def convertReadAlignment(self, read):
"""
Convert a pysam ReadAlignment to a GA4GH ReadAlignment
"""
# TODO fill out remaining fields
# TODO refine in tandem with code in converters module
ret = protocol.ReadAlignment()
ret.alignedQuality = list(read.query_qualities)
ret.alignedSequence = read.query_sequence
ret.alignment = protocol.LinearAlignment()
ret.alignment.mappingQuality = read.mapping_quality
ret.alignment.position = protocol.Position()
ret.alignment.position.referenceName = self._samFile.getrname(
read.reference_id)
ret.alignment.position.position = read.reference_start
ret.alignment.position.strand = \
protocol.Strand.POS_STRAND # TODO fix this!
ret.alignment.cigar = []
for operation, length in read.cigar:
gaCigarUnit = protocol.CigarUnit()
gaCigarUnit.operation = SamCigar.int2ga(operation)
gaCigarUnit.operationLength = length
gaCigarUnit.referenceSequence = None # TODO fix this!
ret.alignment.cigar.append(gaCigarUnit)
ret.duplicateFragment = SamFlags.isFlagSet(read.flag,
SamFlags.DUPLICATE_FRAGMENT)
ret.failedVendorQualityChecks = SamFlags.isFlagSet(
read.flag, SamFlags.FAILED_VENDOR_QUALITY_CHECKS)
ret.fragmentLength = read.template_length
ret.fragmentName = read.query_name
ret.id = "{}:{}".format(self._id, read.query_name)
ret.info = {key: [str(value)] for key, value in read.tags}
ret.nextMatePosition = None
if read.next_reference_id != -1:
ret.nextMatePosition = protocol.Position()
ret.nextMatePosition.referenceName = self._samFile.getrname(
read.next_reference_id)
ret.nextMatePosition.position = read.next_reference_start
ret.nextMatePosition.strand = \
protocol.Strand.POS_STRAND # TODO fix this!
# TODO Is this the correct mapping between numberReads and
# sam flag 0x1? What about the mapping between numberReads
# and 0x40 and 0x80?
ret.numberReads = None
ret.readNumber = None
if SamFlags.isFlagSet(read.flag, SamFlags.NUMBER_READS):
ret.numberReads = 2
if SamFlags.isFlagSet(read.flag, SamFlags.READ_NUMBER_ONE):
ret.readNumber = 0
elif SamFlags.isFlagSet(read.flag, SamFlags.READ_NUMBER_TWO):
ret.readNumber = 1
ret.properPlacement = SamFlags.isFlagSet(read.flag,
SamFlags.PROPER_PLACEMENT)
ret.readGroupId = self._id
ret.secondaryAlignment = SamFlags.isFlagSet(
read.flag, SamFlags.SECONDARY_ALIGNMENT)
ret.supplementaryAlignment = SamFlags.isFlagSet(
read.flag, SamFlags.SUPPLEMENTARY_ALIGNMENT)
return ret
def convertReadAlignment(self, read):
"""
Convert a pysam ReadAlignment to a GA4GH ReadAlignment
"""
samFile = self._parentContainer.getFileHandle(self._parentSamFilePath)
# TODO fill out remaining fields
# TODO refine in tandem with code in converters module
ret = protocol.ReadAlignment()
ret.fragmentId = 'TODO'
if read.query_qualities is None:
ret.alignedQuality = []
else:
ret.alignedQuality = list(read.query_qualities)
ret.alignedSequence = read.query_sequence
if SamFlags.isFlagSet(read.flag, SamFlags.READ_UNMAPPED):
ret.alignment = None
else:
ret.alignment = protocol.LinearAlignment()
ret.alignment.mappingQuality = read.mapping_quality
ret.alignment.position = protocol.Position()
ret.alignment.position.referenceName = samFile.getrname(
read.reference_id)
ret.alignment.position.position = read.reference_start
ret.alignment.position.strand = protocol.Strand.POS_STRAND
if SamFlags.isFlagSet(read.flag, SamFlags.READ_REVERSE_STRAND):
ret.alignment.position.strand = protocol.Strand.NEG_STRAND
ret.alignment.cigar = []
for operation, length in read.cigar:
gaCigarUnit = protocol.CigarUnit()
gaCigarUnit.operation = SamCigar.int2ga(operation)
gaCigarUnit.operationLength = length
gaCigarUnit.referenceSequence = None # TODO fix this!
ret.alignment.cigar.append(gaCigarUnit)
ret.duplicateFragment = SamFlags.isFlagSet(read.flag,
SamFlags.DUPLICATE_READ)
ret.failedVendorQualityChecks = SamFlags.isFlagSet(
read.flag, SamFlags.FAILED_QUALITY_CHECK)
ret.fragmentLength = read.template_length
ret.fragmentName = read.query_name
ret.info = {key: [str(value)] for key, value in read.tags}
if SamFlags.isFlagSet(read.flag, SamFlags.MATE_UNMAPPED):
ret.nextMatePosition = None
else:
ret.nextMatePosition = protocol.Position()
if read.next_reference_id != -1:
ret.nextMatePosition.referenceName = samFile.getrname(
read.next_reference_id)
else:
ret.nextMatePosition.referenceName = ""
ret.nextMatePosition.position = read.next_reference_start
ret.nextMatePosition.strand = protocol.Strand.POS_STRAND
if SamFlags.isFlagSet(read.flag, SamFlags.MATE_REVERSE_STRAND):
ret.nextMatePosition.strand = protocol.Strand.NEG_STRAND
if SamFlags.isFlagSet(read.flag, SamFlags.READ_PAIRED):
ret.numberReads = 2
else:
ret.numberReads = 1
ret.readNumber = None
if SamFlags.isFlagSet(read.flag, SamFlags.FIRST_IN_PAIR):
if SamFlags.isFlagSet(read.flag, SamFlags.SECOND_IN_PAIR):
ret.readNumber = 2
else:
ret.readNumber = 0
elif SamFlags.isFlagSet(read.flag, SamFlags.SECOND_IN_PAIR):
ret.readNumber = 1
ret.properPlacement = SamFlags.isFlagSet(read.flag,
SamFlags.READ_PROPER_PAIR)
ret.readGroupId = self.getId()
ret.secondaryAlignment = SamFlags.isFlagSet(
read.flag, SamFlags.SECONDARY_ALIGNMENT)
ret.supplementaryAlignment = SamFlags.isFlagSet(
read.flag, SamFlags.SUPPLEMENTARY_ALIGNMENT)
ret.id = self.getReadAlignmentId(ret)
return ret