Biostar139647 update to allow selection of a reference in the alignment and creation of insertion - Githubissues

lindenb / jvarkit

Java utilities for Bioinformatics

https://jvarkit.readthedocs.io/

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Biostar139647 update to allow selection of a reference in the alignment and creation of insertion #228

Closed blinard-BIOINFO closed 1 year ago

blinard-BIOINFO commented 1 year ago

To answer Issue #227

Biostar139647 update to allow selection of a reference in the clustal alignment. This allow to include insertions in the output.

Description

the user can now select a reference from the aclustal alignment via its label
this allows to compute insertions in the output sam/bam
the user can set if heading/trailing gaps should be taken into account, which differenciate short reads VS full genome alignments.
if no reference label is selected, the previous behavior is kept (no reference in the alignment, only matches and deletions in the sam).

Checklist

[X ] Code compiles correctly
[ ?] All tests passing
[ X] Extended the README / documentation, if necessary
[ X] Added myself + history to the source file