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initial support for unpaired reads #2

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initial support for unpaired reads #2

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15 changes: 14 additions & 1 deletion splitStrains.py
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Original file line number Diff line number Diff line change
Expand Up @@ -519,7 +519,16 @@ def computeDataFromSam(freqVec, samfile, refFile, baseQuality, mapQuality, regio
chromosome = samfile.references[0]

# flag_filter=3 means we get reads that are mapped in a proper pair, flag_filter=8 ignore reads that have unmapped mate
for pileupcolumn in samfile.pileup(chromosome, regionStart, regionEnd, truncate=True, min_base_quality=baseQuality, min_mapping_quality=mapQuality, fastafile=refFile, stepper='samtools', flag_require=3, flag_filter=3852):
if single_ended == True:
pileup_flag_require = 0
pileup_flag_filter = 3844
else:
pileup_flag_require = 3
pileup_flag_filter = 3852

for pileupcolumn in samfile.pileup(chromosome, regionStart, regionEnd, truncate=True, min_base_quality=baseQuality,
min_mapping_quality=mapQuality, fastafile=refFile, stepper='samtools', flag_require=pileup_flag_require,
flag_filter=pileup_flag_filter):

i = pileupcolumn.pos
pile = ''.join(pileupcolumn.get_query_sequences(mark_ends=False)).lower()
Expand Down Expand Up @@ -793,6 +802,7 @@ def convolveVec(freqVecFlat, proprtionCountThresh=2, boxPoints=4):
parser.add_argument('-l', metavar='n', type=int, default=10, dest='lowerLimit', help='Do not consider proportion of bases below n value. Default=10')
parser.add_argument('-m', metavar='n', type=int, default=40, dest='mapQuality', help='Do not consider reads below n map quality. Default=40')
parser.add_argument('-q', metavar='n', type=int, default=15, dest='baseQuality', help='Do not consider bases below n quality. Default=15')
parser.add_argument('--singleend', action='store_true', help='Allow single-ended reads')
parser.add_argument(dest='bamFilePath', metavar='bamFilePath', help='input bam file')

args = parser.parse_args()
Expand All @@ -817,6 +827,7 @@ def convolveVec(freqVecFlat, proprtionCountThresh=2, boxPoints=4):
useModel = args.model
reuseFreqVec = args.reuse
alpha_level = args.alpha_level
single_ended = args.singleend

logging.basicConfig(format='%(levelname)s:%(message)s', level=logging.INFO, stream=sys.stdout)

Expand Down Expand Up @@ -845,6 +856,8 @@ def convolveVec(freqVecFlat, proprtionCountThresh=2, boxPoints=4):
logging.info(f'regionStart: {regionStart}, regionEnd: {regionEnd}')
logging.info(f'depth threshold: {depthThreshold}')
logging.info(f'entropy threshold: {ethreshold}')
if single_ended:
logging.info(f'Using unpaired reads')

intervals = [] # list of Interval objects. This will be populated if gff file is provided
freqVec = [] # vector format [a prop, c prop, t prop, g prop, position, depth]
Expand Down