* samtools-0.1.5-17 (r422)

 * fixed a but in knetfile.c when seek type is not SEEK_SET
 * write an empty BGZF block to every BGZF file
 * check BGZF EOF marker in bam_header_read()
 * update ChangeLog

diff --git a/ChangeLog b/ChangeLog
index 3bf82a59c9f2f5d0249c9d457022a93f3758d751..d6a6f3340e1e6d46d96d0f7672d5cc4e5a7659d3 100644 (file)
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,287 @@
+------------------------------------------------------------------------
+r421 | lh3lh3 | 2009-07-30 10:03:39 +0100 (Thu, 30 Jul 2009) | 3 lines
+Changed paths:
+   M /trunk/samtools/bam_import.c
+   M /trunk/samtools/bam_plcmd.c
+   M /trunk/samtools/bamtk.c
+   M /trunk/samtools/misc/samtools.pl
+   M /trunk/samtools/sam.c
+   M /trunk/samtools/sam.h
+   M /trunk/samtools/sam_view.c
+
+ * samtools-0.1.5-16 (r421)
+ * in view and pileup, load header from FASTA index if the input is SAM.
+
+------------------------------------------------------------------------
+r420 | lh3lh3 | 2009-07-29 09:18:55 +0100 (Wed, 29 Jul 2009) | 2 lines
+Changed paths:
+   M /trunk/samtools/misc/maq2sam.c
+
+do not set "read 1" if reads are not mapped in the PE mode of maq
+
+------------------------------------------------------------------------
+r419 | lh3lh3 | 2009-07-28 09:52:33 +0100 (Tue, 28 Jul 2009) | 5 lines
+Changed paths:
+   M /trunk/samtools/bam_import.c
+   M /trunk/samtools/bamtk.c
+   M /trunk/samtools/misc/samtools.pl
+   M /trunk/samtools/misc/wgsim_eval.pl
+
+ * samtools-0.1.5-15 (r419)
+ * in sam_open(), return NULL when the file cannot be opened.
+ * make wgsim_eval.pl more robust to imperfect SAM
+ * add "unique" command to samtools.pl
+
+------------------------------------------------------------------------
+r418 | lh3lh3 | 2009-07-24 14:04:19 +0100 (Fri, 24 Jul 2009) | 2 lines
+Changed paths:
+   M /trunk/samtools/misc/wgsim_eval.pl
+
+skip @header lines in SAM
+
+------------------------------------------------------------------------
+r417 | lh3lh3 | 2009-07-24 12:42:38 +0100 (Fri, 24 Jul 2009) | 3 lines
+Changed paths:
+   M /trunk/samtools/bamtk.c
+   M /trunk/samtools/sam_view.c
+
+ * samtools-0.1.5-14 (r417)
+ * more help in "samtools view" due to the recent changes.
+
+------------------------------------------------------------------------
+r416 | lh3lh3 | 2009-07-24 12:34:30 +0100 (Fri, 24 Jul 2009) | 3 lines
+Changed paths:
+   M /trunk/samtools/bam.c
+   M /trunk/samtools/bam.h
+   M /trunk/samtools/bam_import.c
+   M /trunk/samtools/bamtk.c
+   M /trunk/samtools/sam.c
+   M /trunk/samtools/sam.h
+   M /trunk/samtools/sam_view.c
+
+ * samtools-0.1.5-17 (r416)
+ * support import/export SAM with string tags
+
+------------------------------------------------------------------------
+r415 | lh3lh3 | 2009-07-24 11:39:26 +0100 (Fri, 24 Jul 2009) | 3 lines
+Changed paths:
+   M /trunk/samtools/bam.c
+   M /trunk/samtools/bam.h
+   M /trunk/samtools/bam_import.c
+   M /trunk/samtools/bamtk.c
+   M /trunk/samtools/sam.c
+   M /trunk/samtools/sam.h
+   M /trunk/samtools/sam_view.c
+
+ * samtools-0.1.5-12 (r415)
+ * FLAG now can be in HEX
+
+------------------------------------------------------------------------
+r414 | lh3lh3 | 2009-07-22 22:03:49 +0100 (Wed, 22 Jul 2009) | 2 lines
+Changed paths:
+   M /trunk/samtools/kstring.h
+
+fixed a compiling error (thank Ken for fixing it)
+
+------------------------------------------------------------------------
+r412 | lh3lh3 | 2009-07-21 22:19:40 +0100 (Tue, 21 Jul 2009) | 2 lines
