On 17 Apr 2018, at 14:40, Heredia Genestar, Txema <txema.here...@upf.edu> wrote:
> After further reading the documentation I've finally found the part where it
> explains the -0 option.
>
> I was mistaken and the -0 option is not there if you fancy one or another
> indexing. It is there for the ¿rare? cases where your vcf file data is
> written using 0-based positions and you need proper indexing.
Recall that tabix is capable of indexing arbitrary one-record-per-line text
genomics formats. So -0 is really there alongside -b -e etc so that you can
fully describe file formats that use UCSC-style 0-based coordinates. For
example, -p bed is more-or-less equivalent to -s 1 -b 2 -e 3 -0.
Incidentally, old tabix 0.2.5's -0 option also applied only when indexing.
> As it stands now, I cannot use tabix and I have to parse those big vcfs with
> awk. Is there any version without the -h bug that still has the -B option?
The old tabix's -B option simply read a BED file. The new tabix's (and various
bcftools commands') -R option has this crazy thing where it decides whether the
file given is a standard BED file or a file that looks the same but contains
1-based coordinates. It seems to me that for sanity's sake new tabix will need
to regain an option that just takes a BED file, whether that would be -B FILE,
-0 -R FILE, or a somewhat incompatible -R option with less "smarts".
In the meantime, you might like to apply the change below (to current HTSlib
tabix), which will give you a tabix command whose -R option always interprets
its argument as a standard BED file.
John
--- a/tabix.c
+++ b/tabix.c
@@ -100,7 +100,7 @@ static char **parse_regions(char *regions_fname, char
**argv, int argc, int *nre
{
// improve me: this is a too heavy machinery for parsing regions...
- regidx_t *idx = regidx_init(regions_fname, NULL, NULL, 0, NULL);
+ regidx_t *idx = regidx_init(regions_fname, regidx_parse_bed, NULL, 0,
NULL);
if ( !idx ) error("Could not read %s\n", regions_fname);
(*nregs) += regidx_nregs(idx);
------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
_______________________________________________
Samtools-help mailing list
Samtools-help@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/samtools-help
