[med-svn] r12428 - trunk/packages/hmmer/branches/lkajan/debian/patches

[Laszlo Kajan]

Author: lkajan-guest
Date: 2012-10-15 14:18:09 +0000 (Mon, 15 Oct 2012)
New Revision: 12428

Modified:
   trunk/packages/hmmer/branches/lkajan/debian/patches/jackhmmer_chkhmmstop
Log:
moved documentation of --chkhmmskip closer to --chkali

Modified: trunk/packages/hmmer/branches/lkajan/debian/patches/jackhmmer_chkhmmstop
===================================================================
--- trunk/packages/hmmer/branches/lkajan/debian/patches/jackhmmer_chkhmmstop	2012-10-15 13:44:02 UTC (rev 12427)
+++ trunk/packages/hmmer/branches/lkajan/debian/patches/jackhmmer_chkhmmstop	2012-10-15 14:18:09 UTC (rev 12428)
@@ -41,8 +41,8 @@
  	    {
 --- a/documentation/man/jackhmmer.man
 +++ b/documentation/man/jackhmmer.man
-@@ -615,6 +615,21 @@
- .SH OTHER OPTIONS
+@@ -108,6 +108,21 @@
+ is the iteration number (from 1..N).
  
  .TP
 +.BI --chkhmmskip
@@ -60,9 +60,9 @@
 +\&.
 +
 +.TP
- .B --nonull2
- Turn off the null2 score corrections for biased composition.
- 
+ .BI --chkali " <prefix>"
+ At the end of each iteration, checkpoint an alignment of all
+ domains satisfying inclusion thresholds (e.g. what will become the
 @@ -685,7 +700,7 @@
  support. This is the default, but it may have been turned off at
  compile-time for your site or machine for some reason.