- Update to 1.9
* `annotate`
- REF and ALT columns can be now transferred from the annotation
file.
- fixed bug when setting vector_end values.
* `consensus`
- new -M option to control output at missing genotypes
- variants immediately following insersions should not be skipped.
Note however, that the current fix requires normalized VCF and may
still falsely skip variants adjacent to multiallelic indels.
- bug fixed in -H selection handling
* `convert`
- the --tsv2vcf option now makes the missing genotypes diploid,
"./." instead of "."
- the behavior of -i/-e with --gvcf2vcf changed. Previously only
sites with FILTER set to "PASS" or "." were expanded and the -i/-e
options dropped sites completely. The new behavior is to let the -i/-e
options control which records will be expanded. In order to drop
records completely, one can stream through "bcftools view" first.
* `csq`
- since the real consequence of start/splice events are not known,
the aminoacid positions at subsequent variants should stay unchanged
- add `--force` option to skip malformatted transcripts in GFFs
with out-of-phase CDS exons.
* `+dosage`: output all alleles and all their dosages at multiallelic
sites
* `+fixref`: fix serious bug in -m top conversion
* `-i/-e` filtering expressions:
- add two-tailed binomial test
- add functions N_PASS() and F_PASS()
- add support for lists of samples in filtering expressions, with
many samples it was impractical to list them all on the command line.
Samples can be now in a file as, e.g., GT[@samples.txt]="het"
- allow multiple perl functions in the expressions and some bug
fixes
- fix a parsing problem, '@' was not removed from '@filename'
expressions
* `mpileup`: fixed bug where, if samples were renamed using the `-G`
(`--read-groups`) option, some samples could be omitted from the
output file.
* `norm`: update INFO/END when normalizing indels
* `+split`: new -S option to subset samples and to use custom file
names instead of the defaults
* `+smpl-stats`: new plugin
* `+trio-stats`: new plugin
* Fixed build problems with non-functional configure script produced
on some platforms