samtools/htsjdk — pull request #126 by travc (2014-10-04 03:49:52+00:00)
Title: Some support for VCF v4.2 files added

Handles "Number=R" for INFO fields in the header.
Other VCF v4.2 specific additions (Eg: Source and Version fields in INFO header lines) are not handled, but appear to be silently ignored.
Tested on output of samtools mpileup | bcftools call (1.0-17-gfaf4dd6, 1.0-55-gc661821, using htslib 1.0-11-g830ea73)

PS: At least this is sorely needed, since htslib/samtools/bcftools 1.0 produce VCF v4.2.
This is an incomplete fix, since proper v4.2 support should really be added. However it does appear to be sufficient to get IGV to work properly with my v4.2 VCF files.