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 <[email protected]> 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 _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
