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feat: Index for bam::IndexedReader #387

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merged 20 commits into from
May 12, 2023
+281 −14
Merged

feat: Index for bam::IndexedReader #387

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f59e9ee
Add an IndexView for accessing a sam/bam/cram's index
tedil May 2, 2023
b8727dd
fix copy and paste error
tedil May 2, 2023
02e9d56
remove unnecessary cast to u32
tedil May 2, 2023
a924119
index.stats: return Option<_>
tedil May 2, 2023
5d16863
clippy lints
tedil May 2, 2023
74e6d1a
fmt
tedil May 2, 2023
d96be28
add test for idxstats
tedil May 2, 2023
7ceb1ea
add test for number_mapped_unmapped
tedil May 2, 2023
a24b783
add tests for cram index as well
tedil May 2, 2023
24a1a04
set reference for indexed cram reader
tedil May 2, 2023
5804bfd
add slow_idxstats from samtools bam_index.c
tedil May 5, 2023
236c18e
fix slow_idxstats, refactor as methods of IndexedReader
tedil May 11, 2023
5275afe
Add set_read_options 'convenience' method to bam::Read
tedil May 11, 2023
cdab234
cargo fmt
tedil May 11, 2023
4f3d298
add missing test bam/cram indices
tedil May 11, 2023
da63cb6
rename to set_cram_options, add doc
tedil May 11, 2023
9475c99
replace panic with BamUnsorted error
tedil May 11, 2023
bf42d1e
Add tid == -1 comment
tedil May 11, 2023
babb711
remove todo comment
tedil May 11, 2023
36c5cf0
fix doctest path to file
tedil May 11, 2023
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set reference for indexed cram reader
  • Loading branch information
@tedil
tedil committed May 2, 2023
commit 24a1a046683031237eb98fb6a4b74c6a211b45e5
2 changes: 2 additions & 0 deletions src/bam/mod.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -2918,6 +2918,7 @@ CCCCCCCCCCCCCCCCCCC"[..],
#[test]
fn test_idxstats_cram() {
let mut reader = IndexedReader::from_path("test/test_cram.cram").unwrap();
reader.set_reference("test/test_cram.fa").unwrap();
let header = reader.header().clone();
let expected = vec![(0, (120, 2, 0)), (1, (120, 2, 0)), (2, (120, 2, 0))];
let actual = reader.index().stats(header).unwrap();
Expand All @@ -2927,6 +2928,7 @@ CCCCCCCCCCCCCCCCCCC"[..],
#[test]
fn test_number_mapped_and_unmapped_cram() {
let mut reader = IndexedReader::from_path("test/test_cram.cram").unwrap();
reader.set_reference("test/test_cram.fa").unwrap();
let expected = (2, 0);
let actual = reader.index().number_mapped_unmapped(0);
assert_eq!(expected, actual);
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