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Fix QA warnings, due to using incorrect format specifiers in printf:
* contig-cmp.cc:237:50: warning: format ‘%u’ expects argument of type ‘unsigned int’,
* but argument 3 has type ‘std::vector<Contig_t>::size_type {aka long unsigned int}’ [-Wformat=]
* fprintf (stderr, "%u b contigs\n", b . size ());
--- a/src/Align/align.cc
+++ b/src/Align/align.cc
@@ -1936,7 +1936,7 @@
n = align . size ();
con = consensus . c_str ();
- fprintf (fp, "\nConsensus len = %d\n", consensus . length ());
+ fprintf (fp, "\nConsensus len = %zu\n", consensus . length ());
for (i = 0; i < n; i ++)
{
@@ -3936,7 +3936,7 @@
}
// Array of sum of quality scores in the slice for A,C,G,T,- resp.
- for (j = 0; j < 6; j ++)
+ for (j = 0; j < 5; j ++)
qvsum [j] = 0;
int nof_ambiguities = 0;
--- a/src/Align/align_poly.cc
+++ b/src/Align/align_poly.cc
@@ -1761,7 +1761,7 @@
n = align . size ();
con = consensus . c_str ();
- fprintf (fp, "\nConsensus len = %d\n", consensus . length ());
+ fprintf (fp, "\nConsensus len = %zu\n", consensus . length ());
for (i = 0; i < n; i ++)
{
fprintf (fp, "\nString #%d:\n", i);
--- a/src/Align/count-qmers.cc
+++ b/src/Align/count-qmers.cc
@@ -191,8 +191,8 @@
PrintMers(mer_table, min_count);
- fprintf(stderr, "reporter:counter:asm,reads_total,%ld\n", COUNT);
- fprintf(stderr, "reporter:counter:asm,reads_bp,%ld\n", LEN);
+ fprintf(stderr, "reporter:counter:asm,reads_total,%lld\n", COUNT);
+ fprintf(stderr, "reporter:counter:asm,reads_bp,%lld\n", LEN);
}
catch (Exception_t & e)
{
--- a/src/Align/kmer-cov.cc
+++ b/src/Align/kmer-cov.cc
@@ -485,7 +485,7 @@
Kmer_Len = s . length ();
else if (Kmer_Len != int (s . length ()))
{
- sprintf (Clean_Exit_Msg_Line, "New kmer \"%s\" length is %d instead of %d",
+ sprintf (Clean_Exit_Msg_Line, "New kmer \"%s\" length is %zu instead of %d",
s . c_str (), s . length (), Kmer_Len);
Clean_Exit (Clean_Exit_Msg_Line, __FILE__, __LINE__);
}
--- a/src/Align/kmer-cov-plot.cc
+++ b/src/Align/kmer-cov-plot.cc
@@ -316,7 +316,7 @@
}
else if (Kmer_Len != int (s . length ()))
{
- sprintf (Clean_Exit_Msg_Line, "New kmer \"%s\" length is %d instead of %d",
+ sprintf (Clean_Exit_Msg_Line, "New kmer \"%s\" length is %zu instead of %d",
s . c_str (), s . length (), Kmer_Len);
Clean_Exit (Clean_Exit_Msg_Line, __FILE__, __LINE__);
}
--- a/src/Align/make-consensus.cc
+++ b/src/Align/make-consensus.cc
@@ -303,7 +303,7 @@
break;
}
- sprintf (sid, "%ld", ++layout_id);
+ sprintf (sid, "%u", ++layout_id);
cid = string (sid);
ID_t lid = layout.getIID ();
if (lid == 0)
--- a/src/Align/make-consensus_poly.cc
+++ b/src/Align/make-consensus_poly.cc
@@ -279,7 +279,7 @@
break;
}
- sprintf(sid, "%ld", ++layout_id);
+ sprintf(sid, "%u", ++layout_id);
cid = string(sid);
ID_t lid = layout.getIID();
if (lid == 0) {
--- a/src/Align/simple-overlap.cc
+++ b/src/Align/simple-overlap.cc
@@ -422,7 +422,7 @@
"Options:\n"
" -a Also show alignments of overlaps \n"
" -E <x> Maximum error rate for overlaps is <x>\n"
- " e.g., -E 0.06 for 6% error rate\n"
+ " e.g., -E 0.06 for 6%% error rate\n"
" -F Input is a fasta file\n"
" -h Print this usage message\n"
" -o <n> Set minimum overlap length to <n>\n"
--- a/src/Compare/contig-cmp.cc
+++ b/src/Compare/contig-cmp.cc
@@ -145,7 +145,7 @@
fclose (fp);
- fprintf (stderr, "%u a contigs\n", a . size ());
+ fprintf (stderr, "%zu a contigs\n", a . size ());
vector <Unitig_t> a_contig (max_id + 1);
n = a . size ();
for (i = 0; i < n; i ++)
@@ -234,7 +234,7 @@
fclose (fp);
- fprintf (stderr, "%u b contigs\n", b . size ());
+ fprintf (stderr, "%zu b contigs\n", b . size ());
vector <Unitig_t> b_contig (max_id + 1);
n = b . size ();
for (i = 0; i < n; i ++)
--- a/src/Staden/progs/trace_convert.c
+++ b/src/Staden/progs/trace_convert.c
@@ -6,6 +6,9 @@
#include "traceType.h"
#include "seqIOABI.h"
+#include <fcntl.h>
+#include <unistd.h>
+
static char fileIdentifier[] = "$Id$";
struct opts {
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