8000 rust-htslib `read_pos` · Issue #91 · blachlylab/dhtslib · GitHub
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rust-htslib read_pos #91

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rust-htslib read_pos#91
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enhancementNew feature or requestquestionFurther information is requested

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  1. jblachly
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    enhancementNew feature or request
    questionFurther information is requested
    on Aug 3, 2021

  2. charlesgregory commented on Aug 3, 2021

    @charlesgregory
    charlesgregory
    on Aug 3, 2021
    Contributor

    In a way getAlignedPairs can be subsetted.

    dhtslib/source/dhtslib/sam/record.d

    Lines 527 to 531 in 11be3de

    /// get a range of aligned read and reference positions
    /// this is meant to recreate functionality from pysam:
    /// https://pysam.readthedocs.io/en/latest/api.html#pysam.AlignedSegment.get_aligned_pairs
    /// range is 0-based half open using chromosomal coordinates
    auto getAlignedPairs(bool withRefSeq)(long start, long end)

    It returns a range of AlignedPairs that contain rpos, qpos, cigar op, query base, and potentially reference base (if MD tag is present).

  3. jblachly commented on Aug 5, 2021

    @jblachly
    jblachly
    on Aug 5, 2021
    MemberAuthor

    Interesting that rust-htslib wrote a long function for this; seems useful. keep in back of your mind.

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