[med-svn] r15012 - trunk/packages/biosquid/trunk/debian/patches

Andreas Tille tille at alioth.debian.org
Mon Oct 28 13:07:27 UTC 2013 

Author: tille
Date: 2013-10-28 13:07:26 +0000 (Mon, 28 Oct 2013)
New Revision: 15012

Added:
   trunk/packages/biosquid/trunk/debian/patches/series
Modified:
   trunk/packages/biosquid/trunk/debian/patches/Makefile.in.patch
   trunk/packages/biosquid/trunk/debian/patches/afetch.man.patch
   trunk/packages/biosquid/trunk/debian/patches/alistat.man.patch
   trunk/packages/biosquid/trunk/debian/patches/compstruct.man.patch
   trunk/packages/biosquid/trunk/debian/patches/seqstat.man.patch
   trunk/packages/biosquid/trunk/debian/patches/sfetch.man.patch
   trunk/packages/biosquid/trunk/debian/patches/shuffle.man.patch
   trunk/packages/biosquid/trunk/debian/patches/sindex.man.patch
   trunk/packages/biosquid/trunk/debian/patches/sreformat.man.patch
Log:
Refreshed patches for quilt


Modified: trunk/packages/biosquid/trunk/debian/patches/Makefile.in.patch
===================================================================
--- trunk/packages/biosquid/trunk/debian/patches/Makefile.in.patch	2013-10-28 13:05:00 UTC (rev 15011)
+++ trunk/packages/biosquid/trunk/debian/patches/Makefile.in.patch	2013-10-28 13:07:26 UTC (rev 15012)
@@ -1,7 +1,6 @@
-diff -Nur squid/Makefile.in squid.new/Makefile.in
---- squid/Makefile.in	2006-07-30 18:39:11.000000000 -0300
-+++ squid.new/Makefile.in	2006-08-04 18:03:03.000000000 -0300
-@@ -75,10 +75,12 @@
+--- a/Makefile.in
++++ b/Makefile.in
+@@ -75,10 +75,12 @@ PROGS =	afetch\
  
  MANS =  afetch\
  	alistat\
@@ -15,7 +14,7 @@
  
  READMES = 00README INSTALL Makefile.in 
  
-@@ -103,51 +105,80 @@
+@@ -103,51 +105,80 @@ HDRS =	dirichlet.h\
  	stopwatch.h\
  	vectorops.h
  

Modified: trunk/packages/biosquid/trunk/debian/patches/afetch.man.patch
===================================================================
--- trunk/packages/biosquid/trunk/debian/patches/afetch.man.patch	2013-10-28 13:05:00 UTC (rev 15011)
+++ trunk/packages/biosquid/trunk/debian/patches/afetch.man.patch	2013-10-28 13:07:26 UTC (rev 15012)
@@ -1,13 +1,12 @@
-diff -Nur squid/Man/afetch.man squid.new/Man/afetch.man
---- squid/Man/afetch.man	2006-07-30 18:39:11.000000000 -0300
-+++ squid.new/Man/afetch.man	2006-08-05 01:47:12.000000000 -0300
+--- a/Man/afetch.man
++++ b/Man/afetch.man
 @@ -1,4 +1,4 @@
 -.TH "afetch" 1 "@RELEASEDATE@" "@PACKAGE@ @RELEASE@" "@PACKAGE@ Manual"
 +.TH "afetch" 1 "January 2003" "Biosquid 1.9g" "Biosquid Manual"
  
  .SH NAME
  .TP 
-@@ -67,15 +67,23 @@
+@@ -67,15 +67,23 @@ file to prepare it for all future afetch
  
