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thegenemyers / DALIGNER

Find all significant local alignments between reads
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Add optional fix to LAcheck #91

Closed a-ludi closed 4 years ago

a-ludi commented 4 years ago

It would be very useful to have an option that tells LAcheck to try to fix errors it finds - I would suggest -f. The fixable errors are:

  1. "Chains are not sorted" can be fixed by running LAsort.
  2. "Duplicate LAs" can be fixed by removing all duplicates but the first/last.
  3. "Too many/few alignment records" could be fixed by adjusting the file header.

The third case should be maybe only fixed if the user really wants it fixed, e.g. by passing two times the -f option or maybe a -F option.

The second case is of special importance because both daligner and damapper produce duplicate alignments from time to time and it's very easy to fix.