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Disconnect not removing all references?

Open schorlton-bugseq opened this issue 1 year ago • 0 comments

Thanks for the great library! Running gfapy 1.2.3 on the following file: test.gfa.gz

g = gfapy.Gfa.from_file("test.gfa", vlevel=3)
gfa_line = g.line("k141_11431")
gfa_line.disconnect()

Based on the docs, I expected all lines referencing k141_11431 to be removed. Indeed most lines are. However, there is still one line below...am I understanding the library correctly? Thanks!

for line in g.lines: print(line)
H       VN:Z:1.0
S       k141_12728      AGCAGGAGGAGCACTGTTTCACAGTCTTCCTCTCGCCATGATCTATGAGCCTTCTCAACGAATTTGGCGGTCCCGCTATAGGGTGGGTTGATGTAAACAGTCTTCCCGGTCCAGCGCTGCTTCAGACCATCGTCGTCCTGGTAATAGATGCGATCGGCCTGAACCGGACTGTCTGGAAGACCACACGGGTCTATAGAAATCGGGCCTATGACCGAGATGAACCCTTCCAGGAGTTCGGTTCAGGCCGATGAAACGATATGCGCCCGTTTAGGAAGAACACGTCCCCCTGTCCGACGACCTCATTGTGAAACCACCTGTGATG
S       k141_17097      AGCAGGAGGAGCACTGTTTCACAGTCTTCCTCTCGCCATGATCTATGAGCCTTCTCAACGAATTTGGCGGTCCCGCTATAGGGTGGGTTGATGTAAACAGTCTTCCCGGTCCAGCGCTGCTTCAGACCATCGTCGTCCTGGAAAGGATCATCTCGGTCGTAGGCCCAATTTCTATAGACCCGTGTGGTCATCCAGACAGTCCGGTTCAGGCCGATCGCATCTACTACCAGGACGACGATGGTCTGGAGCAGGAGGAGCACTGTTTCACAGTCTTCCTCTCGCCATGATCTATGAGCCTTCTCAACGAATTTGGC
S       k141_6966       GACGATGGTCTGAAGCAGCGCTGGAGCGGGAAGAGTGTTTTCGTCAATCCGCCCTATAGCGGGACGGCCAAATTCGTTGAGAAGGCTCATAGATCATGGCGAGAGGAAGACTGTGAAACAGTGCTCCTCCTGCTCCAGACCATCGTCGTCCTGGTAGTAGATGCGATCGGCCTGAACCGGACTGTCTGGATGACCACACGGGTCTAT
L       k141_11431      +       k141_12728      +       141M
L       k141_6966       +       k141_17097      -       141M

schorlton-bugseq avatar Oct 03 '24 02:10 schorlton-bugseq