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All Samples(1)  |  Call(0)  |  Derive(0)  |  Import(1)
File Parser Class for BAM File.

File is gzip-compatible and binary.
Information available is the same that is in SAM format.

The bitwise flag is made like this:
dec meaning
--- -------
1   paired read
2   proper pair
4   query unmapped
8   mate unmapped
16  strand of the query (1 -> reverse)
32  strand of the mate
64  first read in pair
128 second read in pair
256 alignment is not primary
512 does not pass quality check
1024        PCR or optical duplicate

src/a/r/AREM-1.0.1/AREM/OptValidator.py   AREM(Download)
from subprocess import Popen, PIPE
from math import log
from AREM.IO.Parser import BEDParser, ELANDResultParser, ELANDMultiParser, ELANDExportParser, PairEndELANDMultiParser, SAMParser, BAMParser, BowtieParser,  guess_parser
# ------------------------------------
# constants