diff --git a/RELEASE_HISTORY b/RELEASE_HISTORY index 817db6979e27378311440fb3bd1ac9a413a430d0..5227fd7bb6958327829e6aceb2ef2c9ac341b140 100644 --- a/RELEASE_HISTORY +++ b/RELEASE_HISTORY @@ -1,4 +1,30 @@ -Version 2.9.1 (August-16-2010) +Version 2.10.0 (September-21-2010) +==New tools== +1. annotateBed. Annotates one BED/VCF/GFF file with the coverage and number of overlaps observed +from multiple other BED/VCF/GFF files. In this way, it allows one to ask to what degree one feature coincides with multiple other feature types with a single command. For example, the following will annotate the fraction of the variants in variants.bed that are covered by genes, conservaed regions and know variation, respectively. +$ annotateBed -i variants.bed -files genes.bed conserv.bed known_var.bed + +This tool was suggested by Can Alkan and was motivated by the example source code that he kindly provided. + +==New features== +1. New frequency operations (freqasc and freqdesc) added to groupBy. These operations report a histogram of the frequency that each value is observed in a given column. +2. Support for writing uncompressed bam with the -ubam option. +3. Shorthand arguments for groupBy (-g eq. -grp, -c eq. -opCols, -o eq. -opCols). +4. In addition, all BEDTools that require only one main input file (the -i file) will assume that input is +coming from standard input if the -i parameter is ignored. For example, the following are equivalent: +$ cat snps.bed | sortBed –i stdin +$ cat snps.bed | sortBed + +As are these: +$ cat data.txt | groupBy -i stdin -g 1,2,3 -c 5 -o mean +$ cat data.txt | groupBy -g 1,2,3 -c 5 -o mean + +==Bug fixes== +1. Increased the precision of the output from groupBy. + + + +Version 2.9.0 (August-16-2010) ==New tools== 1. unionBedGraphs. This is a very powerful new tool contributed by Assaf Gordon from CSHL. It will combine/merge multiple BEDGRAPH files into a single file, thus allowing comparisons of coverage (or any text-value) across multiple samples. @@ -14,6 +40,8 @@ Version 2.9.1 (August-16-2010) 4. Fixed other minor parsing and reporting bugs/annoyances. + + Version 2.8.3 (July-25-2010) 1. Fixed bug that caused some GFF files to be misinterpreted as VCF. This prevented the detection of overlaps. 2. Added a new "-tag" option in bamToBed that allows one to choose the _numeric_ tag that will be used to populate the score field. For example, one could populate the score field with the alignment score with "-tag AS".