Goby 1.9.8.4 released (fixes sam-to-compact)

[Fabien Campagne]

Available from http://campagnelab.org/software/goby/download-goby/

This releases fixes various problems with the sam-to-compact mode and makes it possible to efficiently import sorted BAM files. The previous version was compiled with debugging statements on, which slowed down conversions drastically. This version converts about 40,000 BAM entries per second. The sam-to-compact options have also been redesigned to make simple conversions easier. For instance,

goby 1g sam-to-compact --sorted  -i input.bam -o goby-output

will convert input.bam to Goby alignment format preserving sort order (necessary if you want to load the file into IGV). Neither the --third-party option or the -p options are any longer required. Please see help for new option defaults. This should help a lot of people who are trying to get started with Goby and already have many BAM alignments. Please let us know if you encounter any other issues with SAM/BAM to Goby conversions.