Index

Symbols

--actions <actions> ccanalyser-alignments-annotate command line option --annotations <annotations> ccanalyser-alignments-filter command line option --bam <bam> ccanalyser-alignments-filter command line option --bed_files <bed_files> ccanalyser-alignments-annotate command line option --binsize <binsize> ccanalyser-reporters-pileup command line option --binsizes <binsizes> ccanalyser-reporters-store-bins command line option --buffer <buffer> ccanalyser-alignments-deduplicate-identify command line option ccanalyser-alignments-deduplicate-remove command line option --capture_name <capture_name> ccanalyser-reporters-differential command line option ccanalyser-reporters-store-fragments command line option --capture_names <capture_names> ccanalyser-reporters-pileup command line option ccanalyser-reporters-plot command line option --capture_viewpoints <capture_viewpoints> ccanalyser-reporters-differential command line option ccanalyser-reporters-store-fragments command line option --cmap <cmap> ccanalyser-reporters-plot command line option --compression_level <compression_level> ccanalyser-fastq-deduplicate-remove command line option ccanalyser-fastq-digest command line option ccanalyser-fastq-split command line option --conversion_tables <conversion_tables> ccanalyser-reporters-store-bins command line option --coordinates <coordinates> ccanalyser-reporters-plot command line option --custom_filtering <custom_filtering> ccanalyser-alignments-filter command line option --dense ccanalyser-reporters-pileup command line option --design_matrix <design_matrix> ccanalyser-reporters-differential command line option --duplicated_ids <duplicated_ids> ccanalyser-alignments-deduplicate-remove command line option ccanalyser-fastq-deduplicate-remove command line option --duplicates <duplicates> ccanalyser-alignments-annotate command line option --fragment_map <fragment_map> ccanalyser-reporters-store-fragments command line option --genome <genome> ccanalyser-reporters-store-fragments command line option --grouping_col <grouping_col> ccanalyser-reporters-differential command line option --gzip ccanalyser-alignments-filter command line option ccanalyser-fastq-deduplicate-remove command line option ccanalyser-fastq-split command line option ccanalyser-reporters-pileup command line option --help ccanalyser-pipeline command line option --invalid_bed_action <invalid_bed_action> ccanalyser-alignments-annotate command line option --keep_cutsite <keep_cutsite> ccanalyser-fastq-digest command line option --logfile <logfile> ccanalyser-genome-digest command line option --method <method> ccanalyser-fastq-split command line option --minimum_slice_length <minimum_slice_length> ccanalyser-fastq-digest command line option --mode <mode> ccanalyser-fastq-digest command line option --n_cores <n_cores> ccanalyser-alignments-annotate command line option ccanalyser-fastq-digest command line option ccanalyser-reporters-store-bins command line option --n_reads <n_reads> ccanalyser-fastq-split command line option --names <names> ccanalyser-alignments-annotate command line option --no-gzip ccanalyser-alignments-filter command line option ccanalyser-fastq-deduplicate-remove command line option ccanalyser-fastq-split command line option --normalisation <normalisation> ccanalyser-reporters-plot command line option --normalise ccanalyser-reporters-pileup command line option ccanalyser-reporters-store-bins command line option --output <output> ccanalyser-alignments-annotate command line option ccanalyser-alignments-deduplicate-identify command line option ccanalyser-alignments-deduplicate-remove command line option ccanalyser-fastq-deduplicate-identify command line option ccanalyser-fastq-deduplicate-parse command line option ccanalyser-reporters-count command line option ccanalyser-reporters-store-bins command line option ccanalyser-reporters-store-fragments command line option ccanalyser-reporters-store-merge command line option --output_file <output_file> ccanalyser-fastq-digest command line option ccanalyser-genome-digest command line option --output_prefix <output_prefix> ccanalyser-alignments-filter command line option ccanalyser-fastq-deduplicate-remove command line option ccanalyser-fastq-split command line option ccanalyser-reporters-differential command line option ccanalyser-reporters-pileup command line option ccanalyser-reporters-plot command line option --overlap_fraction <overlap_fraction> ccanalyser-reporters-store-bins command line option --overlap_fractions <overlap_fractions> ccanalyser-alignments-annotate command line option --read_buffer <read_buffer> ccanalyser-fastq-deduplicate-parse command line option ccanalyser-fastq-deduplicate-remove command line option ccanalyser-fastq-digest command line option

