| 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 { |