  .SH SEE ALSO
  

Modified: trunk/packages/biosquid/trunk/debian/patches/alistat.man.patch
===================================================================
--- trunk/packages/biosquid/trunk/debian/patches/alistat.man.patch	2013-10-28 13:05:00 UTC (rev 15011)
+++ trunk/packages/biosquid/trunk/debian/patches/alistat.man.patch	2013-10-28 13:07:26 UTC (rev 15012)
@@ -1,13 +1,12 @@
-diff -Nur squid/Man/alistat.man squid.new/Man/alistat.man
---- squid/Man/alistat.man	2006-07-30 18:39:11.000000000 -0300
-+++ squid.new/Man/alistat.man	2006-08-05 02:10:07.000000000 -0300
+--- a/Man/alistat.man
++++ b/Man/alistat.man
 @@ -1,4 +1,4 @@
 -.TH "alistat" 1 "@RELEASEDATE@" "@PACKAGE@ @RELEASE@" "@PACKAGE@ Manual"
 +.TH "alistat" 1 "January 2003" "Biosquid 1.9g" "Biosquid Manual"
  
  .SH NAME
  .TP 
-@@ -109,13 +109,23 @@
+@@ -109,13 +109,23 @@ Babelfish autodetection option.
  
  .SH SEE ALSO
  

Modified: trunk/packages/biosquid/trunk/debian/patches/compstruct.man.patch
===================================================================
--- trunk/packages/biosquid/trunk/debian/patches/compstruct.man.patch	2013-10-28 13:05:00 UTC (rev 15011)
+++ trunk/packages/biosquid/trunk/debian/patches/compstruct.man.patch	2013-10-28 13:07:26 UTC (rev 15012)
@@ -1,13 +1,12 @@
-diff -Nur squid/Man/compstruct.man squid.new/Man/compstruct.man
---- squid/Man/compstruct.man	2006-07-30 18:39:11.000000000 -0300
-+++ squid.new/Man/compstruct.man	2006-08-05 02:11:13.000000000 -0300
+--- a/Man/compstruct.man
++++ b/Man/compstruct.man
 @@ -1,4 +1,4 @@
 -.TH "compstruct" 1 "@RELEASEDATE@" "@PACKAGE@ @RELEASE@" "@PACKAGE@ Manual"
 +.TH "compstruct" 1 "January 2003" "Biosquid 1.9g" "Biosquid Manual"
  
  .SH NAME
  .TP 
-@@ -116,13 +116,23 @@
+@@ -116,13 +116,23 @@ Don't print any verbose header informati
  
  .SH SEE ALSO
  

Modified: trunk/packages/biosquid/trunk/debian/patches/seqstat.man.patch
===================================================================
--- trunk/packages/biosquid/trunk/debian/patches/seqstat.man.patch	2013-10-28 13:05:00 UTC (rev 15011)
+++ trunk/packages/biosquid/trunk/debian/patches/seqstat.man.patch	2013-10-28 13:07:26 UTC (rev 15012)
@@ -1,13 +1,12 @@
-diff -Nur biosquid-1.9g+cvs20050121/Man/seqstat.man biosquid-1.9g+cvs20050121.new/Man/seqstat.man
---- biosquid-1.9g+cvs20050121/Man/seqstat.man	2006-07-30 18:39:11.000000000 -0300
-+++ biosquid-1.9g+cvs20050121.new/Man/seqstat.man	2008-02-21 23:03:22.000000000 -0300
+--- a/Man/seqstat.man
++++ b/Man/seqstat.man
 @@ -1,4 +1,4 @@
 -.TH "seqstat" 1 "@RELEASEDATE@" "@PACKAGE@ @RELEASE@" "@PACKAGE@ Manual"
 +.TH "seqstat" 1 "January 2003" "Biosquid 1.9g" "Biosquid Manual"
  
  .SH NAME
  .TP 
-@@ -16,7 +16,7 @@
+@@ -16,7 +16,7 @@ reads a sequence file
  .I seqfile
  and shows a number of simple statistics about it.
  
