* samtools-0.1.7-6

 * fixed a bug in faidx

diff --git a/ChangeLog b/ChangeLog
index 6b1a695e5918557697bf2c031e2e02236c5733b7..64df707683cb8c2ee3fb4a6cf7f0612482a37413 100644 (file)
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,161 @@
+------------------------------------------------------------------------
+r529 | jmarshall | 2010-01-11 18:51:49 -0500 (Mon, 11 Jan 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/faidx.c
+
+Put the right filename in the error message.
+
+------------------------------------------------------------------------
+r528 | lh3lh3 | 2009-12-14 11:26:47 -0500 (Mon, 14 Dec 2009) | 3 lines
+Changed paths:
+   M /trunk/samtools/bam_plcmd.c
+   M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.7-5 (r528)
+ * further add new consensus generation strategy
+
+------------------------------------------------------------------------
+r527 | petulda | 2009-12-11 12:31:05 -0500 (Fri, 11 Dec 2009) | 1 line
+Changed paths:
+   M /trunk/samtools/knetfile.c
+
+Fixed a bug in knet_seek
+------------------------------------------------------------------------
+r526 | petulda | 2009-12-11 07:51:18 -0500 (Fri, 11 Dec 2009) | 1 line
+Changed paths:
+   M /trunk/samtools/misc/sam2vcf.pl
+
+Small fix in VCF format: dot for the empty INFO field
+------------------------------------------------------------------------
+r525 | petulda | 2009-12-11 04:36:18 -0500 (Fri, 11 Dec 2009) | 1 line
+Changed paths:
+   M /trunk/samtools/sam_header.c
+
+Allow tabs in the CO header field
+------------------------------------------------------------------------
+r524 | jmarshall | 2009-12-10 10:03:58 -0500 (Thu, 10 Dec 2009) | 3 lines
+Changed paths:
+   M /trunk/samtools/Makefile
+   M /trunk/samtools/Makefile.mingw
+
+Depend on libbam.a rather than the phony target, so that samtools is not
+unnecessarily rebuilt every time.  Also clean bgzip.
+
+------------------------------------------------------------------------
+r523 | jmarshall | 2009-12-10 09:45:32 -0500 (Thu, 10 Dec 2009) | 4 lines
+Changed paths:
+   M /trunk/samtools/Makefile
+   M /trunk/samtools/Makefile.mingw
+
+Fix a bug in compiling bgzip: this also needs knetfile.o when _USE_KNETFILE
+is defined.  Also introduce $(KNETFILE_O) which can be set to empty to
+facilitate non-knet builds.
+
+------------------------------------------------------------------------
+r522 | lh3lh3 | 2009-12-01 13:02:36 -0500 (Tue, 01 Dec 2009) | 4 lines
+Changed paths:
+   M /trunk/samtools/bamtk.c
+   M /trunk/samtools/sam_view.c
+
+ * samtools-0.1.7-4 (r522)
+ * fixed a bug in "view -r"
+ * added a new option "view -R" to read required read groups from a file
+
+------------------------------------------------------------------------
+r521 | lh3lh3 | 2009-12-01 10:00:12 -0500 (Tue, 01 Dec 2009) | 3 lines
+Changed paths:
+   M /trunk/samtools/bam_md.c
+   M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.7-3 (r521)
+ * calmd: optionally mask matching bases as N
+
+------------------------------------------------------------------------
+r520 | lh3lh3 | 2009-12-01 09:37:17 -0500 (Tue, 01 Dec 2009) | 4 lines
+Changed paths:
+   M /trunk/samtools/bam_plcmd.c
