+------------------------------------------------------------------------
+r451 | lh3lh3 | 2009-09-02 10:44:48 +0100 (Wed, 02 Sep 2009) | 4 lines
+Changed paths:
+ M /trunk/samtools/bam_md.c
+ M /trunk/samtools/bam_rmdup.c
+ M /trunk/samtools/bam_rmdupse.c
+ M /trunk/samtools/bam_sort.c
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/samtools.1
+
+ * samtools-0.1.5-34 (r451)
+ * applied the patch by John
+ * improved the help message a little bit
+
+------------------------------------------------------------------------
+r450 | lh3lh3 | 2009-09-02 09:55:55 +0100 (Wed, 02 Sep 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam_color.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.5-33 (r450)
+ * fixed a bug in bam_color.c (on behalf of Nils Homer)
+
+------------------------------------------------------------------------
+r449 | lh3lh3 | 2009-08-29 20:36:41 +0100 (Sat, 29 Aug 2009) | 4 lines
+Changed paths:
+ M /trunk/samtools/bam_import.c
+ M /trunk/samtools/bam_md.c
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/misc/samtools.pl
+
+ * samtools-0.1.5-32 (r449)
+ * fillmd: fixed a bug in modifying MD/NM tags
+ * in import, give a warning if the read is aligned but there is no CIGAR.
+
+------------------------------------------------------------------------
+r448 | lh3lh3 | 2009-08-19 09:44:28 +0100 (Wed, 19 Aug 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/ChangeLog
+ M /trunk/samtools/bam_pileup.c
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/misc/wgsim_eval.pl
+
+ * samtools-0.1.5-31 (r448)
+ * fixed an issue when the last CIGAR is I or D
+
------------------------------------------------------------------------
r447 | lh3lh3 | 2009-08-17 09:34:57 +0100 (Mon, 17 Aug 2009) | 3 lines
Changed paths:
+Beta Release 0.1.6 (2 September, 2009)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Notable changes:
+
+ * In tview, do not show a blank screen when no reads mapped to the
+ corresponding region.
+
+ * Implemented native HTTP support in the BGZF library. Samtools is now
+ able to directly open a BAM file on HTTP. HTTP proxy is also
+ supported via the "http_proxy" environmental variable.
+
+ * Samtools is now compitable with the MinGW (win32) compiler and the
+ PDCurses library.
+
+ * The calmd (or fillmd) command now calculates the NM tag and replaces
+ MD tags if they are wrong.
+
+ * The view command now recognizes and optionally prints FLAG in HEXs or
+ strings to make a SAM file more friendly to human eyes. This is a
+ samtools-C extension, not implemented in Picard for the time
+ being. Please type `samtools view -?' for more information.
+
+ * BAM files now have an end-of-file (EOF) marker to facilitate
+ truncation detection. A warning will be given if an on-disk BAM file
+ does not have this marker. The warning will be seen on BAM files
+ generated by an older version of samtools. It does NO harm.
+
+ * New key bindings in tview: `r' to show read names and `s' to show
+ reference skip (N operation) as deletions.
+
+ * Fixed a bug in `samtools merge -n'.
+
+ * Samtools merge now optionally copies the header of a user specified
+ SAM file to the resultant BAM output.
+
+ * Samtools pileup/tview works with a CIGAR with the first or the last
+ operation is an indel.
+
+ * Fixed a bug in bam_aux_get().
+
+
+Changes in other utilies:
+
+ * Fixed wrong FLAG in maq2sam.
+
+
+(0.1.6: 2 September 2009, r453)
+
+
+
Beta Release 0.1.5 (7 July, 2009)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#endif
#ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.1.5-34 (r451)"
+#define PACKAGE_VERSION "0.1.6 (r453)"
#endif
int bam_taf2baf(int argc, char *argv[]);
fprintf(stderr, "Usage: samtools <command> [options]\n\n");
fprintf(stderr, "Command: view SAM<->BAM conversion\n");
fprintf(stderr, " sort sort alignment file\n");
- fprintf(stderr, " merge merge sorted alignments (Picard recommended)\n");
fprintf(stderr, " pileup generate pileup output\n");
fprintf(stderr, " faidx index/extract FASTA\n");
#if _CURSES_LIB != 0
#endif
fprintf(stderr, " index index alignment\n");
fprintf(stderr, " fixmate fix mate information\n");
- fprintf(stderr, " rmdup remove PCR duplicates (Picard recommended)\n");
fprintf(stderr, " glfview print GLFv3 file\n");
fprintf(stderr, " flagstat simple stats\n");
fprintf(stderr, " calmd recalculate MD/NM tags and '=' bases\n");
+ fprintf(stderr, " merge merge sorted alignments (Picard recommended)\n");
+ fprintf(stderr, " rmdup remove PCR duplicates (Picard recommended)\n");
fprintf(stderr, "\n");
return 1;
}
-.TH samtools 1 "6 July 2009" "samtools-0.1.5" "Bioinformatics tools"
+.TH samtools 1 "2 September 2009" "samtools-0.1.6" "Bioinformatics tools"
.SH NAME
.PP
samtools - Utilities for the Sequence Alignment/Map (SAM) format
+++ /dev/null
-digraph {
- faidx[label="faidx.c\n(faidx)"]
- import[label="bam_import.c\n(import)"]
- plcmd[label="bam_plcmd.c\n(pileup)"]
- sort[label="bam_sort.c\n(sort, merge)"]
- index[label="bam_index.c\n(index)"]
- tview[label="bam_tview.c\n(tview)"]
- glf[label="glf.c\n(glfview)"]
- rmdup[label="bam_rmdup.c\n(rmdup)"]
- fixmate[label="bam_mate.c\n(fixmate)"]
- "bam_aux.c" -> {"bam.c", import}
- glf -> {"bam_maqcns.c", plcmd}
- "bgzf.c" -> {"bam.c", glf}
- "bam.c" -> {index, "bam_pileup.c", sort, import, rmdup, fixmate}
- "bam_pileup.c" -> {"bam_lpileup.c", plcmd}
- {"bam_lpileup.c", index, faidx, "bam_maqcns.c"} -> tview
- {import, faidx, "bam_maqcns.c"} -> plcmd
- {tview, plcmd, faidx, sort, import, index, glf, rmdup, fixmate} -> "bamtk.c\n(view)"
-}
\ No newline at end of file
projects / samtools.git / commitdiff