Closes #36 (Adds -l functionality to ignore long indels from assess_assembly)

nanoporetech / pomoxis

Analysis components from Oxford Nanopore Research

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Closes #36 (Adds -l functionality to ignore long indels from assess_assembly) #37

Closed kishwarshafin closed 4 years ago

kishwarshafin commented 5 years ago

Changes: stats_from_bam.py: Now takes the -l parameter to define the longest allowed insertion or deletion. The default is 0 in which it'll count everything. stats_from_aligned_read is changed and masked_stats_from_aligned_read_excluding_longindels is newly added.

The assess_assembly script is also changed to have the -l parameter.

mwykes commented 4 years ago

Thanks for the contribution @kishwarshafin, I'm merging into nanoporetech:long_indels and will make a few tweaks before merging that into master.

kishwarshafin commented 4 years ago

Great! thank you. Let me know if you need any help or have any questions.