From: Heng Li Date: Tue, 7 Jul 2009 09:26:57 +0000 (+0000) Subject: Release samtools-0.1.5 X-Git-Url: https://git.donarmstrong.com/?p=samtools.git;a=commitdiff_plain;h=9f30c9ba76e0266e896f1199b41e0e7ddf6bd648 Release samtools-0.1.5 --- diff --git a/ChangeLog b/ChangeLog index bc7bd9e..3bf82a5 100644 --- a/ChangeLog +++ b/ChangeLog @@ -1,3 +1,38 @@ +------------------------------------------------------------------------ +r372 | lh3lh3 | 2009-07-07 09:49:27 +0100 (Tue, 07 Jul 2009) | 3 lines +Changed paths: + M /trunk/samtools/bamtk.c + M /trunk/samtools/sam.c + + * samtools-0.1.4-23 (r372) + * keep header text if "view -t" is used (by Gerton) + +------------------------------------------------------------------------ +r371 | lh3lh3 | 2009-07-07 01:13:32 +0100 (Tue, 07 Jul 2009) | 2 lines +Changed paths: + M /trunk/samtools/samtools.1 + +update documentation + +------------------------------------------------------------------------ +r370 | bhandsaker | 2009-07-02 22:24:34 +0100 (Thu, 02 Jul 2009) | 2 lines +Changed paths: + M /trunk/samtools/Makefile + +Introduced LIBPATH variable so this could be overridden to allow samtools to build correct at the Broad. + +------------------------------------------------------------------------ +r369 | lh3lh3 | 2009-07-02 13:36:53 +0100 (Thu, 02 Jul 2009) | 4 lines +Changed paths: + M /trunk/samtools/ChangeLog + M /trunk/samtools/bam_aux.c + M /trunk/samtools/bam_plcmd.c + M /trunk/samtools/bamtk.c + + * samtools-0.1.4-22 (r369) + * in pileup, optionally print E2 and U2 + * remove the debugging code in bam_aux_get() (Drat!) + ------------------------------------------------------------------------ r368 | lh3lh3 | 2009-07-02 11:32:26 +0100 (Thu, 02 Jul 2009) | 6 lines Changed paths: diff --git a/NEWS b/NEWS index f0af063..149c090 100644 --- a/NEWS +++ b/NEWS @@ -1,3 +1,64 @@ +Beta Release 0.1.5 (7 July, 2009) +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +Notable changes: + + * Support opening a BAM alignment on FTP. Users can now use "tview" to + view alignments at the NCBI ftp site. Please read manual for more + information. + + * In library, propagate errors rather than exit or complain assertion + failure. + + * Simplified the building system and fixed compiling errors caused by + zlib<1.2.2.1. + + * Fixed an issue about lost header information when a SAM is imported + with "view -t". + + * Implemented "samtool.pl varFilter" which filters both SNPs and short + indels. This command replaces "indelFilter". + + * Implemented "samtools.pl pileup2fq" to generate FASTQ consensus from + pileup output. + + * In pileup, cap mapping quality at 60. This helps filtering when + different aligners are in use. + + * In pileup, allow to output variant sites only. + + * Made pileup generate correct calls in repetitive region. At the same + time, I am considering to implement a simplified model in SOAPsnp, + although this has not happened yet. + + * In view, added '-u' option to output BAM without compression. This + option is preferred when the output is piped to other commands. + + * In view, added '-l' and '-r' to get the alignments for one library or + read group. The "@RG" header lines are now partially parsed. + + * Do not include command line utilities to libbam.a. + + * Fixed memory leaks in pileup and bam_view1(). + + * Made faidx more tolerant to empty lines right before or after FASTA > + lines. + + +Changes in other utilities: + + * Updated novo2sam.pl by Colin Hercus, the key developer of novoalign. + + +This release involves several modifications to the key code base which +may potentially introduce new bugs even though we have tried to minimize +this by testing on several examples. Please let us know if you catch +bugs. + +(0.1.5: 7 July 2009, r373) + + + Beta Release 0.1.4 (21 May, 2009) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ diff --git a/bamtk.c b/bamtk.c index 56cca0a..87b9c13 100644 --- a/bamtk.c +++ b/bamtk.c @@ -4,7 +4,7 @@ #include "bam.h" #ifndef PACKAGE_VERSION -#define PACKAGE_VERSION "0.1.4-23 (r372)" +#define PACKAGE_VERSION "0.1.5 (r373)" #endif int bam_taf2baf(int argc, char *argv[]); diff --git a/samtools.1 b/samtools.1 index d111aa6..45e1612 100644 --- a/samtools.1 +++ b/samtools.1 @@ -23,21 +23,22 @@ samtools tview aln.sorted.bam ref.fasta .SH DESCRIPTION .PP Samtools is a set of utilities that manipulate alignments in the BAM -format. It imports from and exports to the SAM (Sequence -Alignment/Map) format, does sorting, merging and indexing, and -allows to retrieve reads in any regions swiftly. +format. It imports from and exports to the SAM (Sequence Alignment/Map) +format, does sorting, merging and indexing, and allows to retrieve reads +in any regions swiftly. Samtools is designed to work on a stream. It regards an input file `-' -as the standard input (stdin) and an output file `-' as the standard output -(stdout). Several commands can thus be combined with Unix pipes. Samtools -always output warning and error messages to the standard error output (stderr). - -Samtools is also able to open a BAM (not SAM) file on a remote FTP server if the BAM -file name starts with `ftp://'. -Samtools checks the current working directory for the index file and will -download the index upon absence. Samtools achieves random FTP file access -with the `REST' ftp command. It does not retrieve the entire -alignment file unless it is asked to do so. +as the standard input (stdin) and an output file `-' as the standard +output (stdout). Several commands can thus be combined with Unix +pipes. Samtools always output warning and error messages to the standard +error output (stderr). + +Samtools is also able to open a BAM (not SAM) file on a remote FTP +server if the BAM file name starts with `ftp://'. Samtools checks the +current working directory for the index file and will download the index +upon absence. Samtools achieves random FTP file access with the `REST' +ftp command. It does not retrieve the entire alignment file unless it is +asked to do so. .SH COMMANDS AND OPTIONS @@ -106,8 +107,8 @@ is specified, all the alignments will be printed; otherwise only alignments overlapping the specified regions will be output. An alignment may be given multiple times if it is overlapping several regions. A region can be presented, for example, in the following -format: `chr2', `chr2:1000000' or `chr2:1,000,000-2,000,000'. The coordinate -is 1-based. +format: `chr2', `chr2:1000000' or `chr2:1,000,000-2,000,000'. The +coordinate is 1-based. .B OPTIONS: .RS @@ -116,8 +117,9 @@ is 1-based. Output in the BAM format. .TP .B -u -Output uncompressed BAM. This option saves time spent on compression/decomprssion -and is thus preferred when the output is piped to another samtools command. +Output uncompressed BAM. This option saves time spent on +compression/decomprssion and is thus preferred when the output is piped +to another samtools command. .TP .B -h Include the header in the output.