rewrite indel output format

IARCbioinfo / needlestack

Multi-sample somatic variant caller

GNU General Public License v3.0

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rewrite indel output format #173

Closed tdelhomme closed 4 years ago

tdelhomme commented 6 years ago

Change the indel output format:

For deletions, instead of:

chr1 1 ATCT A

write:

chr1 2 TCT -

For insertions, instead of:

chr1 1 A ATCT

write:

chr1 1 - TCT

tdelhomme commented 6 years ago

need to reverse the commits, we finally decided to keep previous version, more consistent with other tools such as annovar which rewrite indels (A -> - becomes A -> 0).