Author: Philipp Benner <philipp@debian.org>
Last-Update: Sun, 07 Jul 2013 13:33:01 +0200
Description: Fix run time errors detected by Mayhem
--- wise-2.4.1.orig/src/models/dbac.c
+++ wise-2.4.1/src/models/dbac.c
@@ -535,8 +535,12 @@
*
*/
- one = read_fasta_file_Sequence(*argv++);
- two = read_fasta_file_Sequence(*argv++);
+ if( (one = read_fasta_file_Sequence(*argv++)) == NULL ) {
+ fatal("Unable to read the sequence in file");
+ }
+ if( (two = read_fasta_file_Sequence(*argv++)) == NULL ) {
+ fatal("Unable to read the sequence in file");
+ }
uppercase_Sequence(one);
uppercase_Sequence(two);
--- wise-2.4.1.orig/src/models/estwise.c
+++ wise-2.4.1/src/models/estwise.c
@@ -313,7 +313,7 @@
}
}
- if( reverse == TRUE ) {
+ if( cdna && reverse == TRUE ) {
if( tstart > tend ) {
warn("You have already reversed the DNA by using %d - %d truncation. Re-reversing",tstart,tend);
}
@@ -323,7 +323,7 @@
cdna = cdna_temp;
}
- if( target_abs == TRUE ) {
+ if( cdna && target_abs == TRUE ) {
cdna->baseseq->offset = 1;
cdna->baseseq->end = strlen(cdna->baseseq->seq);
}
@@ -472,8 +472,11 @@
}
cp = flat_cDNAParser(indel_error);
- cm = flat_CodonMapper(ct);
- sprinkle_errors_over_CodonMapper(cm,subs_error);
+
+ if( ct ) {
+ cm = flat_CodonMapper(ct);
+ sprinkle_errors_over_CodonMapper(cm,subs_error);
+ }
return ret;
--- wise-2.4.1.orig/src/models/genewise.c
+++ wise-2.4.1/src/models/genewise.c
@@ -550,8 +550,10 @@
ret = FALSE;
}
- gen->baseseq->offset = 1;
- gen->baseseq->end = strlen(gen->baseseq->seq);
+ if ( gen ) {
+ gen->baseseq->offset = 1;
+ gen->baseseq->end = strlen(gen->baseseq->seq);
+ }
}
if( alg_str != NULL ) {
--- wise-2.4.1.orig/src/models/estwisedb.c
+++ wise-2.4.1/src/models/estwisedb.c
@@ -688,8 +688,11 @@
cps = flat_cDNAParser(indel_error);
- cm = flat_CodonMapper(ct);
- sprinkle_errors_over_CodonMapper(cm,subs_error);
+
+ if( ct ) {
+ cm = flat_CodonMapper(ct);
+ sprinkle_errors_over_CodonMapper(cm,subs_error);
+ }
return ret;
--- wise-2.4.1.orig/src/models/promoterwise.c
+++ wise-2.4.1/src/models/promoterwise.c
@@ -147,8 +147,12 @@
lchs = standard_LocalCisHitScore(NMaskType_VARIABLE);
- query = read_fasta_file_Sequence(argv[1]);
- target = read_fasta_file_Sequence(argv[2]);
+ if( (query = read_fasta_file_Sequence(argv[1])) == NULL ) {
+ fatal("Unable to read the sequence in query file");
+ }
+ if( (target = read_fasta_file_Sequence(argv[2])) == NULL ) {
+ fatal("Unable to read the sequence in target file");
+ }
for(i=0;i<query->len;i++) {
query->seq[i] = toupper(query->seq[i]);
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