+   M /trunk/samtools/bamtk.c
+   M /trunk/samtools/misc/samtools.pl
+
+ * samtools-0.1.7-2 (r520)
+ * fixed a few issues with compilation in Windows (on behalf of John)
+ * choose a random base as the consensus (for population genetics studies)
+
+------------------------------------------------------------------------
+r519 | jmarshall | 2009-11-30 10:53:02 -0500 (Mon, 30 Nov 2009) | 6 lines
+Changed paths:
+   M /trunk/samtools/Makefile
+
+Put libraries at the end, so they can resolve references from libbam.a
+as well, even with old-fashioned linkers.
+
+Also use libbam.a explicitly rather than "-L. -lbam" to ensure that we get
+the freshly built library, not some other libbam.a lying around the system.
+
+------------------------------------------------------------------------
+r518 | jmarshall | 2009-11-30 08:44:56 -0500 (Mon, 30 Nov 2009) | 2 lines
+Changed paths:
+   M /trunk/samtools/Makefile
+   M /trunk/samtools/misc/Makefile
+
+Also clean *.exe (for Cygwin users using this makefile).
+
+------------------------------------------------------------------------
+r517 | jmarshall | 2009-11-30 07:09:04 -0500 (Mon, 30 Nov 2009) | 2 lines
+Changed paths:
+   M /trunk/samtools/bam_index.c
+
+Index files should be opened in binary mode, not text mode.
+
+------------------------------------------------------------------------
+r516 | lh3lh3 | 2009-11-27 15:18:59 -0500 (Fri, 27 Nov 2009) | 2 lines
+Changed paths:
+   A /trunk/samtools/examples/bam2bed.c
+
+another example program
+
+------------------------------------------------------------------------
+r515 | lh3lh3 | 2009-11-27 10:44:56 -0500 (Fri, 27 Nov 2009) | 3 lines
+Changed paths:
+   M /trunk/samtools/bam_import.c
+   M /trunk/samtools/bamtk.c
+   M /trunk/samtools/misc/wgsim_eval.pl
+   M /trunk/samtools/sam.c
+
+ * samtools-0.1.7-1 (r515)
+ * report an error when .fai contains duplicated names, instead of segfault
+
+------------------------------------------------------------------------
+r514 | jmarshall | 2009-11-24 09:45:35 -0500 (Tue, 24 Nov 2009) | 2 lines
+Changed paths:
+   M /trunk/samtools/bam.c
+
+Format 'c'-encoded auxiliary fields correctly, as *signed* integers.
+
+------------------------------------------------------------------------
+r513 | lh3lh3 | 2009-11-16 10:13:07 -0500 (Mon, 16 Nov 2009) | 2 lines
+Changed paths:
+   M /trunk/samtools/Makefile.mingw
+
+Update Makefile.mingw for the same reason
+
+------------------------------------------------------------------------
+r512 | lh3lh3 | 2009-11-16 10:00:08 -0500 (Mon, 16 Nov 2009) | 2 lines
+Changed paths:
+   M /trunk/samtools/Makefile
+
+Fixed a bug in compiling razip
+
+------------------------------------------------------------------------
+r510 | lh3lh3 | 2009-11-10 10:55:41 -0500 (Tue, 10 Nov 2009) | 2 lines
+Changed paths:
+   M /trunk/samtools/ChangeLog
+   M /trunk/samtools/NEWS
+   M /trunk/samtools/bamtk.c
+   M /trunk/samtools/samtools.1
+
+Release samtools-0.1.7 (r510)
+
 ------------------------------------------------------------------------
 r509 | lh3lh3 | 2009-11-06 09:17:09 -0500 (Fri, 06 Nov 2009) | 3 lines
 Changed paths:

diff --git a/bam_plcmd.c b/bam_plcmd.c
index cbb55cc3a5a7d1643b729c63bd1c36ad206e6387..ccc5eb95a8c397b76729f0d2ff3ce3ea4da77fdc 100644 (file)
--- a/bam_plcmd.c
+++ b/bam_plcmd.c
@@ -174,7 +174,7 @@ static int pileup_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *p
        // update d->ref if necessary
        if (d->fai && (int)tid != d->tid) {
                free(d->ref);
-               d->ref = fai_fetch(d->fai, d->h->target_name[tid], &d->len);
+               d->ref = faidx_fetch_seq(d->fai, d->h->target_name[tid], 0, 0x7fffffff, &d->len);
                d->tid = tid;
        }
        rb = (d->ref && (int)pos < d->len)? d->ref[pos] : 'N';

diff --git a/bamtk.c b/bamtk.c
index 94838a4acc578a97194433091a4046e230cac216..902bd800454d1a338aa605f7e89ea916964eea78 100644 (file)
--- a/bamtk.c
+++ b/bamtk.c
@@ -9,7 +9,7 @@
 #endif
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.1.7-5 (r528)"
+#define PACKAGE_VERSION "0.1.7-6 (r530)"
 #endif
 
 int bam_taf2baf(int argc, char *argv[]);

diff --git a/misc/samtools.pl b/misc/samtools.pl
index 1d9cf59b2ebd84a6ccc5c3bbc8eb48718c555d90..e6dd8e8eac12e659ea0ec12e5bb4ca0572252ed1 100755 (executable)
--- a/misc/samtools.pl
+++ b/misc/samtools.pl
@@ -328,10 +328,11 @@ sub sra2hdr {
 
 sub unique {
   my %opts = (f=>250.0, q=>5, r=>2, a=>1, b=>3);
-  getopts('Qf:q:r:a:b:', \%opts);
+  getopts('Qf:q:r:a:b:m', \%opts);
   die("Usage: samtools.pl unique [-f $opts{f}] <in.sam>\n") if (@ARGV == 0 && -t STDIN);
   my $last = '';
   my $recal_Q = !defined($opts{Q});
+  my $multi_only = defined($opts{m});
   my @a;
   while (<>) {
        my $score = -1;
@@ -349,16 +350,16 @@ sub unique {
        }
        $score = 1 if ($score < 1);
        if ($t[0] ne $last) {
-         &unique_aux(\@a, $opts{f}, $recal_Q) if (@a);
+         &unique_aux(\@a, $opts{f}, $recal_Q, $multi_only) if (@a);
          $last = $t[0];
        }
        push(@a, [$score, \@t]);
   }
-  &unique_aux(\@a, $opts{f}, $recal_Q) if (@a);
+  &unique_aux(\@a, $opts{f}, $recal_Q, $multi_only) if (@a);
 }
 
 sub unique_aux {
-  my ($a, $fac, $is_recal) = @_;
+  my ($a, $fac, $is_recal, $multi_only) = @_;
   my ($max, $max2, $max_i) = (0, 0, -1);
   for (my $i = 0; $i < @$a; ++$i) {
        if ($a->[$i][0] > $max) {
@@ -368,9 +369,11 @@ sub unique_aux {
        }
   }
   if ($is_recal) {
-       my $q = int($fac * ($max - $max2) / $max + .499);
-       $q = 250 if ($q > 250);
-       $a->[$max_i][1][4] = $q < 250? $q : 250;
+       if (!$multi_only || @$a > 1) {
+         my $q = int($fac * ($max - $max2) / $max + .499);
+         $q = 250 if ($q > 250);
+         $a->[$max_i][1][4] = $q < 250? $q : 250;
+       }
   }
   print join("\t", @{$a->[$max_i][1]});
   @$a = ();

diff --git a/misc/wgsim.c b/misc/wgsim.c
index 1522eee484903740390edac608e688f627b77c2e..7b5f095d910b06f3242419066ac8879b7cdb7454 100644 (file)
--- a/misc/wgsim.c
+++ b/misc/wgsim.c
@@ -238,7 +238,7 @@ void maq_print_mutref(const char *name, const seq_t *seq, mutseq_t *hap1, mutseq
                c[0] = nst_nt4_table[(int)seq->s[i]];
                c[1] = hap1->s[i]; c[2] = hap2->s[i];
                if (c[0] >= 4) continue;
-               if ((c[1] & mutmsk) != NOCHANGE || (c[1] & mutmsk) != NOCHANGE) {
+               if ((c[1] & mutmsk) != NOCHANGE || (c[2] & mutmsk) != NOCHANGE) {
                        printf("%s\t%d\t", name, i+1);
                        if (c[1] == c[2]) { // hom
                                if ((c[1]&mutmsk) == SUBSTITUTE) { // substitution
@@ -304,7 +304,7 @@ void wgsim_core(FILE *fpout1, FILE *fpout2, FILE *fp_fa, int is_hap, uint64_t N,
        tmp_seq[1] = (uint8_t*)calloc(l+2, 1);
        size[0] = size_l; size[1] = size_r;
 
-       Q = (int)(-10.0 * log(ERR_RATE) / log(10.0) + 0.499) + 33;
+       Q = (ERR_RATE == 0.0)? 'I' : (int)(-10.0 * log(ERR_RATE) / log(10.0) + 0.499) + 33;
 
        tot_len = n_ref = 0;
        while ((l = seq_read_fasta(fp_fa, &seq, name, 0)) >= 0) {