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#                                #
# Last modified 2019/06/09       # 
#                                #
# Georgi Marinov                 #
#                                # 
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import sys
import string
import pysam
import os

# FLAG field meaning
# 0x0001 1 the read is paired in sequencing, no matter whether it is mapped in a pair
# 0x0002 2 the read is mapped in a proper pair (depends on the protocol, normally inferred during alignment) 1
# 0x0004 4 the query sequence itself is unmapped
# 0x0008 8 the mate is unmapped 1
# 0x0010 16 strand of the query (0 for forward; 1 for reverse strand)
# 0x0020 32 strand of the mate 1
# 0x0040 64 the read is the first read in a pair 1,2
# 0x0080 128 the read is the second read in a pair 1,2
# 0x0100 256 the alignment is not primary (a read having split hits may have multiple primary alignment records)
# 0x0200 512 the read fails platform/vendor quality checks
# 0x0400 1024 the read is either a PCR duplicate or an optical duplicate
# 0x0800 2048 supplementary alignment

def FLAG(FLAG):

    Numbers = [0,1,2,4,8,16,32,64,128,256,512,1024,2048]

    FLAGList=[]

    MaxNumberList=[]
    for i in Numbers:
        if i <= FLAG:
            MaxNumberList.append(i)

    Residual=FLAG
    maxPos = len(MaxNumberList)-1

    while Residual > 0:
        if MaxNumberList[maxPos] <= Residual:
            Residual = Residual - MaxNumberList[maxPos]
            FLAGList.append(MaxNumberList[maxPos])
            maxPos-=1
        else:
            maxPos-=1
  
    return FLAGList

def run():

    if len(sys.argv) < 1:
        print 'usage: python %s FLAG' % sys.argv[0]
        sys.exit(1)

    F = int(sys.argv[1])

    FLAGDict = {1: 'the read is paired in sequencing, no matter whether it is mapped in a pair',
                2: 'the read is mapped in a proper pair (depends on the protocol, normally inferred during alignment) 1',
                4: 'the query sequence itself is unmapped',
                8: 'the mate is unmapped 1',
                16: 'strand of the query (0 for forward; 1 for reverse strand)',
                32: 'strand of the mate 1',
                64: 'the read is the first read in a pair 1,2',
                128: 'the read is the second read in a pair 1,2',
                256: 'the alignment is not primary (a read having split hits may have multiple primary alignment records)',
                512: 'the read fails platform/vendor quality checks',
                1024: 'the read is either a PCR duplicate or an optical duplicate',
                2048: 'supplementary alignmentc'}

    for FFF in FLAG(F):
        print FFF, FLAGDict[FFF]

run ()