secondary_rewriter

Some aligners such as minimap2 do not write the SEQ and QUAL fields to secondary alignments (https://github.com/lh3/minimap2/issues/458) making it hard to analyze them (for example, SNPs will not be visible in a genome browser for secondary alignments). 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-pass program. The first pass collects the secondary alignments and the second adds the SEQ and QUAL fields to the secondaries.

Install

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

Then

cargo install secondary_rewriter

Usage

```

First pass

samtools view -f256 yourfile.bam > secondaries.txt

Second pass

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

```

You can package this into a small bash script (supports CRAM) see write_secondaries.sh

The two-pass strategy works as follows

1. First pass: output ALL secondary alignments (reads with flag 256) to a separate file (plaintext or gzip)
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

It uses a two-pass strategy because otherwise it would have to effectively load the entire SAM/BAM/CRAM into memory

Help

```

% secondary_rewriter --help

secondary_rewriter 0.1.2 Adds SEQ and QUAL fields to secondary alignments from the primary alignment

USAGE: secondary_rewriter [OPTIONS]

OPTIONS: -h, --help Print help information --output-only-new-data -s, --secondaries -V, --version Print version information

```

--output-only-new-data only outputs the secondary alignments with their new SEQ/QUAL fields (and skips all other data). the default mode without this flag passes all other alignments through stdout and adds the secondary alignments at the end

Note

My second rust project!

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