46 releases (18 breaking)

new 0.21.0 Jan 26, 2025
0.19.0 Jan 11, 2025
0.16.0 Dec 20, 2024
0.13.0 Nov 29, 2024

#84 in Biology

Download history 2002/week @ 2024-11-17 531/week @ 2024-11-24 474/week @ 2024-12-01 427/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 @ 2025-01-12 233/week @ 2025-01-19

1,249 downloads per month
Used in 3 crates

MIT license

180KB
2.5K 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

0.20.2

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

~33–45MB
~742K SLoC