maf_stream

maf_stream is a collection of utilities to manipulate multiple alignments in the Multiple Alignment Format (MAF).

Installation

First, install Rust. Then, in the maf_stream directory, run:

cargo install --path .

which will install the program into your Cargo bin directory, or use cargo build --release and use the binary in target/release/maf_stream.

Usage

By default, maf_stream sets the input MAF to stdin and the output to stdout.

Finding duplicated blocks

maf_stream dup_blocks <input maf> <output maf>

Resolving duplicated entries

maf_stream merge_dups <merging mode> <input maf> <output maf> The resulting blocks always contain at most one entry per species; where there were previously duplicated entries only one entry will remain.

Available merging modes:

• consensus: Replace duplicated entries with a single entry (containing a consensus of the dups, with ties broken by consensus with the rest of the column).
• unanimity: Replace duplicated entries with a single entry (containing N if there are different bases within the duplicates, containing the unanimous base if the duplicate entries all agree).
• mask: Replace duplicated entries with single masked entry (containing all Ns).

Splitting a MAF (by reference sequence and maximum length)

maf_stream split <output dir> --max_length <max length per file> <input maf>

Calculating coverage

maf_stream coverage <reference genome> [--bed BED_FILE] <input maf> <output file>

If --bed BED_FILE is provided, coverage is restricted to be of bases within the regions within the BED file. Note that the BED file should not contain overlaps, i.e. it should be run through bedtools merge before being used. BED12 input is also currently disallowed, but will work if split up into BED3.

The output is similar to mafCoverage.