--read_type <read_type> ccanalyser-alignments-deduplicate-identify command line option ccanalyser-alignments-deduplicate-remove command line option ccanalyser-alignments-filter command line option --recognition_site <recognition_site> ccanalyser-genome-digest command line option --remove_capture ccanalyser-reporters-count command line option ccanalyser-reporters-plot command line option --remove_cutsite <remove_cutsite> ccanalyser-genome-digest command line option --remove_exclusions ccanalyser-reporters-count command line option --resolution <resolution> ccanalyser-reporters-plot command line option --restriction_enzyme <restriction_enzyme> ccanalyser-fastq-digest command line option --sample_name <sample_name> ccanalyser-alignments-deduplicate-remove command line option ccanalyser-alignments-filter command line option ccanalyser-fastq-deduplicate-remove command line option ccanalyser-fastq-digest command line option --scale_factor <scale_factor> ccanalyser-reporters-pileup command line option ccanalyser-reporters-store-bins command line option --sort ccanalyser-genome-digest command line option --sparse ccanalyser-reporters-pileup command line option --stats_prefix <stats_prefix> ccanalyser-alignments-deduplicate-remove command line option ccanalyser-alignments-filter command line option ccanalyser-fastq-deduplicate-remove command line option ccanalyser-fastq-digest command line option --subsample <subsample> ccanalyser-reporters-count command line option --suffix <suffix> ccanalyser-reporters-store-fragments command line option --threshold_count <threshold_count> ccanalyser-reporters-differential command line option --threshold_mean <threshold_mean> ccanalyser-reporters-differential command line option --threshold_q <threshold_q> ccanalyser-reporters-differential command line option --version ccanalyser command line option ccanalyser-pipeline command line option --vmax <vmax> ccanalyser-reporters-plot command line option --vmin <vmin> ccanalyser-reporters-plot command line option -a ccanalyser-alignments-annotate command line option ccanalyser-alignments-filter command line option -b ccanalyser-alignments-annotate command line option ccanalyser-alignments-filter command line option ccanalyser-reporters-store-bins command line option -c ccanalyser-reporters-differential command line option ccanalyser-reporters-plot command line option ccanalyser-reporters-store-fragments command line option -d ccanalyser-alignments-deduplicate-remove command line option ccanalyser-fastq-deduplicate-remove command line option -f ccanalyser-alignments-annotate command line option ccanalyser-reporters-store-fragments command line option -g ccanalyser-reporters-store-fragments command line option -h ccanalyser-pipeline command line option -l ccanalyser-genome-digest command line option -m ccanalyser-fastq-digest command line option ccanalyser-fastq-split command line option -n ccanalyser-alignments-annotate command line option ccanalyser-fastq-split command line option ccanalyser-reporters-differential command line option ccanalyser-reporters-pileup command line option ccanalyser-reporters-plot command line option ccanalyser-reporters-store-fragments command line option -o ccanalyser-alignments-annotate command line option ccanalyser-alignments-deduplicate-identify command line option ccanalyser-alignments-deduplicate-remove command line option ccanalyser-alignments-filter command line option ccanalyser-fastq-deduplicate-identify command line option ccanalyser-fastq-deduplicate-parse command line option ccanalyser-fastq-deduplicate-remove command line option ccanalyser-fastq-digest command line option ccanalyser-fastq-split command line option ccanalyser-genome-digest command line option ccanalyser-reporters-count command line option ccanalyser-reporters-differential command line option ccanalyser-reporters-pileup command line option ccanalyser-reporters-plot command line option ccanalyser-reporters-store-bins command line option ccanalyser-reporters-store-fragments command line option ccanalyser-reporters-store-merge command line option -p ccanalyser-alignments-annotate command line option ccanalyser-fastq-digest command line option ccanalyser-reporters-store-bins command line option -r ccanalyser-fastq-digest command line option ccanalyser-genome-digest command line option ccanalyser-reporters-plot command line option

A

alignments_deduplicate_collate() (in module ccanalyser.pipeline.pipeline) alignments_deduplicate_fragments() (in module ccanalyser.pipeline.pipeline) alignments_deduplicate_slices() (in module ccanalyser.pipeline.pipeline) alignments_filter() (in module ccanalyser.pipeline.pipeline) alignments_index() (in module ccanalyser.pipeline.pipeline)

alignments_merge() (in module ccanalyser.pipeline.pipeline) annotate() (in module ccanalyser.cli.alignments_annotate) annotate_alignments() (in module ccanalyser.pipeline.pipeline) annotate_make_exclusion_bed() (in module ccanalyser.pipeline.pipeline) annotate_sort_blacklist() (in module ccanalyser.pipeline.pipeline) annotate_sort_viewpoints() (in module ccanalyser.pipeline.pipeline)

