* fixed a memory violation

 * added splitchr to vcfutils.pl

diff --git a/bam2bcf_indel.c b/bam2bcf_indel.c
index 819c1e7b1371296b7da5536939fab691f53c1722..16241d0c0399fb7e727951f2d8f64d86798e25d1 100644 (file)
--- a/bam2bcf_indel.c
+++ b/bam2bcf_indel.c
@@ -112,7 +112,7 @@ int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_calla
                                          const void *rghash)
 {
        extern void ks_introsort_uint32_t(int, uint32_t*);
-       int i, s, j, k, t, n_types, *types, max_rd_len, left, right, max_ins, *score1, *score2;
+       int i, s, j, k, t, n_types, *types, max_rd_len, left, right, max_ins, *score1, *score2, max_ref2;
        int N, K, l_run, ref_type, n_alt;
        char *inscns = 0, *ref2, *query;
        khash_t(rg) *hash = (khash_t(rg)*)rghash;
@@ -236,7 +236,8 @@ int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_calla
                free(inscns_aux);
        }
        // compute the likelihood given each type of indel for each read
-       ref2  = calloc(right - left + max_ins + 2, 1);
+       max_ref2 = right - left + 2 + 2 * (max_ins > -types[0]? max_ins : -types[0]);
+       ref2  = calloc(max_ref2, 1);
        query = calloc(right - left + max_rd_len + max_ins + 2, 1);
        score1 = calloc(N * n_types, sizeof(int));
        score2 = calloc(N * n_types, sizeof(int));
@@ -264,6 +265,7 @@ int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_calla
                }
                for (; j < right && ref[j]; ++j)
                        ref2[k++] = bam_nt16_nt4_table[bam_nt16_table[(int)ref[j]]];
+               for (; k < max_ref2; ++k) ref2[k] = 4;
                if (j < right) right = j;
                // align each read to ref2
                for (s = K = 0; s < n; ++s) {

diff --git a/bcftools/vcfutils.pl b/bcftools/vcfutils.pl
index 6cc168fb363f59541511429b6e6538e0263acbe1..cd86b0fba041a77bb9d887473fa68cb853f1c597 100755 (executable)
--- a/bcftools/vcfutils.pl
+++ b/bcftools/vcfutils.pl
@@ -14,11 +14,27 @@ sub main {
   my $command = shift(@ARGV);
   my %func = (subsam=>\&subsam, listsam=>\&listsam, fillac=>\&fillac, qstats=>\&qstats, varFilter=>\&varFilter,
                          hapmap2vcf=>\&hapmap2vcf, ucscsnp2vcf=>\&ucscsnp2vcf, filter4vcf=>\&varFilter, ldstats=>\&ldstats,
-                         gapstats=>\&gapstats);
+                         gapstats=>\&gapstats, splitchr=>\&splitchr);
   die("Unknown command \"$command\".\n") if (!defined($func{$command}));
   &{$func{$command}};
 }
 
+sub splitchr {
+  my %opts = (l=>5000000);
+  getopts('l:', \%opts);
+  my $l = $opts{l};
+  die(qq/Usage: vcfutils.pl splitchr [-l $opts{l}] <in.fa.fai>\n/) if (@ARGV == 0 && -t STDIN);
+  while (<>) {
+       my @t = split;
+       my $last = 0;
+       for (my $i = 0; $i < $t[1];) {
+         my $e = ($t[1] - $i) / $l < 1.1? $t[1] : $i + $l;
+         print "$t[0]:".($i+1)."-$e\n";
+         $i = $e;
+       }
+  }
+}
+
 sub subsam {
   die(qq/Usage: vcfutils.pl subsam <in.vcf> [samples]\n/) if (@ARGV == 0);
   my ($fh, %h);