+Changed paths:
+   M /trunk/samtools/kstring.c
+   M /trunk/samtools/kstring.h
+
+Implemented Boyer-Moore search in the kstring library.
+
+------------------------------------------------------------------------
+r409 | lh3lh3 | 2009-07-17 17:10:20 +0100 (Fri, 17 Jul 2009) | 2 lines
+Changed paths:
+   M /trunk/samtools/bam_index.c
+
+do not include knetfile.h when _USE_KNETFILE is not defined
+
+------------------------------------------------------------------------
+r408 | lh3lh3 | 2009-07-17 15:29:21 +0100 (Fri, 17 Jul 2009) | 5 lines
+Changed paths:
+   M /trunk/samtools/bam_md.c
+   M /trunk/samtools/bam_tview.c
+   M /trunk/samtools/bamtk.c
+   M /trunk/samtools/bgzf.c
+
+ * samtools-0.1.5-11 (r408)
+ * force to overwirte existing MD if it is different from the one calculated
+   from fillmd.
+ * bgzf.c: improved the compatibility with Windows headers
+
+------------------------------------------------------------------------
+r407 | lh3lh3 | 2009-07-17 14:46:56 +0100 (Fri, 17 Jul 2009) | 5 lines
+Changed paths:
+   M /trunk/samtools/bam.h
+   M /trunk/samtools/bam_aux.c
+   M /trunk/samtools/bam_md.c
+   M /trunk/samtools/bamtk.c
+   M /trunk/samtools/sam.h
+
+ * samtools-0.1.5-10 (r407)
+ * implemented bam_aux_del() to remove a tag
+ * fillmd: generate the NM tag
+ * fillmd: cmd interface improvement
+
+------------------------------------------------------------------------
+r406 | lh3lh3 | 2009-07-16 23:30:40 +0100 (Thu, 16 Jul 2009) | 2 lines
+Changed paths:
+   M /trunk/samtools/Makefile
+
+Sorry. The old Makefile is for PDCurses...
+
+------------------------------------------------------------------------
+r405 | lh3lh3 | 2009-07-16 23:30:11 +0100 (Thu, 16 Jul 2009) | 3 lines
+Changed paths:
+   M /trunk/samtools/Makefile
+   M /trunk/samtools/bam_tview.c
+   M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.5-9 (r405)
+ * improved the compatibility with PDCurses a little bit
+
+------------------------------------------------------------------------
+r404 | lh3lh3 | 2009-07-16 23:23:52 +0100 (Thu, 16 Jul 2009) | 3 lines
+Changed paths:
+   M /trunk/samtools/Makefile
+   M /trunk/samtools/bam_tview.c
+   M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.5-8 (r404)
+ * compatible with PDCurses
+
+------------------------------------------------------------------------
+r403 | lh3lh3 | 2009-07-16 22:39:39 +0100 (Thu, 16 Jul 2009) | 3 lines
+Changed paths:
+   M /trunk/samtools/bamtk.c
+   M /trunk/samtools/kseq.h
+
+ * samtools-0.1.5-7 (r403)
+ * fixed a bug in kseq.h for binary files (text files are fine)
+
+------------------------------------------------------------------------
+r402 | lh3lh3 | 2009-07-16 11:49:53 +0100 (Thu, 16 Jul 2009) | 4 lines
+Changed paths:
+   M /trunk/samtools/bam_import.c
+   M /trunk/samtools/bam_index.c
+   M /trunk/samtools/bamtk.c
+   M /trunk/samtools/bgzf.c
+
+ * samtools-0.1.5-6 (r402)
+ * fixed compiling error when "-D_USE_NETFILE" is not applied
+ * improve portability to MinGW
+
+------------------------------------------------------------------------
+r398 | lh3lh3 | 2009-07-13 10:21:36 +0100 (Mon, 13 Jul 2009) | 3 lines
+Changed paths:
+   A /trunk/bam-lite/bam.h (from /trunk/samtools/bam.h:395)
+   A /trunk/bam-lite/bam_lite.c (from /trunk/samtools/bam_lite.c:395)
+   D /trunk/samtools/bam_lite.c
+
+ * move bam_lite.c to bam-lite
+ * copy bam.h to bam-lite
+
+------------------------------------------------------------------------
