README.txt

SeqPig is a library of import and export functions for file formats commonly used in bioinformatics for Apache Pig. Additionally, it provides a collection of Pig user-defined functions (UDF's) that allow for processing of aligned and unaligned sequence data. Currently SeqPig supports BAM/SAM, FastQ and Qseq input and output and FASTA input. It is built on top of the Hadoop-BAM library. Fore more information see

http://seqpig.sourceforge.net/

and the documentation that comes with the release.

Releases of SeqPig come bundled with Picard/Samtools, which were developed at the Wellcome Trust Sanger Institute, and Biodoop/Seal, which were developed at the Center for Advanced Studies, Research and Development in Sardinia. See

http://samtools.sourceforge.net/ http://biodoop-seal.sourceforge.net/

Installation with precompiled Seal library

mvn install:install-file -Dfile=lib/seal-0.4.0-with-hadoop-bam-7.4.0.jar -DgroupId=it.crs4 -DartifactId=seal -Dversion=0.4.0-with-hadoop-bam-7.4.0 -Dpackaging=jar -DgeneratePom=true mvn package -DskipTests