Goby 2.0 released

[Fabien Campagne]

We are pleased to announce that Goby 2.0 has been released. Version 2 is a major milestone for the Goby project which brings state of the art alignment compression, very robust SAM/BAM import exports, a parallel large sort implementation, empirical p-values for methylation data and more. See the new tutorial ‘What’s new in Goby 2.0‘ for more information.

We created a summary table to compare features of Goby 1.x, 2.0, BAM, CRAM and FASTQ. Click on the image below to see the full table.


Starting with Goby 2.0, we will be hosting the project source code on GitHub, to facilitate source code discussions and contributions from the community. Also new is a public forum to discuss the project, request new features, ask questions about existing tools, at https://groups.google.com/forum/?fro...goby-framework

[Fabien Campagne]

Goby 2.0.1

We have released 2.0.1. This minor release includes responses to several suggestions we received about 2.0. Thanks to everybody who provided feedback. Here's the detailed list of changes:

– Release Goby C/C++ APIs under the LGPL license version 3 to make it possible for companies to incorporate support for Goby formats in their tools. Thanks to Collin Hercus for the suggestion. Please note that part of the Goby Java APIs are already licensed under the LGPL (anything packaged under the Goby-io.jar file).
– C++ API: Support to set placed unmapped (i.e., mate that does not map is recorded with the read that mapped) and clipleft/clipright with quality scores.
– Fix problem when using a genome backed by a samtools/picard faidx file. In some cases, read bases would be returned shifted by one position. Thanks to James Bonfield for reporting this problem.
– SAM/BAM tags start at column 12, index 11. –preserve-all-tags could skip the first tag on some datasets (e.g., dataset where the first tag was not a MD:Z or RG:Z). Thanks to James Bonfield for reporting this problem.
– Introduce interface for ReadsWriter. Introduce mock implementation to write reads to text. This is useful to write more intelligible JUnit tests.
– mode sam-to-compact now supports option –read-names-are-query-indices to indicate that the read names are integers (typically produced by compact-to-fasta from a chunk of a large file).
– Fix a bug in reformat-compact-reads which did not trim quality scores for paired end reads correctly.

Please address questions/suggestions to the project forum: https://groups.google.com/forum/?fro...goby-framework

[Fabien Campagne]

Goby 2.1

This release includes the following changes:

• Improve compression of hybrid-1 codec by about 8% on average at similar speed. You can enable this improvement with option -x AlignmentCollectionHandler:symbol-modeling=plus. This option will be made the default in a future release. It is not currently the default since Goby 2.1 has just been integrated into IGV and will need time to propagate from IGV dev to production builds.
• compact-file-stats: Add a feature to scan only alignment headers.
• VCFParser group associations: Make it possible to lookup an INFO column by either INFO/colname or colname.
• Remove import of NH:i bam tags as read-origin-index, since the NH tag seems to contain different types of data depending on the aligner that produced the alignment.
• compact-to-sam mode: fix bug where bam tags containing a colon character ':' would be truncated after the first colon. Thanks to Vadim Zalunin for reporting this problem.
• NonAmbiguousAlignmentReader: fix an NPE when reading alignments where all entries have the ambiguity field.
• Fix a problem where AlignmentReaderImpl.canRead would return true when the file ended with an incorrect extension (this problem could create subtle issues when goby tried to access .info.txt files on a web server that did not return 404 errors for missing content). Thanks to Jim Robinson and Helga Thorvaldsdottir for reporting this issue.

You can download this release from http://campagnelab.org/software/goby/download-goby/

Questions, please check/email [email protected] https://groups.google.com/forum/?fro...goby-framework