+r395 | lh3lh3 | 2009-07-13 10:12:57 +0100 (Mon, 13 Jul 2009) | 3 lines
+Changed paths:
+   M /trunk/samtools/bam.h
+   M /trunk/samtools/bam_lite.c
+   M /trunk/samtools/bam_lpileup.c
+   M /trunk/samtools/bam_pileup.c
+   M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.5-5 (r395)
+ * added bam_pileup_file() and removed bam_lpileup_file()
+
+------------------------------------------------------------------------
+r394 | lh3lh3 | 2009-07-13 00:35:10 +0100 (Mon, 13 Jul 2009) | 3 lines
+Changed paths:
+   M /trunk/samtools/bamtk.c
+   M /trunk/samtools/knetfile.c
+   M /trunk/samtools/knetfile.h
+
+ * samtools-0.1.5-4 (r394)
+ * http_proxy support in knetfile library (check http_proxy ENV)
+
+------------------------------------------------------------------------
+r393 | lh3lh3 | 2009-07-12 23:57:07 +0100 (Sun, 12 Jul 2009) | 5 lines
+Changed paths:
+   M /trunk/samtools/bam_index.c
+   M /trunk/samtools/bam_tview.c
+   M /trunk/samtools/bamtk.c
+   M /trunk/samtools/knetfile.c
+   M /trunk/samtools/knetfile.h
+
+ * samtools-0.1.5-3 (r393)
+ * knetfile now supports HTTP (no proxy at the moment)
+ * fixed a potential issue in knetfile on opening ordinary file, although I have
+   not seen the sideeffect so far.
+
+------------------------------------------------------------------------
+r392 | lh3lh3 | 2009-07-12 18:50:55 +0100 (Sun, 12 Jul 2009) | 2 lines
+Changed paths:
+   M /trunk/samtools/samtools.1
+
+Remove the warning in tview
+
+------------------------------------------------------------------------
+r391 | lh3lh3 | 2009-07-12 18:42:43 +0100 (Sun, 12 Jul 2009) | 3 lines
+Changed paths:
+   M /trunk/samtools/bam_tview.c
+   M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.5-2 (r391)
+ * do not show a blank screen when no reads mapped
+
+------------------------------------------------------------------------
+r390 | lh3lh3 | 2009-07-09 14:01:42 +0100 (Thu, 09 Jul 2009) | 4 lines
+Changed paths:
+   M /trunk/samtools/bam.h
+   A /trunk/samtools/bam_lite.c
+   M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.5-1 (r390)
+ * removed useless _IOLIB in bam.h. This should cause no change at all.
+ * added bam_lite.c for light-weight BAM reading
+
+------------------------------------------------------------------------
+r385 | lh3lh3 | 2009-07-07 16:53:29 +0100 (Tue, 07 Jul 2009) | 2 lines
+Changed paths:
+   M /trunk/samtools/bamtk.c
+   M /trunk/samtools/knetfile.c
+
+Release samtools-0.1.5c (fixed a bug in piping)
+
+------------------------------------------------------------------------
+r383 | lh3lh3 | 2009-07-07 11:39:55 +0100 (Tue, 07 Jul 2009) | 2 lines
+Changed paths:
+   M /trunk/samtools/bamtk.c
+   M /trunk/samtools/sam.c
+
+Release samtools-0.1.5b (BUG! so embarrassing!)
+
+------------------------------------------------------------------------
+r381 | lh3lh3 | 2009-07-07 11:20:06 +0100 (Tue, 07 Jul 2009) | 2 lines
+Changed paths:
+   M /trunk/samtools/Makefile
+   M /trunk/samtools/bam.h
+   M /trunk/samtools/bam_aux.c
+   M /trunk/samtools/bamtk.c
+
+Release samtools-0.1.5a (for compatibility with Bio::DB::Sam)
+
+------------------------------------------------------------------------
+r373 | lh3lh3 | 2009-07-07 10:26:57 +0100 (Tue, 07 Jul 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-0.1.5
+
 ------------------------------------------------------------------------
 r372 | lh3lh3 | 2009-07-07 09:49:27 +0100 (Tue, 07 Jul 2009) | 3 lines
 Changed paths:

