mSigSpectra-package	mSigSpectra-package
add_seq_context	add_seq_context
add_transcript_strand	add_transcript_strand
all.abundance	all.abundance
annotate_id_vcf	annotate_id_vcf
annotate_sbs_or_dbs_vcf	annotate_sbs_or_dbs_vcf
annot_vcf_to_476_catalog	annot_vcf_to_476_catalog
annot_vcf_to_83_catalog	annot_vcf_to_83_catalog
annot_vcf_to_89_catalog	annot_vcf_to_89_catalog
as_catalog	as_catalog
catalog_attrs	catalog_attrs
catalog_row_order	catalog_row_order
categorize_1_justified_indel	categorize_1_justified_indel
cbind_catalogs	cbind_catalogs
change_476_type_ids_to_open_intervals	change_476_type_ids_to_open_intervals
change_89_type_ids_to_open_intervals	change_89_type_ids_to_open_intervals
check_and_fix_chrom_names	check_and_fix_chrom_names
check_and_fix_chrom_names_for_trans_ranges	check_and_fix_chrom_names_for_trans_ranges
check_and_remove_discarded_variants	check_and_remove_discarded_variants
check_and_reorder_rownames	check_and_reorder_rownames
collapse_catalog	collapse_catalog
infer_abundance	infer_abundance
infer_catalog_type	infer_catalog_type
infer_ref_genome_name	infer_ref_genome_name
infer_trans_ranges	infer_trans_ranges
is_catalog	is_catalog
is_grch37	is_grch37
is_grch38	is_grch38
is_grcm38	is_grcm38
justify_id_vcf	justify_id_vcf
justify_indel	justify_indel
justify_indels_in_id_vcf_with_contexts	justify_indels_in_id_vcf_with_contexts
lcprefix_fast	lcprefix_fast
mSigSpectra	mSigSpectra-package
normalize_genome_arg	normalize_genome_arg
pyr_penta	pyr_penta
quick_check_vcf	quick_check_vcf
read_catalog	read_catalog
read_transcript_ranges	read_transcript_ranges
read_vcf	read_vcf
read_vcfs	read_vcfs
remove_rows_with_duplicated_chrom_and_pos	remove_rows_with_duplicated_chrom_and_pos
remove_rows_with_pound_sign	remove_rows_with_pound_sign
revc_dbs144	revc_dbs144
revc_sbs96	revc_sbs96
segment_simple_cpp	segment_simple_cpp
seg_simple	seg_simple
select_variants_by_chrom_name	select_variants_by_chrom_name
split_vcf	split_vcf
standard_chrom_name	standard_chrom_name
standard_chrom_name_new	standard_chrom_name_new
stop_if_counts_or_density_illegal	stop_if_counts_or_density_illegal
stop_if_region_illegal	stop_if_region_illegal
stop_if_transcribed_region_illegal	stop_if_transcribed_region_illegal
subset_catalog	subset_catalog
trans.ranges	trans.ranges
trans.ranges.GRCh37	trans.ranges
trans.ranges.GRCh38	trans.ranges
trans.ranges.GRCm38	trans.ranges
transform_catalog	transform_catalog
vcf_to_dbs_catalog	vcf_to_dbs_catalog
vcf_to_id_catalog	vcf_to_id_catalog
vcf_to_sbs_catalog	vcf_to_sbs_catalog
write_catalog	write_catalog
