ngless-toolkit / ngless-toolkit/ngless

mapstats() should error with position sorted sam/bam files

Open
#80 0 comments 0 reactions 0 assignees View on GitHub

Nobody has claimed this yet.

Dominant language
Rust
Stars
152
Forks
23
PR merge metrics
No merged PRs in 30d

Description

Fixing this to handle position sorted bam/sam files will require a similar approach to #72 and keeping an index of read headers in-memory.

An easier solution is to detect if the file is positionally sorted and error informing the user that a name sorted (or unsorted) file is required.
According to this biostars question the HD field can provide this info.

From a local test:

% head -n 1 texpected-unsorted.sam
@SQ	SN:122_DCM_0d2-0d45_scaffold97490_1_gene122702	LN:30803

% head -n 2 texpected-pos_sorted.sam 
@HD	VN:1.3	SO:coordinate
@SQ	SN:122_DCM_0d2-0d45_scaffold97490_1_gene122702	LN:30803

% head -n 2 texpected-name_sorted.sam 
@HD	VN:1.3	SO:queryname
@SQ	SN:122_DCM_0d2-0d45_scaffold97490_1_gene122702	LN:30803

The question above also mentions:

% samtools view -H 5_110118_FC62VT6AAXX-hg18-unsort.bam
@HD    VN:1.0    SO:unsorted

but it seems this field isn't always present in unsorted files.

Regardless, failing in the case of SO:coordinate safeguards the user from erroneous results.

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.

Research direction

Start by locating mapstats() and review issue #72 for the similar in-memory read-header approach. Inspect SAM/BAM header handling, including the HD field and SO:coordinate value, then use the issue's sorted and unsorted examples to verify that position-sorted input is rejected while name-sorted or unsorted input remains supported.

Written by the indexing model from the issue text.

Assessment

Tech stack
rust
Domain
bioinformatics
Issue type
Bug
Difficulty
3/5
Estimated time
1-2 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
48/100

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.