def __iter__(self):
sf = pysam.Samfile(self.filename, "rb")
self.record_no = 0
for pa in sf:
try:
yield SAM_Alignment.from_pysam_AlignedRead(pa, sf)
except OverflowError:
pass
self.record_no += 1
def __iter__( self ):
sf = pysam.Samfile(self.filename, "rb")
self.record_no = 0
for pa in sf:
try:
yield SAM_Alignment.from_pysam_AlignedRead( pa, sf )
except OverflowError:
pass
self.record_no += 1
def fetch(self, reference=None, start=None, end=None, region=None):
sf = pysam.Samfile(self.filename, "rb")
self.record_no = 0
try:
for pa in sf.fetch(reference, start, end, region):
try:
yield SAM_Alignment.from_pysam_AlignedRead(pa, sf)
except OverflowError:
pass
self.record_no += 1
except ValueError as e:
if e.message == "fetch called on bamfile without index":
print "Error: ", e.message
print "Your bam index file is missing or wrongly named, convention is that file 'x.bam' has index file 'x.bam.bai'!"
else:
raise
except:
raise
def fetch( self, reference = None, start = None, end = None, region = None ):
sf = pysam.Samfile(self.filename, "rb")
self.record_no = 0
try:
for pa in sf.fetch( reference, start, end, region ):
try:
yield SAM_Alignment.from_pysam_AlignedRead( pa, sf )
except OverflowError:
pass
self.record_no += 1
except ValueError as e:
if e.message == "fetch called on bamfile without index":
print "Error: ", e.message
print "Your bam index file is missing or wrongly named, convention is that file 'x.bam' has index file 'x.bam.bai'!"
else:
raise
except:
raise