@@ -16,7 +15,7 @@
  The printed statistics include the name of the format, the residue
  type of the first sequence (protein, RNA, or DNA), the number of
  sequences, the total number of residues, and the average and range of
-@@ -69,13 +69,23 @@
+@@ -69,13 +69,23 @@ and date, the parameters and options in
  
  .SH SEE ALSO
  

Added: trunk/packages/biosquid/trunk/debian/patches/series
===================================================================
--- trunk/packages/biosquid/trunk/debian/patches/series	                        (rev 0)
+++ trunk/packages/biosquid/trunk/debian/patches/series	2013-10-28 13:07:26 UTC (rev 15012)
@@ -0,0 +1,9 @@
+afetch.man.patch
+alistat.man.patch
+compstruct.man.patch
+Makefile.in.patch
+seqstat.man.patch
+sfetch.man.patch
+shuffle.man.patch
+sindex.man.patch
+sreformat.man.patch

Modified: trunk/packages/biosquid/trunk/debian/patches/sfetch.man.patch
===================================================================
--- trunk/packages/biosquid/trunk/debian/patches/sfetch.man.patch	2013-10-28 13:05:00 UTC (rev 15011)
+++ trunk/packages/biosquid/trunk/debian/patches/sfetch.man.patch	2013-10-28 13:07:26 UTC (rev 15012)
@@ -1,13 +1,12 @@
-diff -Nur biosquid-1.9g+cvs20050121/Man/sfetch.man biosquid-1.9g+cvs20050121.new/Man/sfetch.man
---- biosquid-1.9g+cvs20050121/Man/sfetch.man	2006-07-30 18:39:11.000000000 -0300
-+++ biosquid-1.9g+cvs20050121.new/Man/sfetch.man	2008-02-21 23:04:12.000000000 -0300
+--- a/Man/sfetch.man
++++ b/Man/sfetch.man
 @@ -1,4 +1,4 @@
 -.TH "sfetch" 1 "@RELEASEDATE@" "@PACKAGE@ @RELEASE@" "@PACKAGE@ Manual"
 +.TH "sfetch" 1 "January 2003" "Biosquid 1.9g" "Biosquid Manual"
  
  .SH NAME
  .TP 
-@@ -64,7 +64,7 @@
+@@ -64,7 +64,7 @@ databases. The program
  .B sindex
  creates SSI indexes for any sequence file.
  
@@ -16,7 +15,7 @@
  .B sfetch
  was originally named 
  .B getseq,
-@@ -191,13 +191,23 @@
+@@ -191,13 +191,23 @@ Babelfish autodetection option.
  
  .SH SEE ALSO
  

Modified: trunk/packages/biosquid/trunk/debian/patches/shuffle.man.patch
===================================================================
--- trunk/packages/biosquid/trunk/debian/patches/shuffle.man.patch	2013-10-28 13:05:00 UTC (rev 15011)
+++ trunk/packages/biosquid/trunk/debian/patches/shuffle.man.patch	2013-10-28 13:07:26 UTC (rev 15012)
@@ -1,13 +1,12 @@
-diff -Nur biosquid-1.9g+cvs20050121/Man/shuffle.man biosquid-1.9g+cvs20050121.new/Man/shuffle.man
---- biosquid-1.9g+cvs20050121/Man/shuffle.man	2006-07-30 18:39:11.000000000 -0300
-+++ biosquid-1.9g+cvs20050121.new/Man/shuffle.man	2008-02-21 23:04:46.000000000 -0300
+--- a/Man/shuffle.man
++++ b/Man/shuffle.man
 @@ -1,4 +1,4 @@
 -.TH "shuffle" 1 "@RELEASEDATE@" "@PACKAGE@ @RELEASE@" "@PACKAGE@ Manual"
 +.TH "shuffle" 1 "January 2003" "Biosquid 1.9g" "Biosquid Manual"
  
  .SH NAME
  .TP 
-@@ -19,7 +19,7 @@
+@@ -19,7 +19,7 @@ in FASTA format on standard output. The
  are unchanged; this allows you to track down the source
  of each randomized sequence if necessary.
  
@@ -16,7 +15,7 @@
  The default is to simply shuffle each input sequence, preserving
  monosymbol composition exactly. To shuffle
  each sequence while preserving both its monosymbol and disymbol
-@@ -27,7 +27,7 @@
+@@ -27,7 +27,7 @@ composition exactly, use the
  .I -d 
  option.
  
