52 releases (21 breaking)

new 0.24.0 Mar 25, 2025
0.22.0 Feb 5, 2025
0.16.0 Dec 20, 2024
0.13.0 Nov 29, 2024

#188 in Biology

Download history 427/week @ 2024-12-08 364/week @ 2024-12-15 85/week @ 2024-12-22 26/week @ 2024-12-29 583/week @ 2025-01-05 407/week @ 2025-01-12 281/week @ 2025-01-19 289/week @ 2025-01-26 202/week @ 2025-02-02 21/week @ 2025-02-09 224/week @ 2025-02-16 327/week @ 2025-02-23 123/week @ 2025-03-02 5/week @ 2025-03-09 1/week @ 2025-03-16 103/week @ 2025-03-23

254 downloads per month
Used in 3 crates

MIT license

200KB
3K SLoC

requirements

# install samtools

cd samtools-1.x    # and similarly for bcftools and htslib
./configure --prefix=/usr/
make
make install
cargo install mm2

gsmm2 align -q query.fa --target target.fa -p query2target

changelog

0.23.0

  • more tags to pass through

0.22.0

  • Pin minimap2 to version 0.1.23

0.21.0

gsmm2-aligned-metric

  • new field: longIndel. only the abs(indel) >=10 will be recorded. 14,-31 means there are two long indels (ins(14), del(31))

0.20.2

gsmm2-aligned-metric

// 1 -> 1000, 0.8 -> 0.2
aligner.mapopt.best_n = 10000; // Output at most INT secondary alignments
aligner.mapopt.pri_ratio = 0.2; // Minimal secondary-to-primary score ratio to output secondary mappings

0.20.0

  • homodel logic

0.18.1

  • primaryCovlen
  • qOvlpRatio
  • rOvlpRatio

0.18.0

  • gsmm2-aligned-metric.rs
  • align_single_query_to_targets TO (align_single_query_to_targets + hits2records)

0.17.0

  • set_primary_alignment_according_2_align_score -> set_primary_supp_alignment_according_2_align_score

0.11.0

  • np_range & rq_range.
  • discard multiple alignment reads

0.9.0

  • dump qual if the query file is bam or fastq. if query file is fa, the qual will be [255; query_len]

0.6.0

  • if the query file is bam format, it will try to dump np & ch & rq to the result bam

0.5.0

  • if the query file is bam format, it will try to dump np & ch to the result bam

Dependencies

~34–46MB
~774K SLoC