fix: fix handle of "6" shape path

[Hocnonsense]

will fix #43

background

in the issue, queries are extended as follow pattern:

and the environment is:

query_set = frozenset((           "AcMG_5518", "AcMG_12242", "AcMG_3793", "AcMG_755", "AcMG_9925", "AcMG_9528"))
contig2assembly = {
    "AcMG_3793" : {"AcMG_925032", "AcMG_5518", "AcMG_12242", "AcMG_3793"},
    "AcMG_755"  : {"AcMG_925032", "AcMG_5518", "AcMG_12242", "AcMG_3793", "AcMG_755", "AcMG_9925"},
    "AcMG_12242": {"AcMG_925032"} | query_set,
    "AcMG_5518" : {"AcMG_925032"} | query_set,
    "AcMG_9925" : {"AcMG_925032"} | query_set,
}
path_circular_potential=frozenset({"AcMG_755"})
contig_link_no_pe=frozenset({"AcMG_9528"})

bug analysis

in this case, a query (AcMG_9528) exists as an arm of a ring (represenated by AcMG_755). In this case, both the ring and the longer path should be marked as failed. A shorter not-ring path inner the failed ring can be reported instead (but failed for bug)

fixes:

1. fix the bug report here. Now the shortest common path are kept.
2. make code easier to read (seperate functions and NamedTuple)
3. fix other bugs via adding tests