gentoo-overlay/sci-biology/amos/files/amos-3.1.0-qa-Wformat.patch

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 {