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add cs_long flag to mappy.Aligner.map, and a "-C" option to minimap2.py #1194

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nickzoic wants to merge 1 commit into lh3:master from nickzoic:nickzoic/python-long-cs

nickzoic commented Apr 18, 2024

Adds a cs_long flag to mappy.Aligner.map, to let Python code get the "long CS" format string.

# generate a short cs string
aligner.map(seq, cs=True)

# generate a long cs string
aligner.map(seq, cs_long=True)

Also adds a -C command line option to minimap2.py by way of example.


          add cs_long flag to mappy.Aligner.map, and a "-C" option to minimap2.py

8a6f18e

nickzoic mentioned this pull request

Add "tseq" output & make available to Python #1201

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