requirements

• samtools : https://www.htslib.org/download/

# 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