B

bed1 (ccanalyser.tools.annotate.BedIntersection attribute) bed2 (ccanalyser.tools.annotate.BedIntersection attribute) bed_has_duplicate_names() (in module ccanalyser.utils) bed_has_name() (in module ccanalyser.utils) bedgraph (ccanalyser.tools.pileup.CoolerBedGraph property) bedgraph() (in module ccanalyser.cli.reporters_pileup) BedIntersection (class in ccanalyser.tools.annotate)

bin_conversion_table (ccanalyser.tools.storage.CoolerBinner property) (ccanalyser.tools.storage.GenomicBinner property) binner (ccanalyser.tools.storage.CoolerBinner attribute) bins (ccanalyser.tools.storage.CoolerBinner property) (ccanalyser.tools.storage.GenomicBinner property) bins() (in module ccanalyser.cli.reporters_store) binsize (ccanalyser.tools.storage.CoolerBinner attribute) (ccanalyser.tools.storage.GenomicBinner attribute)

C

capture capture_bins (ccanalyser.tools.storage.CoolerBinner property) capture_name (ccanalyser.tools.pileup.CoolerBedGraph attribute) capture_site_stats (ccanalyser.tools.filter.CCSliceFilter property) captures (ccanalyser.tools.filter.CCSliceFilter property) categorise_tracks() (in module ccanalyser.utils) ccanalyser command line option --version ccanalyser-alignments-annotate command line option --actions <actions> --bed_files <bed_files> --duplicates <duplicates> --invalid_bed_action <invalid_bed_action> --n_cores <n_cores> --names <names> --output <output> --overlap_fractions <overlap_fractions> -a -b -f -n -o -p SLICES ccanalyser-alignments-deduplicate-identify command line option --buffer <buffer> --output <output> --read_type <read_type> -o FRAGMENTS_FN ccanalyser-alignments-deduplicate-remove command line option --buffer <buffer> --duplicated_ids <duplicated_ids> --output <output> --read_type <read_type> --sample_name <sample_name> --stats_prefix <stats_prefix> -d -o SLICES_FN ccanalyser-alignments-filter command line option --annotations <annotations> --bam <bam> --custom_filtering <custom_filtering> --gzip --no-gzip --output_prefix <output_prefix> --read_type <read_type> --sample_name <sample_name> --stats_prefix <stats_prefix> -a -b -o METHOD ccanalyser-fastq-deduplicate-identify command line option --output <output> -o INPUT_FILES ccanalyser-fastq-deduplicate-parse command line option --output <output> --read_buffer <read_buffer> -o INPUT_FILES ccanalyser-fastq-deduplicate-remove command line option --compression_level <compression_level> --duplicated_ids <duplicated_ids> --gzip --no-gzip --output_prefix <output_prefix> --read_buffer <read_buffer> --sample_name <sample_name> --stats_prefix <stats_prefix> -d -o INPUT_FILES ccanalyser-fastq-digest command line option --compression_level <compression_level> --keep_cutsite <keep_cutsite> --minimum_slice_length <minimum_slice_length> --mode <mode> --n_cores <n_cores> --output_file <output_file> --read_buffer <read_buffer> --restriction_enzyme <restriction_enzyme> --sample_name <sample_name> --stats_prefix <stats_prefix> -m -o -p -r INPUT_FASTQ ccanalyser-fastq-split command line option --compression_level <compression_level> --gzip --method <method> --n_reads <n_reads> --no-gzip --output_prefix <output_prefix> -m -n -o INPUT_FILES ccanalyser-genome-digest command line option --logfile <logfile> --output_file <output_file> --recognition_site <recognition_site> --remove_cutsite <remove_cutsite> --sort -l -o -r INPUT_FASTA ccanalyser-pipeline command line option --help --version -h MODE PIPELINE_OPTIONS ccanalyser-reporters-count command line option --output <output> --remove_capture --remove_exclusions --subsample <subsample> -o REPORTERS ccanalyser-reporters-differential command line option --capture_name <capture_name> --capture_viewpoints <capture_viewpoints> --design_matrix <design_matrix> --grouping_col <grouping_col> --output_prefix <output_prefix> --threshold_count <threshold_count> --threshold_mean <threshold_mean> --threshold_q <threshold_q> -c -n -o UNION_BEDGRAPH ccanalyser-reporters-pileup command line option --binsize <binsize> --capture_names <capture_names> --dense --gzip --normalise --output_prefix <output_prefix> --scale_factor <scale_factor> --sparse -n -o COOLER_FN

