NAMESPACE

# Generated by roxygen2: do not edit by hand

export(calculate_strand_bias_pval_vaf_and_dp_parallel)
export(calculate_strand_bias_pval_vaf_and_dp_parallel_each_indel)
export(convert_cigar_to_verbose_string)
export(filter_and_annotate_calls)
export(getIndelCoverage)
export(getVaf)
export(get_primary_chroms)
export(refine_cigar_string)
export(run_algo_all_reads_each_bam_region_with_simple_indel_padding)
export(run_algo_on_one_read_explicit_args_with_simple_indel_padding)
export(run_indelfindr)
export(seq_with_uneven_last)
export(translate_cigar_index_to_ref_and_query_algo_dev_sliding)
export(translate_cigar_index_to_ref_and_query_v2)
export(translate_cigar_index_to_ref_and_query_v2_with_simple_indel_padding)
export(translate_cigar_index_to_ref_and_query_whole_read)
export(unexplode_cigar_string)
export(write.vcf)
import(dplyr)
import(utils)
importFrom(stringr,str_split)