diff --git a/bam.c b/bam.c
index 2edb2a8b1e339fb99ee3a9c085d1d61bd1881db2..52d97a6959dfad2076afdb3c64f37fd76b87fb40 100644 (file)
--- a/bam.c
+++ b/bam.c
@@ -91,7 +91,11 @@ bam_header_t *bam_header_read(bamFile fp)
 {
        bam_header_t *header;
        char buf[4];
-       int32_t i, name_len;
+       int32_t i = 1, name_len;
+       // check EOF
+       i = bgzf_check_EOF(fp);
+       if (i < 0) fprintf(stderr, "[bam_header_read] read from pipe; skip EOF checking.\n");
+       else if (i == 0) fprintf(stderr, "[bam_header_read] EOF marker is absent.\n");
        // read "BAM1"
        if (bam_read(fp, buf, 4) != 4) return 0;
        if (strncmp(buf, "BAM\001", 4)) {

diff --git a/bamtk.c b/bamtk.c
index 234f465116261df4e10fa0ae01e7ca0184671d65..9e766737e4cfcfd17403bf186fc8cfc43184aa1c 100644 (file)
--- a/bamtk.c
+++ b/bamtk.c
@@ -4,7 +4,7 @@
 #include "bam.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.1.5-16 (r421)"
+#define PACKAGE_VERSION "0.1.5-17 (r422)"
 #endif
 
 int bam_taf2baf(int argc, char *argv[]);

diff --git a/bgzf.c b/bgzf.c
index 71d8c81460044cb8b88c655d41ba918874641f61..2cd1c5e514a94c5569f5819c7f6b23af8985d444 100644 (file)
--- a/bgzf.c
+++ b/bgzf.c
@@ -571,6 +571,14 @@ bgzf_close(BGZF* fp)
         if (flush_block(fp) != 0) {
             return -1;
         }
+               { // add an empty block
+                       int count, block_length = deflate_block(fp, 0);
+#ifdef _USE_KNETFILE
+                       count = fwrite(fp->compressed_block, 1, block_length, fp->x.fpw);
+#else
+                       count = fwrite(fp->compressed_block, 1, block_length, fp->file);
+#endif
+               }
 #ifdef _USE_KNETFILE
         if (fflush(fp->x.fpw) != 0) {
 #else
@@ -610,6 +618,25 @@ void bgzf_set_cache_size(BGZF *fp, int cache_size)
        if (fp) fp->cache_size = cache_size;
 }
 
