Hi Wolfgang, this is only temporary, some of the header APIs got lost in the transition to htslib. We definitely plan to put these back.
Cheers, Petr On Mon, 2014-09-15 at 11:54 +0200, Wolfgang Maier wrote: > Dear all, > SNP calling with samtools/bcftools used to produce a vcf header section > with ##contig lines including all the information found in the input > bam's @SQ lines like: > > ##samtoolsVersion=0.1.19-44428cd > ##contig=<ID=Chromosome,length=3573470,md5=70ad67622b2fbd848ead0f6aeeabf9a7> > > Now with samtools/bcftools-1.0 everything except ID and length seems to > be ignored: > > ##samtoolsVersion=1.0+htslib-1.0 > ##contig=<ID=Chromosome,length=3573470> > > Has this behavior been changed on purpose or is it oversight ? > Thanks, > Wolfgang > > > ------------------------------------------------------------------------------ > Want excitement? > Manually upgrade your production database. > When you want reliability, choose Perforce > Perforce version control. Predictably reliable. > http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg.clktrk > _______________________________________________ > Samtools-help mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/samtools-help -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. ------------------------------------------------------------------------------ Want excitement? Manually upgrade your production database. When you want reliability, choose Perforce Perforce version control. Predictably reliable. http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg.clktrk _______________________________________________ Samtools-help mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/samtools-help
