BamSeqChksumJava

This project contains a prototype implementation of BAM checksumming in Java.

Compilation

The make file can be used to create a JAR file from the Java source files. This requires a JDK.

Running

The program can be run using

java -jar BamSeqChksum.jar < in.bam

It reads the input BAM file from the standard input channel and produces the checksum information on standard output.

The implementation supports three checksums types:

• crc32prod: checksums for single alignments are produced by crc32 and combined over multiple records by multiplication in a prime number field. The prime used is 2^31-1.
• sha512: checksums for single alignments are produced by SHA-512. They are combined over multiple records by adding up and truncating to 512 bit numbers.
• sha512primesums512: checksums for single alignments are produced by SHA-512. They are combined over multiple records by adding up in a prime number field. The prime used is 2^512+75.

The hash type can be set using the hash command line parameter:

java -jar BamSeqChksum.jar hash=sha512 < in.bam