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Author: Andreas Tille <tille@debian.org>
Last-Update: Fri, 26 Oct 2018 20:34:34 +0200
Description: Ensure format security
--- a/src/compute_qv/Btk_qv_io.c
+++ b/src/compute_qv/Btk_qv_io.c
@@ -1426,13 +1426,13 @@
/* Set alignment parameters globally. */
if (set_alignment_parameters(&align_pars, Match, MisMatch, Insertion,
Deletion, &message ) == ERROR) {
- fprintf(stderr, message.text);
+ fprintf(stderr, "%s", message.text);
goto error;
}
if (set_alignment_parameters_IUB(&align_pars_IUB, Match, MisMatch,
Insertion, Deletion, &message ) == ERROR ) {
- fprintf(stderr, message.text);
+ fprintf(stderr, "%s", message.text);
goto error;
}
@@ -1451,7 +1451,7 @@
/* Create reverse complement of consensus. */
if (contig_get_reverse_comp(&consensusrc, &consensus,
&message)==ERROR ) {
- fprintf(stderr, message.text);
+ fprintf(stderr, "%s", message.text);
goto error;
}
FREE(qv);
--- a/src/mktrain/train.c
+++ b/src/mktrain/train.c
@@ -1600,7 +1600,7 @@
/* Set parameters for alignment with consensus */
if (set_alignment_parameters( &align_pars, Match, MisMatch, GapInit,
GapExt , &message ) ==ERROR ) {
- fprintf(stderr, message.text);
+ fprintf(stderr, "%s", message.text);
exit (ERROR);
}
@@ -1608,7 +1608,7 @@
if (set_alignment_parameters_IUB( &align_pars_IUB,
Match * VECTOR_MATCH_MULTIPLIER, MisMatch, GapInit, GapExt,
&message ) ==ERROR ) {
- fprintf(stderr, message.text);
+ fprintf(stderr, "%s", message.text);
exit (ERROR);
}
@@ -1636,7 +1636,7 @@
fprintf(fout, "# Site = %s\n", SiteName);
if (readVector( VectorName, PrimerName, SiteName, &vector,
&align_pars_IUB, &message) ==ERROR ) {
- fprintf(stderr, message.text);
+ fprintf(stderr, "%s", message.text);
exit (ERROR);
}
vecP=&vector;
@@ -1644,7 +1644,7 @@
&& (! PrimerSpecified) && (!SiteSpecified) ) {
fprintf(fout, "# Short Vector = %s\n", VectorName);
if (readShortVector( VectorName, &vector, &message) == ERROR ) {
- fprintf(stderr, message.text);
+ fprintf(stderr, "%s", message.text);
exit (ERROR);
}
vecP=&vector;
@@ -1669,14 +1669,14 @@
/* Read consensus file. */
if (local_read_fasta( ConsensusName, &consensus, &message)
== ERROR) {
- fprintf(stderr, message.text);
+ fprintf(stderr, "%s", message.text);
exit (ERROR);
}
/* Create reverse complement of consensus. */
if (contig_get_reverse_comp( &consensusrc, &consensus, &message)
== ERROR) {
- fprintf(stderr, message.text);
+ fprintf(stderr, "%s", message.text);
exit (ERROR);
}
}
--- a/src/mktrain/trainphd.c
+++ b/src/mktrain/trainphd.c
@@ -928,7 +928,7 @@
if (set_alignment_parameters( &align_pars, Match, MisMatch, GapInit,
GapExt, &message ) != SUCCESS)
{
- fprintf(stderr, message.text);
+ fprintf(stderr, "%s", message.text);
exit (ERROR);
}
@@ -937,7 +937,7 @@
Match * VECTOR_MATCH_MULTIPLIER, MisMatch,
GapInit, GapExt, &message ) != SUCCESS)
{
- fprintf(stderr, message.text);
+ fprintf(stderr, "%s", message.text);
exit (ERROR);
}
@@ -956,7 +956,7 @@
fprintf(fout, "# Site = %s\n", SiteName);
if (readVector( VectorName, PrimerName, SiteName, &vector,
&align_pars_IUB, &message) ==ERROR ) {
- fprintf(stderr, message.text);
+ fprintf(stderr, "%s", message.text);
exit (ERROR);
}
vecP=&vector;
@@ -964,7 +964,7 @@
&& (! PrimerSpecified) && (!SiteSpecified) ) {
fprintf(fout, "# Short Vector = %s\n", VectorName);
if (readShortVector( VectorName, &vector, &message) == ERROR ) {
- fprintf(stderr, message.text);
+ fprintf(stderr, "%s", message.text);
exit (ERROR);
}
vecP=&vector;
@@ -1008,14 +1008,14 @@
/* Read consensus file. */
if (local_read_fasta( ConsensusName, &consensus, &message ) != SUCCESS)
{
- fprintf(stderr, message.text);
+ fprintf(stderr, "%s", message.text);
exit (ERROR);
}
/* Create reverse complement of consensus. */
if (contig_get_reverse_comp( &rev_comp, &consensus, &message )
!= SUCCESS)
{
- fprintf(stderr, message.text);
+ fprintf(stderr, "%s", message.text);
exit (ERROR);
}
@@ -1081,14 +1081,14 @@
fprintf( fout, "#\n");
/* Read consensus file. */
if (local_read_fasta( ConsensusName, &consensus, &message ) != SUCCESS) {
- fprintf(stderr, message.text);
+ fprintf(stderr, "%s", message.text);
exit (ERROR);
}
/* Create reverse complement of consensus. */
if (contig_get_reverse_comp( &rev_comp, &consensus, &message )
!= SUCCESS)
{
- fprintf(stderr, message.text);
+ fprintf(stderr, "%s", message.text);
exit (ERROR);
}
@@ -1120,23 +1120,23 @@
if (!hist)
{
if (alignment_parameters_release( &align_pars, &message ) != SUCCESS) {
- fprintf(stderr, message.text);
+ fprintf(stderr, "%s", message.text);
exit (ERROR);
}
if (alignment_parameters_release( &align_pars_IUB, &message ) != SUCCESS) {
- fprintf(stderr, message.text);
+ fprintf(stderr, "%s", message.text);
exit (ERROR);
}
if ( ( InputType == NAME_FILES ) || ( InputType == NAME_DIR ) ) {
if (contig_release( &consensus, &message ) != SUCCESS) {
- fprintf(stderr, message.text);
+ fprintf(stderr, "%s", message.text);
exit (ERROR);
}
if (contig_release( &rev_comp, &message ) != SUCCESS) {
- fprintf(stderr, message.text);
+ fprintf(stderr, "%s", message.text);
exit (ERROR);
}
}
|
