* 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)

diff --git a/bam_plcmd.c b/bam_plcmd.c
index ba787a98bd78726503f48af1fd16582d89a357dd..1191b582aa7b4faf6c9db06c77f02b3d1c76b1f6 100644 (file)
--- a/bam_plcmd.c
+++ b/bam_plcmd.c
@@ -18,6 +18,7 @@ KHASH_MAP_INIT_INT64(64, indel_list_t)
 #define BAM_PLF_GLF        0x08
 #define BAM_PLF_VAR_ONLY   0x10
 #define BAM_PLF_2ND        0x20
+#define BAM_PLF_RANBASE    0x40
 
 typedef struct {
        bam_header_t *h;
@@ -182,8 +183,15 @@ static int pileup_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *p
                if (i == n) return 0;
        }
        // call the consensus and indel
-       if (d->format & BAM_PLF_CNS) // call consensus
-               cns = bam_maqcns_call(n, pu, d->c);
+       if (d->format & BAM_PLF_CNS) { // call consensus
+               if (d->format & BAM_PLF_RANBASE) {
+                       const bam_pileup1_t *p = pu + (int)(drand48() * n);
+                       int q = bam1_qual(p->b)[p->qpos];
+                       int mapQ = p->b->core.qual < d->c->cap_mapQ? p->b->core.qual : d->c->cap_mapQ;
+                       uint32_t b = bam1_seqi(bam1_seq(p->b), p->qpos);
+                       cns = b<<28 | 0xf<<24 | mapQ<<16 | q<<8;
+               } else cns = bam_maqcns_call(n, pu, d->c);
+       }
        if ((d->format & (BAM_PLF_CNS|BAM_PLF_INDEL_ONLY)) && d->ref && pos < d->len) { // call indels
                if (proposed_indels) // the first element gives the size of the array
                        r = bam_maqindel(n, pos, d->ido, pu, d->ref, proposed_indels[0], proposed_indels+1);
@@ -301,7 +309,7 @@ int bam_pileup(int argc, char *argv[])
        d->tid = -1; d->mask = BAM_DEF_MASK;
        d->c = bam_maqcns_init();
        d->ido = bam_maqindel_opt_init();
-       while ((c = getopt(argc, argv, "st:f:cT:N:r:l:im:gI:G:vM:S2a")) >= 0) {
+       while ((c = getopt(argc, argv, "st:f:cT:N:r:l:im:gI:G:vM:S2aR")) >= 0) {
                switch (c) {
                case 'a': d->c->is_soap = 1; break;
                case 's': d->format |= BAM_PLF_SIMPLE; break;
@@ -318,6 +326,7 @@ int bam_pileup(int argc, char *argv[])
                case 'm': d->mask = strtol(optarg, 0, 0); break;
                case 'g': d->format |= BAM_PLF_GLF; break;
                case '2': d->format |= BAM_PLF_2ND; break;
+               case 'R': d->format |= BAM_PLF_RANBASE; break;
                case 'I': d->ido->q_indel = atoi(optarg); break;
                case 'G': d->ido->r_indel = atof(optarg); break;
                case 'S': is_SAM = 1; break;
@@ -339,6 +348,7 @@ int bam_pileup(int argc, char *argv[])
                fprintf(stderr, "        -l FILE   list of sites at which pileup is output\n");
                fprintf(stderr, "        -f FILE   reference sequence in the FASTA format\n\n");
                fprintf(stderr, "        -c        output the maq consensus sequence\n");
+               fprintf(stderr, "        -R        randomly choose a random base as the consensus (force -c)\n");
                fprintf(stderr, "        -v        print variants only (for -c)\n");
                fprintf(stderr, "        -g        output in the GLFv3 format (suppressing -c/-i/-s)\n");
                fprintf(stderr, "        -T FLOAT  theta in maq consensus calling model (for -c/-g) [%f]\n", d->c->theta);
@@ -350,6 +360,7 @@ int bam_pileup(int argc, char *argv[])
                free(fn_list); free(fn_fa); free(d);
                return 1;
        }
+       if (d->format & BAM_PLF_RANBASE) d->format |= BAM_PLF_CNS;
        if (fn_fa) d->fai = fai_load(fn_fa);
        if (d->format & (BAM_PLF_CNS|BAM_PLF_GLF)) bam_maqcns_prepare(d->c); // consensus calling
        if (d->format & BAM_PLF_GLF) { // for glf output

diff --git a/bamtk.c b/bamtk.c
index 2c7e4f0e773c1190c60df8e93be8b70e41f4dae2..aaa4a3e004a56cb3aae5a5b5e528e44f2546d613 100644 (file)
--- a/bamtk.c
+++ b/bamtk.c
@@ -9,7 +9,7 @@
 #endif
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.1.7-1 (r515)"
+#define PACKAGE_VERSION "0.1.7-2 (r520)"
 #endif
 
 int bam_taf2baf(int argc, char *argv[]);

diff --git a/misc/samtools.pl b/misc/samtools.pl
index 320e8aaeda8ff2fab7fd91ab5e02073d5f3ba8fe..1d9cf59b2ebd84a6ccc5c3bbc8eb48718c555d90 100755 (executable)
--- a/misc/samtools.pl
+++ b/misc/samtools.pl
@@ -11,7 +11,7 @@ my $version = '0.3.3';
 
 my $command = shift(@ARGV);
 my %func = (showALEN=>\&showALEN, pileup2fq=>\&pileup2fq, varFilter=>\&varFilter,
-                       unique=>\&unique, uniqcmp=>\&uniqcmp, sra2hdr=>\&sra2hdr);
+                       unique=>\&unique, uniqcmp=>\&uniqcmp, sra2hdr=>\&sra2hdr, sam2fq=>\&sam2fq);
 
 die("Unknown command \"$command\".\n") if (!defined($func{$command}));
 &{$func{$command}};
@@ -226,6 +226,49 @@ sub p2q_print_str {
   }
 }
 
+#
+# sam2fq
+#
+
+sub sam2fq {
+  my %opts = (n=>20, p=>'');
+  getopts('n:p:', \%opts);
+  die("Usage: samtools.pl sam2fq [-n 20] [-p <prefix>] <inp.sam>\n") if (@ARGV == 0 && -t STDIN);
+  if ($opts{p} && $opts{n} > 1) {
+       my $pre = $opts{p};
+       my @fh;
+       for (0 .. $opts{n}-1) {
+         open($fh[$_], sprintf("| gzip > $pre.%.3d.fq.gz", $_)) || die;
+       }
+       my $i = 0;
+       while (<>) {
+         next if (/^@/);
+         chomp;
+         my @t = split("\t");
+         next if ($t[9] eq '*');
+         my ($name, $seq, $qual);
+         if ($t[1] & 16) { # reverse strand
+               $seq = reverse($t[9]);
+               $qual = reverse($t[10]);
+               $seq =~ tr/ACGTacgt/TGCAtgca/;
+         } else {
+               ($seq, $qual) = @t[9,10];
+         }
+         $name = $t[0];
+         $name .= "/1" if ($t[1] & 0x40);
+         $name .= "/2" if ($t[1] & 0x80);
+         print {$fh[$i]} "\@$name\n$seq\n";
+         if ($qual ne '*') {
+               print {$fh[$i]} "+\n$qual\n";
+         }
+         $i = 0 if (++$i == $opts{n});
+       }
+       close($fh[$_]) for (0 .. $opts{n}-1);
+  } else {
+       die("To be implemented.\n");
+  }
+}
+
 #
 # sra2hdr
 #