@@ -25,7 +24,7 @@
  The
  .I -0
  and 
-@@ -44,7 +44,7 @@
+@@ -44,7 +44,7 @@ the generated sequence has the same 1st
  Markov properties as the input sequence (e.g.
  the same disymbol frequencies). 
  
@@ -34,7 +33,7 @@
  Note that the default and
  .I -0,
  or 
-@@ -56,7 +56,7 @@
+@@ -56,7 +56,7 @@ composition exactly, while the Markov al
  only expect to generate a sequence of similar
  composition on average.
  
@@ -43,7 +42,7 @@
  Other shuffling algorithms are also available,
  as documented below in the options.
  
-@@ -175,13 +175,23 @@
+@@ -175,13 +175,23 @@ the same output in subsequent runs with
  
  .SH SEE ALSO
  

Modified: trunk/packages/biosquid/trunk/debian/patches/sindex.man.patch
===================================================================
--- trunk/packages/biosquid/trunk/debian/patches/sindex.man.patch	2013-10-28 13:05:00 UTC (rev 15011)
+++ trunk/packages/biosquid/trunk/debian/patches/sindex.man.patch	2013-10-28 13:07:26 UTC (rev 15012)
@@ -1,13 +1,12 @@
-diff -Nur squid/Man/sindex.man squid.new/Man/sindex.man
---- squid/Man/sindex.man	2006-07-30 18:39:11.000000000 -0300
-+++ squid.new/Man/sindex.man	2006-08-05 02:01:43.000000000 -0300
+--- a/Man/sindex.man
++++ b/Man/sindex.man
 @@ -1,4 +1,4 @@
 -.TH "sindex" 1 "@RELEASEDATE@" "@PACKAGE@ @RELEASE@" "@PACKAGE@ Manual"
 +.TH "sindex" 1 "January 2003" "Biosquid 1.9g" "Biosquid Manual"
  
  .SH NAME
  .TP 
-@@ -83,12 +83,24 @@
+@@ -83,12 +83,24 @@ and accession (as a secondary key).
  .SH SEE ALSO
  
  .PP

Modified: trunk/packages/biosquid/trunk/debian/patches/sreformat.man.patch
===================================================================
--- trunk/packages/biosquid/trunk/debian/patches/sreformat.man.patch	2013-10-28 13:05:00 UTC (rev 15011)
+++ trunk/packages/biosquid/trunk/debian/patches/sreformat.man.patch	2013-10-28 13:07:26 UTC (rev 15012)
@@ -1,13 +1,12 @@
-diff -Nur biosquid-1.9g+cvs20050121/Man/sreformat.man biosquid-1.9g+cvs20050121.new/Man/sreformat.man
---- biosquid-1.9g+cvs20050121/Man/sreformat.man	2006-07-30 18:39:11.000000000 -0300
-+++ biosquid-1.9g+cvs20050121.new/Man/sreformat.man	2008-02-21 23:05:16.000000000 -0300
+--- a/Man/sreformat.man
++++ b/Man/sreformat.man
 @@ -1,4 +1,4 @@
 -.TH "sreformat" 1 "@RELEASEDATE@" "@PACKAGE@ @RELEASE@" "@PACKAGE@ Manual"
 +.TH "sreformat" 1 "January 2003" "Biosquid 1.9g" "Biosquid Manual"
  
  .SH NAME
  .TP 
-@@ -43,7 +43,7 @@
+@@ -43,7 +43,7 @@ include
  .I raw
  (raw sequence, no other information).
  
@@ -16,7 +15,7 @@
  The available aligned output file format
  codes include
  .I stockholm
-@@ -59,7 +59,7 @@
+@@ -59,7 +59,7 @@ codes include
  .I selex
  (the old SELEX/HMMER/Pfam annotated alignment format);
  
@@ -25,7 +24,7 @@
  All thee codes are interpreted case-insensitively
  (e.g. MSF, Msf, or msf all work).
  
-@@ -231,13 +231,23 @@
+@@ -231,13 +231,23 @@ markup.
  
  .SH SEE ALSO

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