* samtools-0.1.5-32 (r449)

 * fillmd: fixed a bug in modifying MD/NM tags
 * in import, give a warning if the read is aligned but there is no CIGAR.

diff --git a/bam_import.c b/bam_import.c
index 19cd75f4352f2d144b1d0a36ed0925cab6a50cc8..1dc906eb49f36428460be547b1582ab52432f651 100644 (file)
--- a/bam_import.c
+++ b/bam_import.c
@@ -374,7 +374,10 @@ int sam_read1(tamFile fp, bam_header_t *header, bam1_t *b)
                        c->bin = bam_reg2bin(c->pos, bam_calend(c, bam1_cigar(b)));
                        doff += c->n_cigar * 4;
                } else {
-                       if (!(c->flag&BAM_FUNMAP)) parse_error(fp->n_lines, "mapped sequence without CIGAR");
+                       if (!(c->flag&BAM_FUNMAP)) {
+                               fprintf(stderr, "Parse warning at line %lld: mapped sequence without CIGAR\n", (long long)fp->n_lines);
+                               c->flag |= BAM_FUNMAP;
+                       }
                        c->bin = bam_reg2bin(c->pos, c->pos + 1);
                }
        }

diff --git a/bam_md.c b/bam_md.c
index ead2346e4ec21f75b8ceb88a4b78690d2a3d3b39..e2fdff801aebf4cf8e28d8e620434ec21a48ac69 100644 (file)
--- a/bam_md.c
+++ b/bam_md.c
@@ -16,10 +16,6 @@ void bam_fillmd1(bam1_t *b, char *ref, int is_equal)
        uint8_t *old_md, *old_nm;
        int32_t old_nm_i = -1, nm = 0;
 
-       old_md = bam_aux_get(b, "MD");
-       old_nm = bam_aux_get(b, "NM");
-       if (c->flag & BAM_FUNMAP) return;
-       if (old_nm) old_nm_i = bam_aux2i(old_nm);
        str = (kstring_t*)calloc(1, sizeof(kstring_t));
        for (i = y = 0, x = c->pos; i < c->n_cigar; ++i) {
                int j, l = cigar[i]>>4, op = cigar[i]&0xf;
@@ -57,12 +53,19 @@ void bam_fillmd1(bam1_t *b, char *ref, int is_equal)
                }
        }
        ksprintf(str, "%d", u);
+       // update NM
+       old_nm = bam_aux_get(b, "NM");
+       if (c->flag & BAM_FUNMAP) return;
+       if (old_nm) old_nm_i = bam_aux2i(old_nm);
        if (!old_nm) bam_aux_append(b, "NM", 'i', 4, (uint8_t*)&nm);
        else if (nm != old_nm_i) {
+               uint8_t *old_data = b->data;
                fprintf(stderr, "[bam_fillmd1] different NM for read '%s': %d -> %d\n", bam1_qname(b), old_nm_i, nm);
                bam_aux_del(b, old_nm);
                bam_aux_append(b, "NM", 'i', 4, (uint8_t*)&nm);
        }
+       // update MD
+       old_md = bam_aux_get(b, "MD");
        if (!old_md) bam_aux_append(b, "MD", 'Z', str->l + 1, (uint8_t*)str->s);
        else {
                int is_diff = 0;

diff --git a/bamtk.c b/bamtk.c
index c6a571463cb608639dd23d71251ad2c70210c649..41b3bc8c26a78bc71042eb2474a8855a6f635adc 100644 (file)
--- a/bamtk.c
+++ b/bamtk.c
@@ -9,7 +9,7 @@
 #endif
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.1.5-31 (r448)"
+#define PACKAGE_VERSION "0.1.5-32 (r449)"
 #endif
 
 int bam_taf2baf(int argc, char *argv[]);

diff --git a/misc/samtools.pl b/misc/samtools.pl
index 8c64de85297a20593f9bcadabb021c952c2fdb8e..86b285c5fa6c144a1d60ed61cb48a23bde7f134f 100755 (executable)
--- a/misc/samtools.pl
+++ b/misc/samtools.pl
@@ -302,7 +302,11 @@ sub uniqcmp {
                $p->[0][5]-$p->[1][5], "\n" if ($z && defined($opts{p}) && ($p->[0][3] >= $opts{q} || $p->[1][3] >= $opts{q}));
        } elsif (defined($p->[0])) {
          ++$cnt[$p->[0][3]>=$opts{q}? 6 : 7];
+         print STDERR "$x\t$p->[0][1]:$p->[0][2]\t$p->[0][3]\t$p->[0][4]\t*\t0\t*\t",
+               $p->[0][5], "\n" if (defined($opts{p}) && $p->[0][3] >= $opts{q});
        } else {
+         print STDERR "$x\t*\t0\t*\t$p->[1][1]:$p->[1][2]\t$p->[1][3]\t$p->[1][4]\t",
+               -$p->[1][5], "\n" if (defined($opts{p}) && $p->[1][3] >= $opts{q});
          ++$cnt[$p->[1][3]>=$opts{q}? 8 : 9];
        }
   }
@@ -326,7 +330,8 @@ sub uniqcmp_aux {
   while (<$fh>) {
        my @t = split;
        next if (@t < 11);
-       my $l = ($t[5] =~ /^(\d+)S/)? $1 : 0;
+#      my $l = ($t[5] =~ /^(\d+)S/)? $1 : 0;
+       my $l = 0;
        my ($x, $nm) = (0, 0);
        $nm = $1 if (/NM:i:(\d+)/);
        $_ = $t[5];