ccanalyser-reporters-plot command line option --capture_names <capture_names> --cmap <cmap> --coordinates <coordinates> --normalisation <normalisation> --output_prefix <output_prefix> --remove_capture --resolution <resolution> --vmax <vmax> --vmin <vmin> -c -n -o -r COOLER_FN ccanalyser-reporters-store-bins command line option --binsizes <binsizes> --conversion_tables <conversion_tables> --n_cores <n_cores> --normalise --output <output> --overlap_fraction <overlap_fraction> --scale_factor <scale_factor> -b -o -p COOLER_FN ccanalyser-reporters-store-fragments command line option --capture_name <capture_name> --capture_viewpoints <capture_viewpoints> --fragment_map <fragment_map> --genome <genome> --output <output> --suffix <suffix> -c -f -g -n -o COUNTS ccanalyser-reporters-store-merge command line option --output <output> -o COOLERS ccanalyser.cli.alignments_annotate module ccanalyser.cli.alignments_deduplicate module ccanalyser.cli.alignments_filter module ccanalyser.cli.fastq_deduplicate module ccanalyser.cli.fastq_digest module ccanalyser.cli.fastq_split module ccanalyser.cli.genome_digest module ccanalyser.cli.reporters_count module ccanalyser.cli.reporters_differential module ccanalyser.cli.reporters_heatmap module ccanalyser.cli.reporters_pileup module ccanalyser.cli.reporters_store module ccanalyser.cli.tsv_aggregate module ccanalyser.pipeline.pipeline module ccanalyser.tools.annotate module ccanalyser.tools.deduplicate module ccanalyser.tools.digest module ccanalyser.tools.filter module ccanalyser.tools.io module ccanalyser.tools.pileup module ccanalyser.tools.plotting module ccanalyser.tools.statistics module ccanalyser.tools.storage module ccanalyser.utils module CCBedgraph (class in ccanalyser.tools.pileup) CCMatrix (class in ccanalyser.tools.plotting) CCSliceFilter (class in ccanalyser.tools.filter) check_config() (in module ccanalyser.pipeline.pipeline) check_user_supplied_paths() (in module ccanalyser.pipeline.pipeline) chrom (ccanalyser.tools.digest.DigestedChrom attribute) chromsizes (ccanalyser.tools.storage.GenomicBinner attribute) cis_or_trans_stats (ccanalyser.tools.filter.CCSliceFilter property) (ccanalyser.tools.filter.TiledCSliceFilter property) collate_cis_trans_data() (in module ccanalyser.tools.statistics) collate_histogram_data() (in module ccanalyser.tools.statistics) collate_read_data() (in module ccanalyser.tools.statistics) collate_slice_data() (in module ccanalyser.tools.statistics) collate_statistics() (in module ccanalyser.cli.fastq_digest) concat_tsvs() (in module ccanalyser.cli.tsv_aggregate) convert_bed_to_dataframe() (in module ccanalyser.utils) convert_interval_to_coords() (in module ccanalyser.utils) convert_to_bedtool() (in module ccanalyser.utils) cooler (ccanalyser.tools.pileup.CoolerBedGraph attribute) (ccanalyser.tools.storage.CoolerBinner attribute) COOLER_FN ccanalyser-reporters-pileup command line option ccanalyser-reporters-plot command line option ccanalyser-reporters-store-bins command line option CoolerBedGraph (class in ccanalyser.tools.pileup) CoolerBedGraphWindowed (class in ccanalyser.tools.pileup) CoolerBinner (class in ccanalyser.tools.storage) COOLERS ccanalyser-reporters-store-merge command line option coordinates (ccanalyser.tools.pileup.CCBedgraph property) count() (in module ccanalyser.cli.reporters_count) count_re_site_combinations() (in module ccanalyser.cli.reporters_count) COUNTS ccanalyser-reporters-store-fragments command line option create_cooler_cc() (in module ccanalyser.tools.storage) cycle_argument() (in module ccanalyser.cli.alignments_annotate)

D

DeduplicationStatistics (class in ccanalyser.tools.statistics) df (ccanalyser.tools.statistics.DeduplicationStatistics property) differential() (in module ccanalyser.cli.reporters_differential) digest() (in module ccanalyser.cli.fastq_digest) (in module ccanalyser.cli.genome_digest)

