Incorporate patches by Marcel Martin for read counting.

diff --git a/ChangeLog b/ChangeLog
index 12908c968c54e264baff1562e7cea623fb145dcb..d43635f959b10163635da118160e55b0ed886f0e 100644 (file)
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,162 @@
+------------------------------------------------------------------------
+r797 | lh3lh3 | 2010-11-08 13:39:52 -0500 (Mon, 08 Nov 2010) | 3 lines
+Changed paths:
+   M /trunk/samtools/bam2bcf.c
+   M /trunk/samtools/bam2bcf.h
+   M /trunk/samtools/bam2bcf_indel.c
+   M /trunk/samtools/bam_plcmd.c
+   M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.9-2 (r797)
+ * mpileup: indel calling seems to be working
+
+------------------------------------------------------------------------
+r796 | lh3lh3 | 2010-11-08 10:54:46 -0500 (Mon, 08 Nov 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/bam2bcf.c
+   M /trunk/samtools/bam2bcf.h
+   M /trunk/samtools/bam2bcf_indel.c
+   M /trunk/samtools/bam_plcmd.c
+   M /trunk/samtools/kaln.c
+
+indel calling is apparently working, but more information needs to be collected
+
+------------------------------------------------------------------------
+r795 | lh3lh3 | 2010-11-08 00:39:18 -0500 (Mon, 08 Nov 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/bam2bcf.c
+   M /trunk/samtools/bam2bcf_indel.c
+
+fixed a few bugs in the indel caller. Probably there are more.
+
+------------------------------------------------------------------------
+r794 | lh3lh3 | 2010-11-07 22:23:16 -0500 (Sun, 07 Nov 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/Makefile
+   M /trunk/samtools/bam.h
+   M /trunk/samtools/bam2bcf.c
+   M /trunk/samtools/bam2bcf.h
+   A /trunk/samtools/bam2bcf_indel.c
+   M /trunk/samtools/bam_plcmd.c
+   M /trunk/samtools/kaln.c
+   M /trunk/samtools/kaln.h
+
+prepare for the indel caller. It is not ready yet.
+
+------------------------------------------------------------------------
+r793 | lh3lh3 | 2010-11-05 11:28:23 -0400 (Fri, 05 Nov 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/bam2bcf.c
+   M /trunk/samtools/bam2bcf.h
+   M /trunk/samtools/bam_plcmd.c
+
+Revert to r790. The recent changes are not good...
+
+------------------------------------------------------------------------
+r792 | lh3lh3 | 2010-11-05 00:19:14 -0400 (Fri, 05 Nov 2010) | 6 lines
+Changed paths:
+   M /trunk/samtools/bam2bcf.c
+   M /trunk/samtools/bam2bcf.h
+   M /trunk/samtools/bam_plcmd.c
+
+ * this revision is UNSTABLE
+
+ * indel caller seems working, but it is very insensitive and has
+   several things I do not quite understand.
+
+
+------------------------------------------------------------------------
+r791 | lh3lh3 | 2010-11-04 22:58:43 -0400 (Thu, 04 Nov 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/bam2bcf.c
+   M /trunk/samtools/bam2bcf.h
+   M /trunk/samtools/bam_plcmd.c
+
+for backup. no effective changes
+
+------------------------------------------------------------------------
+r790 | lh3lh3 | 2010-11-03 15:51:24 -0400 (Wed, 03 Nov 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/bcftools/vcfutils.pl
+   M /trunk/samtools/kprobaln.c
+
+fixed a minor problem in the example coming with kprobaln.c
+
+------------------------------------------------------------------------
+r789 | lh3lh3 | 2010-11-02 15:41:27 -0400 (Tue, 02 Nov 2010) | 4 lines
+Changed paths:
+   M /trunk/samtools/Makefile
+   M /trunk/samtools/bam_md.c
+   M /trunk/samtools/kaln.c
+   M /trunk/samtools/kaln.h
+   A /trunk/samtools/kprobaln.c
+   A /trunk/samtools/kprobaln.h
+
+Separate kaln and kprobaln as I am preparing further changes. At
+present, the results should be identical to the previous.
+
+
+------------------------------------------------------------------------
+r788 | petulda | 2010-11-02 12:19:04 -0400 (Tue, 02 Nov 2010) | 1 line
+Changed paths:
+   M /trunk/samtools/bam_plcmd.c
+
+Added -b option: read file names from a file
+------------------------------------------------------------------------
+r787 | lh3lh3 | 2010-10-29 23:17:22 -0400 (Fri, 29 Oct 2010) | 7 lines
+Changed paths:
+   M /trunk/samtools/bam.h
+   M /trunk/samtools/bam_pileup.c
+   M /trunk/samtools/bam_plcmd.c
+   M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.9-2 (r787)
+
+ * Allow to set a maximum per-sample depth to reduce memory. However,
+   BAQ computation is still applied to every read. The speed is not
+   improved.
+
+
+------------------------------------------------------------------------
+r786 | lh3lh3 | 2010-10-29 12:10:40 -0400 (Fri, 29 Oct 2010) | 3 lines
+Changed paths:
+   M /trunk/samtools/bam2bcf.c
+   M /trunk/samtools/bam2bcf.h
+   M /trunk/samtools/bam_plcmd.c
+   M /trunk/samtools/bamtk.c
+   M /trunk/samtools/bcftools/bcf.c
+   M /trunk/samtools/bcftools/vcf.c
+
+ * samtools-0.1.9-1 (r786)
+ * samtools: optionally perform exact test for each sample
+
+------------------------------------------------------------------------
+r785 | lh3lh3 | 2010-10-29 09:42:25 -0400 (Fri, 29 Oct 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/bam2bcf.c
+   M /trunk/samtools/bam2bcf.h
+   M /trunk/samtools/bam_plcmd.c
+   M /trunk/samtools/bcftools/bcf.c
+
+Optionally output "DP", the individual read depth
+
+------------------------------------------------------------------------
+r784 | lh3lh3 | 2010-10-27 23:10:27 -0400 (Wed, 27 Oct 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/samtools.1
+
+acknowledge Petr and John who have greatly contributed to the project.
+
+------------------------------------------------------------------------
+r783 | lh3lh3 | 2010-10-27 22:47:47 -0400 (Wed, 27 Oct 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/ChangeLog
+   M /trunk/samtools/NEWS
+   M /trunk/samtools/bamtk.c
+   M /trunk/samtools/samtools.1
+
+Release samtools-0.1.9 (r783)
+
 ------------------------------------------------------------------------
 r782 | lh3lh3 | 2010-10-27 19:58:54 -0400 (Wed, 27 Oct 2010) | 2 lines
 Changed paths:

diff --git a/sam_view.c b/sam_view.c
index d0fdad25445508e90052970a90de92e1f0f61ae5..eb69449f9e44d643ef43f31638fd8534c454c940 100644 (file)
--- a/sam_view.c
+++ b/sam_view.c
@@ -9,6 +9,13 @@
 #include "khash.h"
 KHASH_SET_INIT_STR(rg)
 
+// When counting records instead of printing them,
+// data passed to the bam_fetch callback is encapsulated in this struct.
+typedef struct {
+       bam_header_t *header;
+       int *count;
+} count_func_data_t;
+
 typedef khash_t(rg) *rghash_t;
 
 rghash_t g_rghash = 0;
@@ -54,7 +61,7 @@ static inline int __g_skip_aln(const bam_header_t *h, const bam1_t *b)
        return 0;
 }
 
-// callback function for bam_fetch()
+// callback function for bam_fetch() that prints nonskipped records
 static int view_func(const bam1_t *b, void *data)
 {
        if (!__g_skip_aln(((samfile_t*)data)->header, b))
@@ -62,19 +69,30 @@ static int view_func(const bam1_t *b, void *data)
        return 0;
 }
 
+// callback function for bam_fetch() that counts nonskipped records
+static int count_func(const bam1_t *b, void *data)
+{
+       if (!__g_skip_aln(((count_func_data_t*)data)->header, b)) {
+               (*((count_func_data_t*)data)->count)++;
+       }
+       return 0;
+}
+
 static int usage(int is_long_help);
 
 int main_samview(int argc, char *argv[])
 {
-       int c, is_header = 0, is_header_only = 0, is_bamin = 1, ret = 0, is_uncompressed = 0, is_bamout = 0, slx2sngr = 0;
+       int c, is_header = 0, is_header_only = 0, is_bamin = 1, ret = 0, is_uncompressed = 0, is_bamout = 0, slx2sngr = 0, is_count = 0;
        int of_type = BAM_OFDEC, is_long_help = 0;
+       int count = 0;
        samfile_t *in = 0, *out = 0;
        char in_mode[5], out_mode[5], *fn_out = 0, *fn_list = 0, *fn_ref = 0, *fn_rg = 0;
 
