hts_itr_t reuse

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#527 opened on May 4, 2017 0 comments 0 reactions 0 assignees View on GitHub

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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: api, bioinformatics

Research direction

Start by reviewing the hts_itr_t lifecycle described here, including sam_itr_queryi() and sam_itr_next(), and the linked mailing-list discussion. Compare the proposed clone/fork and reset behaviors, then define the API and tests needed to show that repeated iteration over the same file and region is safe.

Written by the indexing model from the issue text.

Description

This is a follow-up to a question I asked in the samtools-devel mailinglist found here.

The problem in question arises if one wants to use an identical instance of a hts_itr_t struct multiple times (same file, same region). Since the struct gets changed during the iteration process (e.g. through sam_itr_next()) it would be ideal to have a sort of "source" iterator which stays in the iterators original state (e.g. created through sam_itr_queryi()), from which the iterator used within sam_itr_next() gets cloned so only the clone gets changed. Alternatively, if the iterator could be reset safely in between uses that would also solve the problem. At present, this seems to be not safe without destroying and recreating the struct.

The two scenarios I describe above could be handled with something like a hts_itr_clone()/hts_itr_fork() function, or with a hts_itr_reset() function as Rob proposes in his mailing list answer. Would an implementation of something like that be feasible?

Thanks!

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