DigestedChrom (class in ccanalyser.tools.digest) DigestedRead (class in ccanalyser.tools.digest) DigestionStats (class in ccanalyser.tools.statistics) duplicated_ids (ccanalyser.tools.deduplicate.ReadDuplicateRemovalProcess attribute)

E

extract_trimming_stats() (in module ccanalyser.tools.statistics)

F

fastq_alignment() (in module ccanalyser.pipeline.pipeline) fastq_digest_combined() (in module ccanalyser.pipeline.pipeline) fastq_digest_non_combined() (in module ccanalyser.pipeline.pipeline) fastq_duplicates_identify() (in module ccanalyser.pipeline.pipeline) fastq_duplicates_parse() (in module ccanalyser.pipeline.pipeline) fastq_duplicates_remove() (in module ccanalyser.pipeline.pipeline) fastq_flash() (in module ccanalyser.pipeline.pipeline) fastq_multiqc() (in module ccanalyser.pipeline.pipeline) fastq_preprocessing() (in module ccanalyser.pipeline.pipeline) fastq_qc() (in module ccanalyser.pipeline.pipeline) fastq_split() (in module ccanalyser.pipeline.pipeline) fastq_trim() (in module ccanalyser.pipeline.pipeline) FastqReaderProcess (class in ccanalyser.tools.io) FastqReadFormatterProcess (class in ccanalyser.tools.io) FastqWriterProcess (class in ccanalyser.tools.io) FastqWriterSplitterProcess (class in ccanalyser.tools.io) filter() (in module ccanalyser.cli.alignments_filter) filter_slices() (ccanalyser.tools.filter.SliceFilter method) filter_stages (ccanalyser.tools.filter.CCSliceFilter attribute) (ccanalyser.tools.filter.SliceFilter attribute) (ccanalyser.tools.filter.TiledCSliceFilter attribute) (ccanalyser.tools.filter.TriCSliceFilter attribute) filter_stats (ccanalyser.tools.filter.CCSliceFilter attribute) (ccanalyser.tools.filter.SliceFilter attribute) (ccanalyser.tools.filter.SliceFilter property) (ccanalyser.tools.filter.TiledCSliceFilter attribute) (ccanalyser.tools.filter.TriCSliceFilter attribute)

filtered (ccanalyser.tools.statistics.DigestionStats attribute) filters (ccanalyser.tools.filter.SliceFilter property) format_coordinates() (in module ccanalyser.utils) format_index_var() (in module ccanalyser.cli.tsv_aggregate) frag_stats (ccanalyser.tools.filter.CCSliceFilter property) fragment fragment_indexes (ccanalyser.tools.digest.DigestedChrom attribute) fragment_min_len (ccanalyser.tools.digest.DigestedChrom attribute) fragment_number_offset (ccanalyser.tools.digest.DigestedChrom attribute) fragments (ccanalyser.tools.digest.DigestedChrom property) (ccanalyser.tools.filter.CCSliceFilter attribute) (ccanalyser.tools.filter.CCSliceFilter property) (ccanalyser.tools.filter.SliceFilter attribute) (ccanalyser.tools.filter.SliceFilter property) (ccanalyser.tools.filter.TiledCSliceFilter attribute) (ccanalyser.tools.filter.TiledCSliceFilter property) (ccanalyser.tools.filter.TriCSliceFilter attribute) (ccanalyser.tools.storage.GenomicBinner attribute) fragments() (in module ccanalyser.cli.reporters_store) FRAGMENTS_FN ccanalyser-alignments-deduplicate-identify command line option full() (in module ccanalyser.pipeline.pipeline)

G

generate_bin_conversion_tables() (in module ccanalyser.pipeline.pipeline) genome_digest() (in module ccanalyser.pipeline.pipeline) GenomicBinner (class in ccanalyser.tools.storage) get_capture_bins() (in module ccanalyser.tools.storage) get_capture_coords() (in module ccanalyser.tools.storage) get_chromosome_from_name() (in module ccanalyser.cli.reporters_differential) get_human_readable_number_of_bp() (in module ccanalyser.utils)

get_matrix() (ccanalyser.tools.plotting.CCMatrix method) get_matrix_normalised() (ccanalyser.tools.plotting.CCMatrix method) get_re_site() (in module ccanalyser.utils) get_recognition_site_indexes() (ccanalyser.tools.digest.DigestedChrom method) (ccanalyser.tools.digest.DigestedRead method) get_timing() (in module ccanalyser.utils) get_unfiltered_slices() (ccanalyser.tools.filter.SliceFilter method)

