def __analyze(self, bwsa, seq_pairs_read):
##################################################
# This method performs the actual analysis work.
# BWA writes its results directly into the bwsa structures.
##################################################
if not self.reference_loaded():
self.load_reference()
ii = bwa.isize_info_t()
self.visitor.start("cal_sa_reg_gap")
for i in 0, 1:
bwa.cal_sa_reg_gap_mt(self.__bwts, seq_pairs_read, bwsa[i],
self.gopt)
self.visitor.stop("cal_sa_reg_gap")
self.visitor.start("cal_pac_pos_pe")
bwa.cal_pac_pos_pe(self.__bwts, seq_pairs_read, bwsa, ii, self.popt,
self.gopt, self.__last_ii)
self.visitor.stop("cal_pac_pos_pe")
self.__last_ii = ii
if ii.avg > self.max_isize:
self.visitor.log_warning("skipping S-W, isize is too big (%.3f)" %
ii.avg)
else:
self.visitor.start("paired_sw")
if 0 < self.pairing_batch_size < seq_pairs_read:
for offset in xrange(0, seq_pairs_read,
self.pairing_batch_size):
nseq = min(self.pairing_batch_size,
seq_pairs_read - offset)
self.visitor.start("paired_sw_batch")
bwa.paired_sw(self.__bnsp, self.__pacseq, nseq, bwsa,
self.popt, ii, offset)
self.visitor.stop_batch("paired_sw_batch", offset, nseq)
else:
bwa.paired_sw(self.__bnsp, self.__pacseq, seq_pairs_read, bwsa,
self.popt, ii)
self.visitor.stop("paired_sw")
self.visitor.start("refine_gapped")
for i in 0, 1:
bwa.refine_gapped(self.__bnsp, seq_pairs_read, bwsa[i],
self.__pacseq)
self.visitor.stop("refine_gapped")
def __analyze(self, bwsa, seq_pairs_read):
##################################################
# This method performs the actual analysis work.
# BWA writes its results directly into the bwsa structures.
##################################################
if not self.reference_loaded():
self.load_reference()
ii = bwa.isize_info_t()
self.visitor.start("cal_sa_reg_gap")
for i in 0, 1:
bwa.cal_sa_reg_gap_mt(self.__bwts, seq_pairs_read, bwsa[i], self.gopt)
self.visitor.stop("cal_sa_reg_gap")
self.visitor.start("cal_pac_pos_pe")
bwa.cal_pac_pos_pe(self.__bwts, seq_pairs_read, bwsa, ii,
self.popt, self.gopt, self.__last_ii)
self.visitor.stop("cal_pac_pos_pe")
self.__last_ii = ii
if ii.avg > self.max_isize:
self.visitor.log_warning("skipping S-W, isize is too big (%.3f)" % ii.avg)
else:
self.visitor.start("paired_sw")
if 0 < self.pairing_batch_size < seq_pairs_read:
for offset in xrange(0, seq_pairs_read, self.pairing_batch_size):
nseq = min(self.pairing_batch_size, seq_pairs_read - offset)
self.visitor.start("paired_sw_batch")
bwa.paired_sw(self.__bnsp, self.__pacseq, nseq, bwsa, self.popt, ii, offset)
self.visitor.stop_batch("paired_sw_batch", offset, nseq)
else:
bwa.paired_sw(self.__bnsp, self.__pacseq, seq_pairs_read, bwsa, self.popt, ii)
self.visitor.stop("paired_sw")
self.visitor.start("refine_gapped")
for i in 0, 1:
bwa.refine_gapped(self.__bnsp, seq_pairs_read, bwsa[i], self.__pacseq)
self.visitor.stop("refine_gapped")
def clean_isize_statistics(self): self.__last_ii = bwa.isize_info_t() self.__last_ii.avg = -1.0
def clean_isize_statistics(self):
self.__last_ii = bwa.isize_info_t()
self.__last_ii.avg = -1.0
