X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=samtools.git;a=blobdiff_plain;f=NEWS;h=946ba7b4e98d584081b846105bde5f438f6e3ba1;hp=478e718c79963a052e682bbc33cfa0de695076e0;hb=ced7709f121a00d5049d99ee8576037994aab1d1;hpb=6a0c6f060a60789b48e10a72b1381f6e54599302 diff --git a/NEWS b/NEWS index 478e718..946ba7b 100644 --- a/NEWS +++ b/NEWS @@ -1,3 +1,135 @@ +Beta release 0.1.14 (16 March, 2011) +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +This release implements a method for testing associations for case-control +data. The method does not call genotypes but instead sums over all genotype +configurations to compute a chi^2 based test statistics. It can be potentially +applied to comparing a pair of samples (e.g. a tumor-normal pair), but this +has not been evaluated on real data. + +Another new feature is to make X chromosome variant calls when female and male +samples are both present. The user needs to provide a file indicating the +ploidy of each sample. + +Other new features: + + * Added `samtools mpileup -L' to skip INDEL calling in regions with + excessively high coverage. Such regions dramatically slow down mpileup. + + * Added `bcftools view -F' to parse BCF files generated by samtools r921 or + older which encode PL in a different way. + +(0.1.14: 16 March 2011, r930:163) + + + +Beta release 0.1.13 (1 March, 2011) +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +The most important though largely invisible modification is the change of the +order of genotypes in the PL VCF/BCF tag. This is to conform the upcoming VCF +spec v4.1. The change means that 0.1.13 is not backward compatible with VCF/BCF +generated by samtools older than r921 inclusive. VCF/BCF generated by the new +samtools will contain a line `##fileformat=VCFv4.1' as well as the samtools +version number. + +Single Individual Haplotyping (SIH) is added as an experimental feature. It +originally aims to produce haploid consensus from fosmid pool sequencing, but +also works with short-read data. For short reads, phased blocks are usually too +short to be useful in many applications, but they can help to rule out part of +SNPs close to INDELs or between copies of CNVs. + + +Other notable changes in samtools: + + * Construct per-sample consensus to reduce the effect of nearby SNPs in INDEL + calling. This reduces the power but improves specificity. + + * Improved sorting order checking in indexing. Now indexing is the preferred way + to check if a BAM is sorted. + + * Added a switch `-E' to mpileup and calmd. This option uses an alternative way + to apply BAQ, which increases sensistivity, especially to MNPs, at the cost of + a little loss in specificity. + + * Added `mpileup -A' to allow to use reads in anomalous pairs in SNP calling. + + * Added `mpileup -m' to allow fine control of the collection of INDEL candidates. + + * Added `mpileup -S' to compute per-sample strand bias P-value. + + * Added `mpileup -G' to exclude read groups in variant calling. + + * Fixed segfault in indel calling related to unmapped and refskip reads. + + * Fixed an integer overflow in INDEL calling. This bug produces wrong INDEL + genotypes for longer short INDELs, typically over 10bp. + + * Fixed a bug in tview on big-endian machines. + + * Fixed a very rare memory issue in bam_md.c + + * Fixed an out-of-boundary bug in mpileup when the read base is `N'. + + * Fixed a compiling error when the knetfile library is not used. Fixed a + library compiling error due to the lack of bam_nt16_nt4_table[] table. + Suppress a compiling warning related to the latest zlib. + + +Other notable changes in bcftools: + + * Updated the BCF spec. + + * Added the `FQ' VCF INFO field, which gives the phred-scaled probability + of all samples being the same (identical to the reference or all homozygous + variants). Option `view -f' has been dropped. + + * Implementated of "vcfutils.pl vcf2fq" to generate a consensus sequence + similar to "samtools.pl pileup2fq". + + * Make sure the GT FORMAT field is always the first FORMAT to conform the VCF + spec. Drop bcf-fix.pl. + + * Output bcftools specific INFO and FORMAT in the VCF header. + + * Added `view -s' to call variants from a subset of samples. + + * Properly convert VCF to BCF with a user provided sequence dictionary. Nonetheless, + custom fields are still unparsed and will be stored as a missing value. + + * Fixed a minor bug in Fisher's exact test; the results are rarely changed. + + +(0.1.13: 1 March 2011, r926:134) + + + +Beta release 0.1.12a (2 December, 2010) +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +This is another bug fix release: + + * Fixed a memory violation in mpileup, which causes segfault. Release + 0.1.9 and above are affected. + + * Fixed a memory violation in the indel caller, which does not causes + segfault, but may potentially affect deletion calls in an unexpected + way. Release 0.1.10 and above are affected. + + * Fixed a bug in computing r-square in bcftools. Few are using this + functionality and it only has minor effect. + + * Fixed a memory leak in bam_fetch(). + + * Fixed a bug in writing meta information to the BAM index for the last + sequence. This bug is invisible to most users, but it is a bug anyway. + + * Fixed a bug in bcftools which causes false "DP4=0,0,0,0" annotations. + +(0.1.12: 2 December 2010, r862) + + + Beta release 0.1.11 (21 November, 2010) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -506,4 +638,4 @@ Beta Release 0.1.1 (22 December, 2008) The is the first public release of samtools. For more information, please check the manual page `samtools.1' and the samtools website -http://samtools.sourceforge.net \ No newline at end of file +http://samtools.sourceforge.net