        /* parse command-line options */
        strcpy(in_mode, "r"); strcpy(out_mode, "w");
-       while ((c = getopt(argc, argv, "Sbt:hHo:q:f:F:ul:r:xX?T:CR:")) >= 0) {
+       while ((c = getopt(argc, argv, "Sbct:hHo:q:f:F:ul:r:xX?T:CR:")) >= 0) {
                switch (c) {
+               case 'c': is_count = 1; break;
                case 'C': slx2sngr = 1; break;
                case 'S': is_bamin = 0; break;
                case 'b': is_bamout = 1; break;
@@ -133,7 +151,7 @@ int main_samview(int argc, char *argv[])
                ret = 1;
                goto view_end;
        }
-       if ((out = samopen(fn_out? fn_out : "-", out_mode, in->header)) == 0) {
+       if (!is_count && (out = samopen(fn_out? fn_out : "-", out_mode, in->header)) == 0) {
                fprintf(stderr, "[main_samview] fail to open \"%s\" for writing.\n", fn_out? fn_out : "standard output");
                ret = 1;
                goto view_end;
@@ -146,7 +164,8 @@ int main_samview(int argc, char *argv[])
                while ((r = samread(in, b)) >= 0) { // read one alignment from `in'
                        if (!__g_skip_aln(in->header, b)) {
                                if (slx2sngr) sol2sanger(b);
-                               samwrite(out, b); // write the alignment to `out'
+                               if (!is_count) samwrite(out, b); // write the alignment to `out'
+                               count++;
                        }
                }
                if (r < -1) {
@@ -164,14 +183,19 @@ int main_samview(int argc, char *argv[])
                        goto view_end;
                }
                for (i = optind + 1; i < argc; ++i) {
-                       int tid, beg, end;
+                       int tid, beg, end, result;
                        bam_parse_region(in->header, argv[i], &tid, &beg, &end); // parse a region in the format like `chr2:100-200'
                        if (tid < 0) { // reference name is not found
                                fprintf(stderr, "[main_samview] region \"%s\" specifies an unknown reference name. Continue anyway.\n", argv[i]);
                                continue;
                        }
                        // fetch alignments
-                       if (bam_fetch(in->x.bam, idx, tid, beg, end, out, view_func) < 0) {
+                       if (is_count) {
+                               count_func_data_t count_data = { in->header, &count };
+                               result = bam_fetch(in->x.bam, idx, tid, beg, end, &count_data, count_func);
+                       } else
+                               result = bam_fetch(in->x.bam, idx, tid, beg, end, out, view_func);
+                       if (result < 0) {
                                fprintf(stderr, "[main_samview] retrieval of region \"%s\" failed due to truncated file or corrupt BAM index file\n", argv[i]);
                                ret = 1;
                                break;
@@ -181,6 +205,9 @@ int main_samview(int argc, char *argv[])
        }
 
 view_end:
+       if (is_count && ret == 0) {
+               printf("%d\n", count);
+       }
        // close files, free and return
        free(fn_list); free(fn_ref); free(fn_out); free(g_library); free(g_rg); free(fn_rg);
        if (g_rghash) {
@@ -190,7 +217,8 @@ view_end:
                kh_destroy(rg, g_rghash);
        }
        samclose(in);
-       samclose(out);
+       if (!is_count)
+               samclose(out);
        return ret;
 }
 
@@ -205,6 +233,7 @@ static int usage(int is_long_help)
        fprintf(stderr, "         -u       uncompressed BAM output (force -b)\n");
        fprintf(stderr, "         -x       output FLAG in HEX (samtools-C specific)\n");
        fprintf(stderr, "         -X       output FLAG in string (samtools-C specific)\n");
+       fprintf(stderr, "         -c       print only the count of matching records\n");
        fprintf(stderr, "         -t FILE  list of reference names and lengths (force -S) [null]\n");
        fprintf(stderr, "         -T FILE  reference sequence file (force -S) [null]\n");
        fprintf(stderr, "         -o FILE  output file name [stdout]\n");

diff --git a/samtools.1 b/samtools.1
index 09cb14765df6cde33503e9eebd4a84577edd4f6c..7de9857245ca6debe24abaa4d6786f942886035e 100644 (file)
--- a/samtools.1
+++ b/samtools.1
@@ -47,7 +47,7 @@ entire alignment file unless it is asked to do so.
 
 .TP 10
 .B view
-samtools view [-bhuHS] [-t in.refList] [-o output] [-f reqFlag] [-F
+samtools view [-bchuHS] [-t in.refList] [-o output] [-f reqFlag] [-F
 skipFlag] [-q minMapQ] [-l library] [-r readGroup] [-R rgFile] <in.bam>|<in.sam> [region1 [...]]
 
 Extract/print all or sub alignments in SAM or BAM format. If no region
@@ -100,6 +100,15 @@ Input is in SAM. If @SQ header lines are absent, the
 .B `-t'
 option is required.
 .TP
+.B -c
+Instead of printing the alignments, only count them and print the
+total number. All filter options, such as
+.B `-f',
+.B `-F'
+and
+.B `-q'
+, are taken into account.
+.TP
 .BI -t " FILE"
 This file is TAB-delimited. Each line must contain the reference name
 and the length of the reference, one line for each distinct reference;