Filter SAM file by sequence identity and alignment ratio

usage

Filters CIGAR strings by sequence identity and alignment ratio in SAM files

Usage: sam_filter [OPTIONS] --identity <min_identity> --ratio <min_ratio>

Options:
  -i, --identity <min_identity>  Minimum matching identity as a float
  -r, --ratio <min_ratio>        Minimum query alignment ratio as a float
      --reverse                  If used, print lines where identity <= min_identity (ignoring ratio), otherwise print lines where identity > min_identity and ratio > min_ratio
  -h, --help                     Print help
  -V, --version                  Print version

Generate sensitive mappings without SAM header

bowtie2 -p 64 -f --interleaved ./359250487_S94_L007_interleaved.fasta --seed 42 --very-sensitive -k 16 --np 1 --mp "1,1" --rdg "0,1" --rfg "0,1" --score-min "L,0,-0.05" --no-head --no-unal -S 359250487_S94_L007.sam -x pUC57.fasta

git clone https://github.com/jianshu93/sam_filter.git
cd sam_filter
cargo build --release
### extract high identity matches
cat data/test.sam | ./target/release/sam_filter -i 0.98 -r 0.90 > test.filtered.sam

### extract low identity matches
cat data/test.sam | ./target/release/sam_filter -i 0.98 -r 0.90 --reverse > test.filtered.sam