* samtools-0.1.2-12

 * optionally print SAM header

diff --git a/ChangeLog b/ChangeLog
index 887cc605a03818d3767347536069ce0dd0f27151..8f0ba4d865fc88f5ba0444904a64eefdadf0d51b 100644 (file)
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,79 @@
+------------------------------------------------------------------------
+r153 | lh3lh3 | 2009-03-02 10:45:28 +0000 (Mon, 02 Mar 2009) | 3 lines
+Changed paths:
+   M /trunk/samtools/bamtk.c
+   M /trunk/samtools/glf.c
+
+ * samtools-0.1.2-11
+ * use "GLF\3" as the magic for GLFv3 files
+
+------------------------------------------------------------------------
+r152 | lh3lh3 | 2009-03-02 10:39:09 +0000 (Mon, 02 Mar 2009) | 5 lines
+Changed paths:
+   M /trunk/samtools/Makefile
+   M /trunk/samtools/bam_import.c
+   M /trunk/samtools/bam_index.c
+   M /trunk/samtools/bam_plcmd.c
+   M /trunk/samtools/bamtk.c
+   M /trunk/samtools/glf.c
+   M /trunk/samtools/glf.h
+
+ * samtools-0.1.2-10
+ * fixed a bug in import: core.bin is undefined for unmapped reads
+ * this bug can be alleviated (not completely solved) in bam_index.c
+ * update to GLFv3: pos is changed to offset for better compression
+
+------------------------------------------------------------------------
+r151 | lh3lh3 | 2009-03-01 15:18:43 +0000 (Sun, 01 Mar 2009) | 3 lines
+Changed paths:
+   M /trunk/samtools/misc/wgsim.c
+
+ * wgsim-0.2.3
+ * fixed a bug in simulating indels
+
+------------------------------------------------------------------------
+r145 | lh3lh3 | 2009-02-26 19:43:57 +0000 (Thu, 26 Feb 2009) | 4 lines
+Changed paths:
+   M /trunk/samtools/misc/wgsim.c
+
+ * wgsim-0.2.2
+ * allow to print mismatch information as fastq comment. MAQ does
+   not like long read names.
+
+------------------------------------------------------------------------
+r141 | lh3lh3 | 2009-02-26 14:53:03 +0000 (Thu, 26 Feb 2009) | 6 lines
+Changed paths:
+   M /trunk/samtools/ChangeLog
+   M /trunk/samtools/misc/wgsim.c
+   M /trunk/samtools/misc/wgsim_eval.pl
+
+ * wgsim-0.2.1
+ * fixed a bug about color read coordinates
+ * fixed a bug in read names
+ * wgsim_eval.pl-0.1.3
+ * make the script work with color reads
+
+------------------------------------------------------------------------
+r140 | lh3lh3 | 2009-02-26 14:02:57 +0000 (Thu, 26 Feb 2009) | 2 lines
+Changed paths:
+   M /trunk/samtools/misc/Makefile
+   M /trunk/samtools/misc/wgsim.c
+
+ * wgsim: added a note
+
+------------------------------------------------------------------------
+r139 | lh3lh3 | 2009-02-26 11:39:08 +0000 (Thu, 26 Feb 2009) | 7 lines
+Changed paths:
+   M /trunk/samtools/misc/wgsim.c
+   M /trunk/samtools/misc/wgsim_eval.pl
+
+ * wgsim-0.2.0
+ * considerable code clean up
+ * print number of substitutions/indels/errors on each read
+ * potentially support SOLiD simulation, though not tested at the moment
+ * wgsim_eval.pl-0.1.2
+ * change in accordant with wgsim
+
 ------------------------------------------------------------------------
 r129 | lh3lh3 | 2009-02-18 22:23:27 +0000 (Wed, 18 Feb 2009) | 3 lines
 Changed paths:

diff --git a/bamtk.c b/bamtk.c
index dc1805cb73ad8ccc049d66abed05ce05de6bcb26..b55415ed6a9286b7e50366fdb8f8815399332a71 100644 (file)
--- a/bamtk.c
+++ b/bamtk.c
@@ -3,7 +3,7 @@
 #include "bam.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.1.2-11"
+#define PACKAGE_VERSION "0.1.2-12"
 #endif
 
 int bam_taf2baf(int argc, char *argv[]);
@@ -35,15 +35,17 @@ int bam_view(int argc, char *argv[])
        bamFile fp, fpout = 0;
        bam_header_t *header;
        bam1_t *b;
-       int ret, c, is_bam = 0;
-       while ((c = getopt(argc, argv, "b")) >= 0) {
+       int ret, c, is_bam = 0, is_header = 0, is_headeronly = 0;
+       while ((c = getopt(argc, argv, "bhH")) >= 0) {
                switch (c) {
                case 'b': is_bam = 1; break;
+               case 'h': is_header = 1; break;
+               case 'H': is_headeronly = 1; break;
                default: fprintf(stderr, "Unrecognized option: -%c\n", c); return 1;
                }
        }
        if (argc == optind) {
-               fprintf(stderr, "Usage: samtools view [-b] <in.bam> [<region> [...]]\n");
+               fprintf(stderr, "Usage: samtools view [-bhH] <in.bam> [<region> [...]]\n");
                return 1;
        }
        fp = strcmp(argv[optind], "-")? bam_open(argv[optind], "r") : bam_dopen(fileno(stdin), "r");
@@ -53,6 +55,16 @@ int bam_view(int argc, char *argv[])
                assert(fpout = bam_dopen(fileno(stdout), "w"));
                bam_header_write(fpout, header);
        }
+       if (is_header || is_headeronly) {
+               int i;
+               for (i = 0; i < header->n_targets; ++i)
+                       printf("@SQ\tSN:%s\tLN:%d\n", header->target_name[i], header->target_len[i]);
+               if (is_headeronly) {
+                       bam_header_destroy(header);
+                       bam_close(fp);
+                       return 0;
+               }
+       }
        if (optind + 1 == argc) {
                b = (bam1_t*)calloc(1, sizeof(bam1_t));
                while ((ret = bam_read1(fp, b)) >= 0) bam_view1(header, b);