Author: tille
Date: 2008-12-10 16:22:25 +0000 (Wed, 10 Dec 2008)
New Revision: 2767
Added:
trunk/packages/euler2/trunk/debian/patches/20_exit_better_than_crash.patch
Modified:
trunk/packages/euler2/trunk/debian/patches/20_perl_warnings.patch
trunk/packages/euler2/trunk/debian/patches/series
Log:
Euler2 has a limit of 75000 sequences hardcoded. I have no idea in how far it
might make
sense to simply increase this number or whether there are other constraints
given the fact
that there does not exist a check for exceeding this limit.
Added:
trunk/packages/euler2/trunk/debian/patches/20_exit_better_than_crash.patch
===================================================================
--- trunk/packages/euler2/trunk/debian/patches/20_exit_better_than_crash.patch
(rev 0)
+++ trunk/packages/euler2/trunk/debian/patches/20_exit_better_than_crash.patch
2008-12-10 16:22:25 UTC (rev 2767)
@@ -0,0 +1,20 @@
+File readpar.c contains the definition of the maximum number of sequences:
+ max_seq = 75000;
+but there is no check whether this limit is exceeded somewhere. If you have
+larger data sets the program trans_qual (and probably others using readseq1by1)
+will just crash. This check at least results in an error message and exiting
+the program (harsh but at least more helpful than a crash).
+--- euler-2.0.orig/readseq1by1.c
++++ euler-2.0/readseq1by1.c
+@@ -171,6 +171,11 @@
+ }
+ n = 0;
+ k ++;
++ if ( k > max_seq ) {
++ fprintf(stderr, "Number of sequence exceeds
maximum allowed number (%i)\n", max_seq);
++ fprintf(stderr, "The first string that can not
be read is '%s'\n", str);
++ exit(-1);
++ }
+ sscanf(&str[1], "%s", src_name[k]);
+ } else {
+ for(i = 0; i < strlen(str); i ++) {
Modified: trunk/packages/euler2/trunk/debian/patches/20_perl_warnings.patch
===================================================================
--- trunk/packages/euler2/trunk/debian/patches/20_perl_warnings.patch
2008-12-10 12:38:53 UTC (rev 2766)
+++ trunk/packages/euler2/trunk/debian/patches/20_perl_warnings.patch
2008-12-10 16:22:25 UTC (rev 2767)
@@ -23,3 +23,14 @@
system("mv reads.tmp.score reads.txt.score");
system("$MYHOME/overlapper-all -i reads.txt -q reads.txt.score -o
reads.aln -l $overlen -p 200 -d $min_id -H");
$i = $i + 1;
+--- euler-2.0.orig/eubatch.pl
++++ euler-2.0/eubatch.pl
+@@ -455,7 +455,7 @@
+ if(${quality_file} ne "${fasta_file}.qual") {
+ `cp ${quality_file} ${fasta_file}.qual`;
+ }
+- do_cmd($params, "trans_qual", "$EBIN/trans_qual -i $fasta_file -o
$fasta_file.reads $cmdhtml ");
++ do_cmd($params, "trans_qual", "$EBIN/trans_qual -i $fasta_file -o
$fasta_file.reads $cmdhtml ") || die("Command trans_qual failed.");
+ do_cmd($params, "errcorr-lapper-pair-mem",
+ "$EBIN/errcorr-lapper-pair-mem.pl ${fasta_file}.reads
${fasta_file}.reads.score $min_length $min_id");
+ } else {
Modified: trunk/packages/euler2/trunk/debian/patches/series
===================================================================
--- trunk/packages/euler2/trunk/debian/patches/series 2008-12-10 12:38:53 UTC
(rev 2766)
+++ trunk/packages/euler2/trunk/debian/patches/series 2008-12-10 16:22:25 UTC
(rev 2767)
@@ -2,3 +2,4 @@
20_gcc4_static.patch
10_euler2_path_on_debian.patch
20_perl_warnings.patch
+20_exit_better_than_crash.patch
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