Commit ca999082 authored by MARIJON Pierre's avatar MARIJON Pierre

_add_internal become just a proxy to add link

parent 8974149e
......@@ -145,12 +145,14 @@ class Parser:
for line in str(self.__graph).split("\n"):
yield line
else:
segment = set()
yield str(self.__graph.header)
for line in self.__graph.segments:
segment.add(line.name)
yield str(line)
for line in self.__graph.dovetails:
if line.to_segment in self.__graph.segments \
and line.from_segment in self.__graph.segments:
if line.to_segment.name in segment \
and line.from_segment in segment:
yield str(line)
......@@ -198,12 +200,8 @@ class Parser:
def _add_internal(self, name_a, strand_a, name_b, strand_b, ov_len,
nb_match, overhang_maplen):
signature = (name_a, strand_a, name_b, strand_b)
value = (name_a, strand_a, name_b, strand_b, ov_len+"M",
"NM:i:"+str(int(ov_len) - int(nb_match)),
"om:f:{:.2f}".format(overhang_maplen))
self.__graph.add_line("L\t"+"\t".join(value))
self._add_link(self, name_a, strand_a, name_b, strand_b, ov_len,
nb_match, overhang_maplen)
def _add_containment(self, container, strand_ner, contained, strand_ned, pos, length):
self.__graph.add_line("C\t"+"\t".join([container, strand_ner, contained,
......
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