H

has_slices (ccanalyser.tools.digest.DigestedRead attribute) hash_column() (in module ccanalyser.utils)

hash_seed (ccanalyser.tools.deduplicate.ReadDeduplicationParserProcess attribute) (ccanalyser.tools.deduplicate.ReadDuplicateRemovalProcess attribute) hub_make() (in module ccanalyser.pipeline.pipeline)

I

identify() (in module ccanalyser.cli.alignments_deduplicate) (in module ccanalyser.cli.fastq_deduplicate) identify_differential_interactions() (in module ccanalyser.pipeline.pipeline) INPUT_FASTA ccanalyser-genome-digest command line option INPUT_FASTQ ccanalyser-fastq-digest command line option input_file (ccanalyser.tools.io.FastqReaderProcess attribute) INPUT_FILES ccanalyser-fastq-deduplicate-identify command line option ccanalyser-fastq-deduplicate-parse command line option ccanalyser-fastq-deduplicate-remove command line option ccanalyser-fastq-split command line option

inq (ccanalyser.tools.deduplicate.ReadDeduplicationParserProcess attribute) (ccanalyser.tools.deduplicate.ReadDuplicateRemovalProcess attribute) intersect_bins() (in module ccanalyser.utils) intersection (ccanalyser.tools.annotate.BedIntersection property) intersection_name (ccanalyser.tools.annotate.BedIntersection attribute) invalid_bed_action (ccanalyser.tools.annotate.BedIntersection attribute) invert_dict() (in module ccanalyser.utils) is_compressed() (in module ccanalyser.cli.tsv_aggregate) is_none() (in module ccanalyser.utils) is_off() (in module ccanalyser.utils) is_on() (in module ccanalyser.utils) is_valid_bed() (in module ccanalyser.utils)

J

join_tsvs() (in module ccanalyser.cli.tsv_aggregate)

L

link_bins() (in module ccanalyser.tools.storage)

load_json() (in module ccanalyser.utils) load_tsv() (in module ccanalyser.cli.tsv_aggregate)

M

main() (in module ccanalyser.cli.tsv_aggregate) merge() (in module ccanalyser.cli.reporters_store) merge_annotations() (in module ccanalyser.cli.alignments_filter) merged_captures_and_reporters (ccanalyser.tools.filter.CCSliceFilter property) METHOD ccanalyser-alignments-filter command line option min_frac (ccanalyser.tools.annotate.BedIntersection attribute) min_overlap (ccanalyser.tools.storage.GenomicBinner attribute) min_slice_len (ccanalyser.tools.digest.DigestedRead attribute) MODE ccanalyser-pipeline command line option modify_pipeline_params_dict() (in module ccanalyser.pipeline.pipeline) module ccanalyser.cli.alignments_annotate ccanalyser.cli.alignments_deduplicate ccanalyser.cli.alignments_filter ccanalyser.cli.fastq_deduplicate ccanalyser.cli.fastq_digest ccanalyser.cli.fastq_split ccanalyser.cli.genome_digest ccanalyser.cli.reporters_count ccanalyser.cli.reporters_differential ccanalyser.cli.reporters_heatmap ccanalyser.cli.reporters_pileup ccanalyser.cli.reporters_store ccanalyser.cli.tsv_aggregate ccanalyser.pipeline.pipeline ccanalyser.tools.annotate ccanalyser.tools.deduplicate ccanalyser.tools.digest ccanalyser.tools.filter ccanalyser.tools.io ccanalyser.tools.pileup ccanalyser.tools.plotting ccanalyser.tools.statistics ccanalyser.tools.storage ccanalyser.utils

N

n_cis_interactions (ccanalyser.tools.storage.CoolerBinner attribute) n_cores (ccanalyser.tools.annotate.BedIntersection attribute) (ccanalyser.tools.storage.CoolerBinner attribute) (ccanalyser.tools.storage.GenomicBinner attribute)

n_subproceses (ccanalyser.tools.io.FastqReaderProcess attribute) normalise_bedgraph() (ccanalyser.tools.pileup.CoolerBedGraph method) (ccanalyser.tools.pileup.CoolerBedGraphWindowed method) normalise_pixels() (ccanalyser.tools.storage.CoolerBinner method)

O

only_cis (ccanalyser.tools.pileup.CoolerBedGraph attribute) outq (ccanalyser.tools.deduplicate.ReadDeduplicationParserProcess attribute) (ccanalyser.tools.deduplicate.ReadDuplicateRemovalProcess attribute) (ccanalyser.tools.io.FastqReaderProcess attribute)

