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diff -urbN src/tigr.orig/annotate.cc src/tigr/annotate.cc
--- src/tigr.orig/annotate.cc 2007-07-13 19:06:58.000000000 +0200
+++ src/tigr/annotate.cc 2007-11-07 21:47:03.000000000 +0100
@@ -10,6 +10,7 @@
*/
#include "tigrinc.hh"
+#include <assert.h>
#define FIELD_LEN 20
#define MAX_ALIGN 10000
@@ -138,19 +139,19 @@
// Print the alignment between strings A [1 .. M] and B [1 .. N] .
{
- static int D [MAX_ALIGN] [MAX_ALIGN];
- static char Op [MAX_ALIGN] [MAX_ALIGN];
- static char Show_A [2 * MAX_ALIGN];
- static char Show_B [2 * MAX_ALIGN];
+ int **D, *D_buf;
+ char **Op, *Op_buf;
+ char *Show_A;
+ char *Show_B;
int Errors, Tmp;
long int i, j, Ct;
- if (M >= MAX_ALIGN || N >= MAX_ALIGN)
- {
- printf ("\n *** Too long ***\n\n");
- fprintf (Gaps_With_Errors_File, "%s %7s\n", Line, "-");
- return;
- }
+ assert ( D_buf = (int *) calloc ( (M+1)*(N+1), sizeof(int) ) ) ;
+ D = &D_buf ;
+ assert ( Op_buf = (char *) calloc ( (M+1)*(N+1), sizeof(char) ) ) ;
+ Op = &Op_buf ;
+ assert ( Show_A = (char *) calloc ( 2*(M+1) , sizeof(char) ) ) ;
+ assert ( Show_B = (char *) calloc ( 2*(N+1) , sizeof(char) ) ) ;
D [0] [0] = 0;
Op [0] [0] = 'a';
@@ -229,5 +230,10 @@
putchar ('\n');
Ct -= WIDTH;
} while (Ct > 0);
+
+ free ( D_buf ) ;
+ free ( Op_buf ) ;
+ free ( Show_A ) ;
+ free ( Show_B ) ;
return;
}
diff -urbN src/tigr.orig/Makefile src/tigr/Makefile
--- src/tigr.orig/Makefile 2007-07-13 19:06:58.000000000 +0200
+++ src/tigr/Makefile 2007-11-07 21:47:03.000000000 +0100
@@ -2,23 +2,20 @@
# BIN_DIR AUX_BIN_DIR CXX CC CPPFLAGS LDFLAGS
ifndef BIN_DIR
-BIN_DIR := $(CURDIR)
+BIN_DIR := ../../bin
endif
ifndef AUX_BIN_DIR
-AUX_BIN_DIR := $(CURDIR)
+AUX_BIN_DIR := ../../aux_bin
endif
OBJ_RULE = $(CXX) $(CPPFLAGS) $< -c -o $@
-BIN_RULE = $(CXX) $(CPPFLAGS) $^ -o $(BIN_DIR)/$@; \
- chmod 755 $(BIN_DIR)/$@
-AUX_BIN_RULE = $(CXX) $(CPPFLAGS) $^ -o $(AUX_BIN_DIR)/$@; \
- chmod 755 $(AUX_BIN_DIR)/$@
+BIN_RULE = $(CXX) $(CPPFLAGS) $^ -o $(BIN_DIR)/$@ && chmod 755 $(BIN_DIR)/$@
+AUX_BIN_RULE = $(CXX) $(CPPFLAGS) $^ -o $(AUX_BIN_DIR)/$@ && chmod 755 $(AUX_BIN_DIR)/$@
VPATH := $(AUX_BIN_DIR):$(BIN_DIR)
ALL := annotate combineMUMs delta-filter gaps mgaps \
postnuc postpro prenuc prepro repeat-match \
- show-aligns show-coords show-tiling show-snps \
- show-diff
+ show-aligns show-coords show-tiling show-snps
#-- PHONY rules --#
@@ -30,10 +27,8 @@
clean:
rm -f *.o *~
- cd $(BIN_DIR); rm -f $(ALL)
- cd $(AUX_BIN_DIR); rm -f $(ALL)
-
-
+ ( cd $(BIN_DIR) && rm -f $(ALL) )
+ ( cd $(AUX_BIN_DIR) && rm -f $(ALL) )
#-- not so PHONY rules --#
@@ -92,5 +87,3 @@
show-snps: show-snps.cc tigrinc.o translate.o delta.o
$(BIN_RULE)
-show-diff: show-diff.cc tigrinc.o delta.o
- $(BIN_RULE)
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