Can you backport the fixes to bioc-release which is also affected? Best Julian
Valerie Obenchain (12/09/14 03:24): > Thanks to Michael and Julian for taking care of this. Fixes are in > devel, >= 1.13.15. > > Valerie > > > On 12/03/14 08:44, Michael Lawrence wrote: >> Looks like an issue when expand()ing the VCF. Maybe Val could take a look? >> >> On Wed, Dec 3, 2014 at 7:39 AM, Julian Gehring <julian.gehr...@embl.de> >> wrote: >> >>> Hi, >>> >>> The conversion from a 'VCF' to 'VRanges' object fails if an INFO field >>> with multiple values for different ALT alleles is present: >>> >>> Here an example VCF entry for which this fails (line 71151250 in >>> 'ALL.wgs.phase3_shapeit2_mvncall_integrated_v5.20130502.sites.vcf.gz' >>> , taken from >>> >>> ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.wgs.phase3_shapeit2_mvncall_integrated_v5.20130502.sites.vcf.gz >>> ): >>> >>> 10001541 rs12451372 C G,T 100 PASS >>> >>> AC=700,298;AF=0.139776,0.0595048;AN=5008;NS=2504;DP=17289;EAS_AF=0.2421,0;AMR_AF=0.1801,0.0115;AFR_AF=0.0749,0.2194;EUR_AF=0.0915,0;SAS_AF=0.1431,0;AA=T||| >>> >>> The respective code to reproduce this: >>> >>> library(VariantAnnotation) >>> roi = GRanges("17", IRanges(1e7+1541, width = 1)) >>> vcf = readVcf(path, "GRCh37", ScanVcfParam(which = roi, info = "AF")) >>> ## 'info = character()' and other versions also cause the error >>> >>> vrc = as(vcf, "VRanges") ## error >>> >>> fails with >>> >>> Error in colSums(ielt) : 'x' must be an array of at least two dimensions >>> >>> This occurs both with the latest version of VariantAnnotation in >>> bioc-release and bioc-devel. >>> >>> Best >>> Julian >>> >>> _______________________________________________ >>> Bioc-devel@r-project.org mailing list >>> https://stat.ethz.ch/mailman/listinfo/bioc-devel >>> >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioc-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel >> > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
