samtools/bcftools — pull request #25 by sm15 (2014-02-07 16:57:47+00:00)
Title: bcftools index to work on VCF and BCF

* add `vcfindex.c` to do indexing of vcf and bcf; default at the moment to `.csi`

* move `bcf_idx.c` to `bcf_idx.unused.c`.

* hide `bcftools tabix` command. if we're going to remove it, we need to rejigger the tests that need to index tab delimited files. can assume `tabix` somehow like bgzip??

* add `index` to the man

* test limits of index retrival

* tbi limit is (`1<<29`). no error reported when creating the index though

* csi index is (`1<<31-1`). bcf creation and indexing a problem above this

* added commented out test for region specified as `chr20` rather than `chr20:1-2147483647`; fails at the moment, but shouldn't