ComputeGain
Manipulator
This program computes the read correction tool metric GAIN. It takes a genome FASTA file and two SAM file with read alignments before and after correction. It then computes various statistics and computes the GAIN, based on the edit or Hamming distance for reach read before and after correction.
Input ports
- Type: URI Object Genome file. [fq,fq.bgzf,fq.gz,fastq,fastq.bgzf,fastq.gz,fa,fa.bgzf,fa.gz,fasta,fasta.bgzf,fasta.gz,faa,faa.bgzf,faa.gz,ffn,ffn.bgzf,ffn.gz,fna,fna.bgzf,fna.gz,frn,frn.bgzf,frn.gz,embl,embl.bgzf,embl.gz,gbk,gbk.bgzf,gbk.gz,raw,raw.bgzf,raw.gz,sam,sam.bgzf,sam.gz,bam]
- Type: URI Object Pre-correction SAM file. [sam,bam]
- Type: URI Object Post-correction SAM file. [sam,opt.]
- Type: URI Object Post-correction FASTQ or FASTA file. [fastq,fq,fastq.gz,fq.gz,fasta,fa,fasta.gz,fa.gz,opt.]
Output ports
- Type: URI Object Write log about introduced/removed errors to this file. []