A Yara fork for automatically expanding BioSeqZip collapsed sequences

This repository contains a fork of the Yara mapper (v0.9.11) from the SeqAn2 library (v2.4.0). It works exactly as the original Yara tool, but it was hacked for automatically expanding SAM/BAM records after the mapping phase.

Notice that this works properly ONLY if the input file was previously collapsed with BioSeqZip as long as all read headers are supposed to have the BioSeqZip format (BIOSEQZIP|ID:<id>|CN:<count>)

Prerequisites

A modern C++11 compiler with OpenMP 3.0 extensions is required to build Yara. If unsure, use GNU G++ 4.9 or newer.

• Git
• CMake 3.2 or newer
• G++ 4.9 or newer

Install from source

The BioSeqZip-Yara tool can be installed executing the following commands:

# Download the repository
git clone https://github.com/bioinformatics-polito/BioSeqZip-Yara.git bsz_yara

# Make the build directory
mkdir bsz_yara/build
cd bsz_yara/build

# Configure and build the tool
cmake .. -DCMAKE_BUILD_TYPE=Release -DSEQAN_BUILD_SYSTEM=APP:yara
make

# Install the binaries
cp bin/yara* /usr/local/bin

Contact

• Gianvito Urgese gianvito.urgese@polito.it
• Emanuele Parisi emanuele.parisi@polito.it