P

parse() (in module ccanalyser.cli.fastq_deduplicate) parse_alignment() (in module ccanalyser.tools.io) parse_bam() (in module ccanalyser.tools.io) parse_chromosomes() (in module ccanalyser.cli.genome_digest) pipeline_make_report() (in module ccanalyser.pipeline.pipeline) pipeline_merge_stats() (in module ccanalyser.pipeline.pipeline) PIPELINE_OPTIONS ccanalyser-pipeline command line option

pixel_conversion_table (ccanalyser.tools.storage.CoolerBinner property) pixels (ccanalyser.tools.storage.CoolerBinner property) plot() (in module ccanalyser.cli.reporters_heatmap) plot_matrix() (in module ccanalyser.cli.reporters_heatmap) post_annotation() (in module ccanalyser.pipeline.pipeline) post_ccanalyser_analysis() (in module ccanalyser.pipeline.pipeline) pre_annotation() (in module ccanalyser.pipeline.pipeline) PysamFakeEntry (class in ccanalyser.utils)

R

read (ccanalyser.tools.digest.DigestedRead attribute) read_buffer (ccanalyser.tools.io.FastqReaderProcess attribute) read_counter (ccanalyser.tools.io.FastqReaderProcess attribute) read_number (ccanalyser.tools.statistics.DigestionStats attribute) read_stats (ccanalyser.tools.filter.CCSliceFilter attribute) (ccanalyser.tools.filter.SliceFilter attribute) (ccanalyser.tools.filter.SliceFilter property) (ccanalyser.tools.filter.TiledCSliceFilter attribute) (ccanalyser.tools.filter.TriCSliceFilter attribute) read_type (ccanalyser.tools.statistics.DigestionStats attribute) ReadDeduplicationParserProcess (class in ccanalyser.tools.deduplicate) ReadDigestionProcess (class in ccanalyser.tools.digest) ReadDuplicateRemovalProcess (class in ccanalyser.tools.deduplicate) reads_total (ccanalyser.tools.deduplicate.ReadDuplicateRemovalProcess attribute) reads_unique (ccanalyser.tools.deduplicate.ReadDuplicateRemovalProcess attribute) recognition_len (ccanalyser.tools.digest.DigestedChrom attribute) (ccanalyser.tools.digest.DigestedRead attribute) recognition_seq (ccanalyser.tools.digest.DigestedChrom attribute), [1] (ccanalyser.tools.digest.DigestedRead attribute), [1] remove() (in module ccanalyser.cli.alignments_deduplicate) (in module ccanalyser.cli.fastq_deduplicate) remove_blacklisted_slices() (ccanalyser.tools.filter.SliceFilter method) remove_dual_capture_fragments() (ccanalyser.tools.filter.TiledCSliceFilter method) remove_duplicate_re_frags() (ccanalyser.tools.filter.SliceFilter method) remove_duplicate_slices() (ccanalyser.tools.filter.SliceFilter method) remove_duplicate_slices_pe() (ccanalyser.tools.filter.SliceFilter method) remove_duplicates_from_bed() (in module ccanalyser.cli.alignments_annotate) remove_excluded_slices() (ccanalyser.tools.filter.SliceFilter method) remove_multi_capture_fragments() (ccanalyser.tools.filter.CCSliceFilter method) remove_multicapture_reporters() (ccanalyser.tools.filter.CCSliceFilter method) remove_non_capture_fragments() (ccanalyser.tools.filter.TiledCSliceFilter method) remove_non_reporter_fragments() (ccanalyser.tools.filter.CCSliceFilter method) remove_orphan_slices() (ccanalyser.tools.filter.SliceFilter method) remove_slices_outside_capture() (ccanalyser.tools.filter.TiledCSliceFilter method)

