Added FilterParam option to exclude multi-allelic sites report_multiallelic, or to exclude reporting a variant in the Var assay based on allelic frequency (min_allelic_freq). The two parameters, if used in combination, will exclude multiallelic sites with high primary and secondary variant allele frequencies.
changed filterParam argument in pileup_sites and pileup_cells to param for simplicity.
renamed FilterParam parameter min_nucleotide_depth to min_depth
renamed FilterParam parameter min_read_bqual to read_bqual
moved bam_flags parameters to FilterParams class
the bedindex parameter for pileup_sites has been removed. This option is not needed
at the user level and is planned to be replaced by the regional indexing used in pileup_cells().
related to #72
FilterParam
option to exclude multi-allelic sitesreport_multiallelic
, or to exclude reporting a variant in the Var assay based on allelic frequency (min_allelic_freq
). The two parameters, if used in combination, will exclude multiallelic sites with high primary and secondary variant allele frequencies.filterParam
argument inpileup_sites
andpileup_cells
toparam
for simplicity.min_nucleotide_depth
tomin_depth
min_read_bqual
toread_bqual
bam_flags
parameters toFilterParams
classbedindex
parameter forpileup_sites
has been removed. This option is not needed at the user level and is planned to be replaced by the regional indexing used inpileup_cells()
.