def downgrade_read_edges(in_fpath,
out_fpath,
size,
qual_to_substract=QUAL_TO_SUBSTRACT):
in_sam = AlignmentFile(in_fpath)
out_sam = AlignmentFile(out_fpath, 'wb', template=in_sam)
for aligned_read in in_sam:
_downgrade_edge_qualities(aligned_read,
size,
qual_to_substract=qual_to_substract)
out_sam.write(aligned_read)
def downgrade_read_edges(in_fpath,
out_fpath,
size,
qual_to_substract=QUAL_TO_SUBSTRACT):
in_sam = AlignmentFile(in_fpath)
out_sam = AlignmentFile(out_fpath, 'wb', template=in_sam)
for aligned_read in in_sam:
if (aligned_read.has_tag(LEFT_DOWNGRADED_TAG)
or aligned_read.has_tag(RIGTH_DOWNGRADED_TAG)):
raise RuntimeError('Edge qualities already downgraded\n')
_downgrade_edge_qualities(aligned_read,
size,
qual_to_substract=qual_to_substract)
out_sam.write(aligned_read)
