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

The application is written in Java 11 and built as a Maven project. To build fromsource, simply runmvn package on the main directory, which compiles and buildsthe Java project, producing an artifact undertarget/mapper-1.0-jar-with-dependencies.jar.

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

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

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

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

• 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

• -h prints this message

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