This is a port from BWA on Linux. The original project is here: http://bio-bwa.sourceforge.net/ and the base code we took is bwa-0.6.1.tar.bz2, 2011-11-28, 130.0 kB.
Support: 64bit Windows, tested on Windows Server 2003 R2 x64, Windows Vista x64, Windows Server 2008 x64. 8GB memory.
1, This release is the miminum change on the Linux source code so that: the code compiles with Visual Studio 2010; all features/behaviours work the same way as on Linux. No further work planned on this except bug fix.
2, Later will be another branch of release on BWA, with improvements on performance and memory footprints etc. Eventually will diverge from above branch to fully utilize the advanced Windows OS ability.
3, Due to our own project usage pattern and limited resources, not all sub command of BWA is tested fully. But the following is tested and compared with Linux run info:
3.1 BWA INDEX, on human decoy reference hs37d5
3.2 BWA ALN, on human paired end short reads about 100x
3.3 BWA SAMPE, on above output SAI files
Memory footprints and runtimes are similar, output files identical for binary (e.g. .BWT, .SA, .PAC, .SAI); and identical for text except New-Line difference (e.g. .AMB, .ANN, .SAM). We could change the new line to Unix format if there is demand.
Other sub commands are not tested but should work in general, please test it before you do real work, or you can fill bug report from the Issue Tracker.
Please also let us know how you plan to use this, on what size machine and what kind of workload so that we could improve the Windows specific branch to suit the needs. (Use Discussions please).