[med-svn] r19043 - in trunk/packages/mummer/trunk/debian: . patches

[Andreas Tille]

Author: tille
Date: 2015-04-14 06:34:01 +0000 (Tue, 14 Apr 2015)
New Revision: 19043

Added:
   trunk/packages/mummer/trunk/debian/README.Debian
Modified:
   trunk/packages/mummer/trunk/debian/patches/addition_from_mugsy.patch
Log:
Fix patches and add README.Debian about additional tools from mugsy


Added: trunk/packages/mummer/trunk/debian/README.Debian
===================================================================
--- trunk/packages/mummer/trunk/debian/README.Debian	                        (rev 0)
+++ trunk/packages/mummer/trunk/debian/README.Debian	2015-04-14 06:34:01 UTC (rev 19043)
@@ -0,0 +1,14 @@
+Mummer for Debian
+=================
+
+Debian will also package mugsy (http://mugsy.sourceforge.net/) that
+contains a patched copy of the mummer code.  This patch contains two
+additional tools
+
+   delta2blocks
+   delta2maf
+
+These tools are taken over to Debian's mummer code base to enable
+droping the extra code copy in mugsy.
+
+ -- Andreas Tille <tille at debian.org>  Mon, 13 Apr 2015 22:29:27 +0200

Modified: trunk/packages/mummer/trunk/debian/patches/addition_from_mugsy.patch
===================================================================
--- trunk/packages/mummer/trunk/debian/patches/addition_from_mugsy.patch	2015-04-13 20:31:06 UTC (rev 19042)
+++ trunk/packages/mummer/trunk/debian/patches/addition_from_mugsy.patch	2015-04-14 06:34:01 UTC (rev 19043)
@@ -1491,7 +1491,7 @@
     return;
    }
  
-+int Read_File  (FILE * fp, long int & Size, map<string,char *> & seqsMap,
++int Read_File  (FILE * fp, long int & Size, std::map<std::string,char *> & seqsMap,
 +		  int Partial)
 +
 +/* Read next string from  fp  (assuming FASTA format) into  T [1 ..]
@@ -1521,7 +1521,7 @@
 +	 if  (P != NULL){
 +	   //save previous seq
 +	   T [Len] = '\0';
-+	   string sP(P);
++	   std::string sP(P);
 +	   //printf("Saving seq %s of length %d %d\n",sP.c_str(),Len,strlen(T));
 +	   seqsMap.insert(make_pair(sP,T));
 +	   assert(seqsMap.find(P) != seqsMap.end());
@@ -1565,7 +1565,7 @@
 +   if  (P != NULL){
 +     //save previous seq
 +     T [Len] = '\0';
-+     string sP(P);
++     std::string sP(P);
 +     //printf("Saving seq %s of length %d %d\n",sP.c_str(),Len,strlen(T));
 +     seqsMap.insert(make_pair(sP,T));
 +     assert(seqsMap.find(P) != seqsMap.end());
@@ -1577,11 +1577,20 @@
 +
 --- a/src/tigr/tigrinc.hh
 +++ b/src/tigr/tigrinc.hh
-@@ -37,6 +37,7 @@ void *  Safe_realloc  (void *, size_t);
+@@ -12,6 +12,8 @@
+ #include  <ctime>
+ #include  <cassert>
+ #include  <cerrno>
++#include  <map>
++#include  <string>
+ #include  <unistd.h>
+ 
+ 
+@@ -37,6 +39,7 @@ void *  Safe_realloc  (void *, size_t);
  char  Complement  (char);
  bool CompareIUPAC (char, char);
  int  Read_String  (FILE *, char * &, long int &, char [], int);
-+int  Read_File  (FILE *, long int &, map<string, char *> &, int);
++int  Read_File  (FILE *, long int &, std::map<std::string, char *> &, int);
  void  Reverse_Complement (char S [], long int Lo, long int Hi);
  
  #endif