Fix handling chimeric alignments in hicBuildMatrix #151
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added 2 commits
November 17, 2017 15:57
SAM format specification does not impose an order of alignment lines (i.e. supplementary alignments might appear before or after the representative alignment). Here in code, the first alignment is taken as "primary", all the following as "supplementary", hence the flag is_supplementary should be ignored. The decision regarding which alignment is representative is usually arbitrary.
This should depend on the position of the first match (operation M in CIGAR string) in the read sequence. Currently, it depends on the number of CIGAR tuples before the first match. The fix makes e.g. 1H64M36H rank higher than 65S36M.
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@ajank I will take care of the flake8 error. Meanwhile, can you document a bit the lines that you modified? Simply add something similar to the git commit message to the file. |
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