README.md

Multi-Seed Consensus Reference-Based Mapper (MSCRM)

MSCRM is a reference-based read-mapper which performs ungapped alignment of sample reads on reference sequence.

Compiling from Source

The application is written in Java 11 and built as a Maven project. To build from source, simply run mvn package on the main directory, which compiles and builds the Java project, producing an artifact under target/mapper-1.0-jar-with-dependencies.jar.

While building the project, Maven runs provided JUnit tests to ensure that all unit-tests pass before producing the artifact. All unit-tests can be found under src/test/java/ directory.

All source code can be found under src/main/java/edu/rice/comp416/mapper/ directory.

Requirements

• Java JRE >= 11.0.12
• Apache Maven >= 3.8.2

Command Syntax

java -jar target/mapper-1.0-jar-with-dependencies.jar [OPTIONS] REF SAMPLE SAMPLE OUT

Required Arguments

• REF is the pathname (absolute or relative) to the reference fastq file
• SAMPLE is the pathname (absolute or relative) to the sample fasta file
• OUT is the pathname (absolute or relative) to the output sam file

Optional Flags

• -h prints this message

Example Use

java -jar target/mapper-1.0-jar-with-dependencies.jar reference.fasta sample1.fastq sample2.fastq out.sam