remove_slices_with_one_reporter() (ccanalyser.tools.filter.TriCSliceFilter method) remove_slices_without_re_frag_assigned() (ccanalyser.tools.filter.SliceFilter method) remove_unmapped_slices() (ccanalyser.tools.filter.SliceFilter method) replace_na() (in module ccanalyser.cli.tsv_aggregate) reporter REPORTERS ccanalyser-reporters-count command line option reporters (ccanalyser.tools.filter.CCSliceFilter attribute) (ccanalyser.tools.filter.CCSliceFilter property) (ccanalyser.tools.filter.SliceFilter attribute) (ccanalyser.tools.filter.SliceFilter property) (ccanalyser.tools.filter.TiledCSliceFilter attribute) (ccanalyser.tools.filter.TriCSliceFilter attribute) (ccanalyser.tools.pileup.CoolerBedGraph property) reporters_binned (ccanalyser.tools.pileup.CoolerBedGraphWindowed property) reporters_collate() (in module ccanalyser.pipeline.pipeline) reporters_count() (in module ccanalyser.pipeline.pipeline) reporters_make_bedgraph() (in module ccanalyser.pipeline.pipeline) reporters_make_bedgraph_normalised() (in module ccanalyser.pipeline.pipeline) reporters_make_bigwig() (in module ccanalyser.pipeline.pipeline) reporters_make_comparison_bedgraph() (in module ccanalyser.pipeline.pipeline) reporters_make_union_bedgraph() (in module ccanalyser.pipeline.pipeline) reporters_plot_heatmap() (in module ccanalyser.pipeline.pipeline) reporters_store_binned() (in module ccanalyser.pipeline.pipeline) reporters_store_merged() (in module ccanalyser.pipeline.pipeline) reporters_store_restriction_fragment() (in module ccanalyser.pipeline.pipeline) run() (ccanalyser.tools.deduplicate.ReadDeduplicationParserProcess method) (ccanalyser.tools.deduplicate.ReadDuplicateRemovalProcess method) (ccanalyser.tools.digest.ReadDigestionProcess method) (ccanalyser.tools.io.FastqReaderProcess method) (ccanalyser.tools.io.FastqReadFormatterProcess method) (ccanalyser.tools.io.FastqWriterProcess method) (ccanalyser.tools.io.FastqWriterSplitterProcess method) run_unix_split() (in module ccanalyser.cli.fastq_split)

S

save_hash_dict_path (ccanalyser.tools.deduplicate.ReadDeduplicationParserProcess attribute) scale_factor (ccanalyser.tools.storage.CoolerBinner attribute) score (ccanalyser.tools.pileup.CCBedgraph property) set_up_chromsizes() (in module ccanalyser.pipeline.pipeline) slice slice_indexes (ccanalyser.tools.digest.DigestedRead attribute) slice_number_offset (ccanalyser.tools.digest.DigestedRead attribute) slice_stats (ccanalyser.tools.filter.CCSliceFilter attribute) (ccanalyser.tools.filter.CCSliceFilter property) (ccanalyser.tools.filter.SliceFilter attribute) (ccanalyser.tools.filter.SliceFilter property) (ccanalyser.tools.filter.TiledCSliceFilter attribute) (ccanalyser.tools.filter.TiledCSliceFilter property) (ccanalyser.tools.filter.TriCSliceFilter attribute) SliceFilter (class in ccanalyser.tools.filter) SLICES ccanalyser-alignments-annotate command line option

slices (ccanalyser.tools.digest.DigestedRead attribute) (ccanalyser.tools.filter.CCSliceFilter attribute) (ccanalyser.tools.filter.SliceFilter attribute) (ccanalyser.tools.filter.TiledCSliceFilter attribute) (ccanalyser.tools.filter.TriCSliceFilter attribute) SLICES_FN ccanalyser-alignments-deduplicate-remove command line option sparse (ccanalyser.tools.pileup.CoolerBedGraph attribute) split() (in module ccanalyser.cli.fastq_split) split_intervals_on_chrom() (in module ccanalyser.utils) statq (ccanalyser.tools.deduplicate.ReadDuplicateRemovalProcess attribute) (ccanalyser.tools.io.FastqReaderProcess attribute) stats_alignment_filtering_collate() (in module ccanalyser.pipeline.pipeline) stats_deduplication_collate() (in module ccanalyser.pipeline.pipeline) stats_digestion_collate() (in module ccanalyser.pipeline.pipeline) stats_trim_collate() (in module ccanalyser.pipeline.pipeline)

T

TiledCSliceFilter (class in ccanalyser.tools.filter) to_bedtool() (ccanalyser.tools.pileup.CCBedgraph method) to_cooler() (ccanalyser.tools.storage.CoolerBinner method)

to_file() (ccanalyser.tools.pileup.CCBedgraph method) (ccanalyser.tools.pileup.CoolerBedGraph method) TriCSliceFilter (class in ccanalyser.tools.filter)

U

unfiltered (ccanalyser.tools.statistics.DigestionStats attribute)

UNION_BEDGRAPH ccanalyser-reporters-differential command line option

V

viewpoints_to_bigbed() (in module ccanalyser.pipeline.pipeline)