+int bgzf_check_EOF(BGZF *fp)
+{
+       static uint8_t magic[28] = "\037\213\010\4\0\0\0\0\0\377\6\0\102\103\2\0\033\0\3\0\0\0\0\0\0\0\0\0";
+       uint8_t buf[28];
+       off_t offset;
+#ifdef _USE_KNETFILE
+       offset = knet_tell(fp->x.fpr);
+       if (knet_seek(fp->x.fpr, -28, SEEK_END) != 0) return -1;
+       knet_read(fp->x.fpr, buf, 28);
+       knet_seek(fp->x.fpr, offset, SEEK_SET);
+#else
+       offset = ftello(fp->file);
+       if (fseeko(fp->file, -28, SEEK_END) != 0) return -1;
+       fread(buf, 1, 28, fp->file);
+       fseeko(fp->file, offset, SEEK_SET);
+#endif
+       return (memcmp(magic, buf, 28) == 0)? 1 : 0;
+}
+
 int64_t
 bgzf_seek(BGZF* fp, int64_t pos, int where)
 {
@@ -636,4 +663,3 @@ bgzf_seek(BGZF* fp, int64_t pos, int where)
     fp->block_offset = block_offset;
     return 0;
 }
-

diff --git a/bgzf.h b/bgzf.h
index d5eeafe7e527c57823b8b68cb2c32511f1b0fadd..f685c4455eea660cfadd9f61cdbcf5f9aea0613b 100644 (file)
--- a/bgzf.h
+++ b/bgzf.h
@@ -113,6 +113,8 @@ int64_t bgzf_seek(BGZF* fp, int64_t pos, int where);
  */
 void bgzf_set_cache_size(BGZF *fp, int cache_size);
 
+int bgzf_check_EOF(BGZF *fp);
+
 #ifdef __cplusplus
 }
 #endif

diff --git a/knetfile.c b/knetfile.c
index bcf74a89024b5533941cf322ccc6e83c6d28210d..358ee6482c67619efc567355761655f517bb640d 100644 (file)
--- a/knetfile.c
+++ b/knetfile.c
@@ -344,11 +344,12 @@ int knet_seek(knetFile *fp, off_t off, int whence)
 {
        if (whence == SEEK_SET && off == fp->offset) return 0;
        if (fp->type == KNF_TYPE_LOCAL) {
-               if (lseek(fp->fd, off, whence) == -1) {
+               off_t offset = lseek(fp->fd, off, whence);
+               if (offset == -1) {
                        perror("lseek");
                        return -1;
                }
-               fp->offset = off;
+               fp->offset = offset;
                return 0;
        } else if (fp->type == KNF_TYPE_FTP || fp->type == KNF_TYPE_HTTP) {
                if (whence != SEEK_SET) { // FIXME: we can surely allow SEEK_CUR and SEEK_END in future

diff --git a/sam.c b/sam.c
index b8e7350f3bebd70cd043bf54de02c77315092ee9..a74c557bad9aa83d274ea44bdfe1a16dfbc4d5a6 100644 (file)
--- a/sam.c
+++ b/sam.c
@@ -158,6 +158,7 @@ int sampileup(samfile_t *fp, int mask, bam_pileup_f func, void *func_data)
 char *samfaipath(const char *fn_ref)
 {
        char *fn_list = 0;
+       if (fn_ref == 0) return 0;
        fn_list = calloc(strlen(fn_ref) + 5, 1);
        strcat(strcpy(fn_list, fn_ref), ".fai");
        if (access(fn_list, R_OK) == -1) { // fn_list is unreadable

diff --git a/sam_view.c b/sam_view.c
index 1776b8eb586b99b3123b8dffaeb39849179d30cc..c2056bafecf266904172ddf68f40266329ba8bea 100644 (file)
--- a/sam_view.c
+++ b/sam_view.c
@@ -86,7 +86,7 @@ int main_samview(int argc, char *argv[])
                goto view_end;
        }
        if (in->header == 0) {
-               fprintf(stderr, "[main_samview] fail to read SAM header.\n");
+               fprintf(stderr, "[main_samview] fail to read the header.\n");
                goto view_end;
        }
        if ((out = samopen(fn_out? fn_out : "-", out_mode, in->header)) == 0) {