104 lines
2.7 KiB
Diff
104 lines
2.7 KiB
Diff
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]);
|