Merge adjacent sites into a complex

Open
#2,229 1 comment 0 reactions 0 assignees View on GitHub

Nobody has claimed this yet.

Assessment

Difficulty
5/5
Estimated time
Over a week
Newbie friendliness
25/100
Issue type
Feature
Clarity
Needs clarification
Activity status
Stale
Tech stack
c
Domain
bioinformatics

Research direction

Start with bcftools' handling of the two adjacent VCF records shown in the issue and check whether it supports producing the requested single-record representation. The work is complete when the capability is either confirmed and documented or implemented with coverage for this example.

Written by the indexing model from the issue text.

Description

D1: Difficult P2: Desirable

17 37880996 . T TTTA . PASS AS_FilterStatus=SITE;AS_SB_TABLE=2337,1597|178,137;DP=4390;ECNT=2;GERMQ=93;MBQ=35,36;MFRL=184,191;MMQ=60,60;MPOS=26;NALOD=2.09;NLOD=506.28;POPAF=6.00;TLOD=1053.35
17 37880997 . G T . PASS AS_FilterStatus=SITE;AS_SB_TABLE=2337,1597|178,137;DP=4408;ECNT=2;GERMQ=93;MBQ=35,34;MFRL=184,191;MMQ=60,60;MPOS=26;NALOD=2.09;NLOD=506.29;POPAF=6.00;TLOD=1053.34

These two sites are close to each other and should be merged into the following format. Can bcftools do it?

17 37880997 . G TTAT . PASS

Dominant language
C
Stars
891
Forks
277
Avg merge
2d 23h
Merged PRs (30d)
2

Contributor guide

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

More from samtools/bcftools

All issues in samtools/bcftools

Similar issues

More C issues

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.