[Bio-bwa-help] clarification on color-space support in BWA 0.6.1

[Phillipe L. <Phi...@je...>]

I saw the following in the NEWS file of BWA 0.6.1.  While it looks like color-space alignment is now disabled in BWA-short, what about BWA-SW?  Is color-space still enabled and working there?  I found the following thread 'http://kevin-gattaca.blogspot.com/2011/11/bio-bwa-help-color-space-support-may-be.html' which mentions that color-space support is dropping in 0.6, but from below want to confirm if it's being dropped from BWA-short, BWA-SW, or both.

Thanks you,
Phillipe





Release 0.6.1 (28 November, 2011)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Notable changes to BWA-short:

 * Bugfix: duplicated alternative hits in the XA tag.

 * Bugfix: when trimming enabled, bwa-aln trims 1bp less.

 * Disabled the color-space alignment. 0.6.x is not working with SOLiD reads at
   present.

Notable changes to BWA-SW:

 * Bugfix: segfault due to excessive ambiguous bases.

 * Bugfix: incorrect mate position in the SE mode.

 * Bugfix: rare segfault in the PE mode

 * When macro _NO_SSE2 is in use, fall back to the standard Smith-Waterman
   instead of SSE2-SW.

 * Optionally mark split hits with lower alignment scores as secondary.

Changes to fastmap:

 * Bugfix: infinite loop caused by ambiguous bases.

 * Optionally output the query sequence.

(0.6.1: 28 November 2011, r104)