Index

A

aggregate() (in module amplimap.coverage) align_and_find_cigar() (in module amplimap.naive_mapper) amplimap.common (module) amplimap.coverage (module) amplimap.merge_folders (module) amplimap.naive_mapper (module) amplimap.parse_reads (module) amplimap.pileup (module)

amplimap.reader (module) amplimap.run (module) amplimap.simulate (module) amplimap.stats_alignment (module) amplimap.variants (module) AMPLIMAP_CONFIG AmplimapNoAlignment AmplimapReaderException

C

calculate_del_score() (in module amplimap.variants) check_config_keys() (in module amplimap.run)

compare_config_dicts() (in module amplimap.run) create_bam() (in module amplimap.naive_mapper)

E

environment variable AMPLIMAP_CONFIG

F

find_cigar_for_alignment() (in module amplimap.naive_mapper) find_closest_exon() (in module amplimap.variants) find_umi_groups() (in module amplimap.common)

fraction_10x_coverage() (in module amplimap.coverage) fraction_30x_coverage() (in module amplimap.coverage) fraction_zero_coverage() (in module amplimap.coverage)

G

get_al_mate_starts() (in module amplimap.pileup) get_code_versions() (in module amplimap.reader)

get_file_hashes() (in module amplimap.reader) get_group_consensus() (in module amplimap.pileup) get_pileup_row() (in module amplimap.pileup)

L

load_gene_exons() (in module amplimap.variants)

M

main() (in module amplimap.run) make_extended_read_name() (in module amplimap.common) make_summary() (in module amplimap.variants) make_summary_condensed() (in module amplimap.variants)

make_summary_dataframe() (in module amplimap.variants) make_trimmed_read() (in module amplimap.parse_reads) merge_probes_by_id() (in module amplimap.reader) merge_variants_from_annovar() (in module amplimap.variants) merge_variants_unannotated() (in module amplimap.variants)

P

parse_extended_read_name() (in module amplimap.common) parse_read_pairs() (in module amplimap.parse_reads) PileupGroupFilterException PileupRowFilterException process_file() (in module amplimap.coverage) (in module amplimap.stats_alignment)

process_pileup_base() (in module amplimap.pileup) process_pileup_read() (in module amplimap.pileup) process_pileup_row() (in module amplimap.pileup) process_probe_design() (in module amplimap.reader)

Q

quality_trim_read() (in module amplimap.parse_reads)

R

read_and_convert_heatseq_probes() (in module amplimap.reader) read_and_convert_mipgen_probes() (in module amplimap.reader) read_config_file() (in module amplimap.run) read_new_probe_design() (in module amplimap.reader)

read_sample_info() (in module amplimap.reader) read_snps_txt() (in module amplimap.reader) read_targets() (in module amplimap.reader) record_read_in_group() (in module amplimap.pileup)

W

write_targets_bed() (in module amplimap.reader)