From: Heng Li Date: Wed, 2 Sep 2009 12:56:33 +0000 (+0000) Subject: Release samtools-0.1.6 X-Git-Url: https://git.donarmstrong.com/?p=samtools.git;a=commitdiff_plain;h=0746c10643c92a4e8c7dc9663b2cc0c63249e683 Release samtools-0.1.6 --- diff --git a/ChangeLog b/ChangeLog index 969fb28..c0afc45 100644 --- a/ChangeLog +++ b/ChangeLog @@ -1,3 +1,49 @@ +------------------------------------------------------------------------ +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: diff --git a/NEWS b/NEWS index 149c090..8e0ba35 100644 --- a/NEWS +++ b/NEWS @@ -1,3 +1,54 @@ +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) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ diff --git a/bamtk.c b/bamtk.c index 3742bb2..ea66672 100644 --- a/bamtk.c +++ b/bamtk.c @@ -9,7 +9,7 @@ #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[]); @@ -78,7 +78,6 @@ static int usage() fprintf(stderr, "Usage: samtools [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 @@ -86,10 +85,11 @@ static int usage() #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; } diff --git a/samtools.1 b/samtools.1 index 7b50ef9..d2c78f1 100644 --- a/samtools.1 +++ b/samtools.1 @@ -1,4 +1,4 @@ -.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 diff --git a/source.dot b/source.dot deleted file mode 100644 index 1735774..0000000 --- a/source.dot +++ /dev/null @@ -1,19 +0,0 @@ -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