Implement pileup() for unindexed files and/or SAM files #916
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
…opers#916) Reorganise pileup() so that it chooses between IteratorColumnRegion/ IteratorColumnAllRefs/IteratorColumnAll primarily by has_coord (i.e., whether contig+etc/region was specified) and secondarily by has_index. Add IteratorColumnAll() which iterates as per HTS_IDX_REST, piling up the entire file, which works without an index and for SAM files. Fixes pysam-developers#915. Unfortunately sam_itr_next() does not work for SAM files (even for HTS_IDX_REST) prior to HTSlib 1.10. Instead we follow samtools mpileup's lead and special case this to use sam_read1() at the bottom level instead of an HTS_IDX_REST iterator. We duplicate __advance_all() and __advance_nofilter() functions, but __advance_samtools() is itself complicated enough that we just make it handle both cases instead.
jmarshall
force-pushed
the
pileup-no-index
branch
from
5731505 to
9e7bc31
Compare
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Reorganise
pileupso that it chooses betweenIteratorColumnRegion/IteratorColumnAllRefs/IteratorColumnAllprimarily byhas_coord(i.e., whethercontig+etc/regionwas specified) and secondarily byhas_index.Add
IteratorColumnAll()which iterates as per HTS_IDX_REST, piling up the entire file, which works without an index and for SAM files. (Unfortunatelysam_itr_next()does not work for SAM files (even for HTS_IDX_REST) prior to HTSlib 1.10. Instead we followsamtools mpileup'slead and special case this to use
sam_read1()at the bottom level instead ofsam_itr_next().)The common parts of the two
_setup_iteratorfunctions could in future be refactored…