fRagmentomics-package	fRagmentomics-package
apply_bcftools_norm	apply_bcftools_norm
check_bcftools_is_installed	check_bcftools_is_installed
check_parameters	check_parameters
compare_read_to_ref_wt_and_mut	compare_read_to_ref_wt_and_mut
extract_fragment_features	extract_fragment_features
fRagmentomics	fRagmentomics-package
get_base_basq_from_read_at_pos	get_base_basq_from_read_at_pos
get_base_basq_mstat_from_read	get_base_basq_mstat_from_read
get_fragment_bases_5p_3p	get_fragment_bases_5p_3p
get_fragment_bases_5p_3p_softclip	get_fragment_bases_5p_3p_softclip
get_fragment_size	get_fragment_size
get_index_aligning_with_pos	get_index_aligning_with_pos
get_mutation_status_of_fragment	get_mutation_status_of_fragment
get_mutation_status_of_read	get_mutation_status_of_read
get_number_of_common_first_char	get_number_of_common_first_char
normalize_mut	normalize_mut
normalize_to_vcf_rep	normalize_to_vcf_rep
plot_freq_barplot	plot_freq_barplot
plot_ggseqlogo_meme	plot_ggseqlogo_meme
plot_motif_barplot	plot_motif_barplot
plot_size_distribution	plot_size_distribution
read_bam	read_bam
read_mut	read_mut
remove_bad_mut	remove_bad_mut
run_fRagmentomics	run_fRagmentomics
search_for_indel_in_cigar	search_for_indel_in_cigar
