Code

feat: Index for bam::IndexedReader#387

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johanneskoester merged 20 commits intomasterrust-bio/rust-htslib:masterfrom index-for-indexed-readerrust-bio/rust-htslib:index-for-indexed-readerCopy head branch name to clipboardMay 12, 2023

+281-14

Commits

Commits on May 2, 2023

• Add an IndexView for accessing a sam/bam/cram's index

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  f59e9ee

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• fix copy and paste error

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  b8727dd

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• remove unnecessary cast to u32

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• index.stats: return Option<_>

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• clippy lints

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• fmt

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  74e6d1a

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• add test for idxstats

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• add test for number_mapped_unmapped

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• add tests for cram index as well

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  a24b783

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• set reference for indexed cram reader

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Commits on May 5, 2023

• add slow_idxstats from samtools bam_index.c

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Commits on May 11, 2023

• fix slow_idxstats, refactor as methods of IndexedReader

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• Add set_read_options 'convenience' method to bam::Read

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• cargo fmt

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• add missing test bam/cram indices

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• rename to set_cram_options, add doc

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• replace panic with BamUnsorted error

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• Add tid == -1 comment

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• remove todo comment

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  babb711

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• fix doctest path to file

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