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