secondary_rewriter

Some aligners such as minimap2 do not write the SEQ and QUAL fields to secondary alignments making it hard to analyze them. This program adds these back, referring to the primary alignment to get the SEQ and QUAL, and adding them to the secondaries. This is a two (or three for sorted output) pass program, one collects the secondaries and the other adds the tags to the secondaries.

Install

First install rust, probably with rustup https://rustup.rs/

Then

cargo install secondary_rewriter

Usage

```

First pass

samtools view yourfile.bam | secondary_rewriter --pass1 > secondaries.txt

Second pass

samtools view -h yourfile.bam | secondary_rewriter --pass2 --secondaries secondaries.txt | samtools view -o out.bam

Third pass, sort the BAM since all the new secondaries are added at the end of the file

samtools sort out.bam -o out.sorted.bam ```

The two-pass strategy works as follows

1. First pass: output ALL secondary alignments (reads with flag 256) to a separate file
2. Second pass: reading secondary alignments into memory, and then scan original SAM/BAM/CRAM to add SEQ and QUAL fields encountered during scan to the secondary alignments that are stored in a hashmap

Note

My second rust project!