Add soft/hard clipping support to FragmentStore

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#535 4 comments 0 reactions 0 assignees View on GitHub

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Assessment

Difficulty
4/5
Estimated time
3-5 days
Newbie friendliness
35/100
Issue type
Feature
Clarity
Mostly clear
Activity status
Stale
Tech stack
cpp
Domain
bioinformatics

Research direction

Start by tracing FragmentStore's SAM loading and anchor-gap handling, using the issue's distinction between soft and hard clipping as the behavioral guide. Verify how clipped sequence data is represented and define done as correctly supporting both clipping modes without losing sequence characters across regions.

Written by the indexing model from the issue text.

Description

bug enhancement Port to SeqAn3

The FragmentStore does neither support soft nor hard clipping.

For soft-clipping, the full sequence is in the SEQ field of SAM files and the anchor gaps data structure supports clipping with anchors. This should not be a problem.

For hard clipping, one would have to assume that the full sequence can be loaded into RAM (FragmentStore is not meant for genome alignment). When loading, one could fill the hard clipped region with N characters and when another region is found for the same sequence one could replace N by the actual sequence characters.

Dominant language
C++
Stars
502
Forks
172
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