 0x80),
    ("not primary alignment", 0x100),
    ("read fails platform/vendor quality checks", 0x200),
    ("read is PCR or optical duplicate", 0x400)
    ]
    

def explain_sam_flags(iFlags):
    print iFlags, ":"
    for strFlagName, iMask in lstFlags:
        if iFlags & iMask:
            print "\t" + strFlagName

def main(argv=None):
    if argv is None:
        argv = sys.argv

    for strArg in argv[1:]:
        explain_sam_flags(int(strArg))

if __name__ == "__main__":
    sys.exit(main())