Commit 3c6f8f33 by Eric Coissac

Adds a low memory option

parent 5640db43
......@@ -39,7 +39,8 @@ default_config = { 'reformat' : False,
"phix" : True,
"fastqdump": False,
'shift' : 33,
"direct" : False
"direct" : False,
"zip" : False
}
def addOptions(parser):
......@@ -175,6 +176,11 @@ def addOptions(parser):
default=False,
help='ensure that forward and reverse files are correctly paired')
parser.add_argument('--low-memory', dest='index:zip',
action='store_true',
default=None,
help='Reduce memory usage for optimal length computation')
parser.add_argument('--quality-encoding-offset', dest='index:shift',
type=int,
action='store',
......@@ -407,7 +413,8 @@ def run(config):
skip = config['index']['skip'],
maxread = config['index']['maxread'],
phix = config['index']['phix'],
shift = config['index']['shift']
shift = config['index']['shift'],
zip = config['index']['zip']
)
if config['index']['fastqdump']:
......
......@@ -492,7 +492,8 @@ def readPairedEnd(filenames,
int skip=0,
int maxread=0,
bint phix=True,
int shift=33
int shift=33,
bint zip=False
):
PEI = None
......@@ -542,7 +543,7 @@ def readPairedEnd(filenames,
if length>0 :
PEI = PELengthCut(PEI,length)
elif lengthestimate > 0:
PEI = PELengthEstimate(PEI,lengthestimate,minlength)
PEI = PELengthEstimate(PEI,lengthestimate,minlength,zip)
if maxread > 0:
PEI = PEMaxReadCount(PEI,maxread)
......
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