Pore-C Tools
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Command Line Interface
Schemas
API
pore_c package
pore_c.analyses package
pore_c.analyses.alignments module
pore_c.analyses.contacts module
pore_c.analyses.reads module
pore_c.analyses.reference module
pore_c.catalogs module
pore_c.cli module
pore_c.cli_utils module
pore_c.config module
pore_c.datasources module
pore_c.io module
pore_c.model module
pore_c.settings module
pore_c.utils module
Development
GitHub Repository
GitHub Snakemake Pipeline
repository
Index
A
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B
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C
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D
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E
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F
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G
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H
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I
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K
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L
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M
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N
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O
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P
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R
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S
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T
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U
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V
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W
A
align1_align_base_qscore (pore_c.model.PoreCContactRecord attribute)
align1_align_idx (pore_c.model.PoreCContactRecord attribute)
align1_align_score (pore_c.model.PoreCContactRecord attribute)
align1_chrom (pore_c.model.PoreCContactRecord attribute)
align1_end (pore_c.model.PoreCContactRecord attribute)
align1_fragment_end (pore_c.model.PoreCContactRecord attribute)
align1_fragment_id (pore_c.model.PoreCContactRecord attribute)
align1_fragment_start (pore_c.model.PoreCContactRecord attribute)
align1_haplotype (pore_c.model.PoreCContactRecord attribute)
align1_mapping_quality (pore_c.model.PoreCContactRecord attribute)
align1_phase_qual (pore_c.model.PoreCContactRecord attribute)
align1_phase_set (pore_c.model.PoreCContactRecord attribute)
align1_start (pore_c.model.PoreCContactRecord attribute)
align1_strand (pore_c.model.PoreCContactRecord attribute)
align2_align_base_qscore (pore_c.model.PoreCContactRecord attribute)
align2_align_idx (pore_c.model.PoreCContactRecord attribute)
align2_align_score (pore_c.model.PoreCContactRecord attribute)
align2_chrom (pore_c.model.PoreCContactRecord attribute)
align2_end (pore_c.model.PoreCContactRecord attribute)
align2_fragment_end (pore_c.model.PoreCContactRecord attribute)
align2_fragment_id (pore_c.model.PoreCContactRecord attribute)
align2_fragment_start (pore_c.model.PoreCContactRecord attribute)
align2_haplotype (pore_c.model.PoreCContactRecord attribute)
align2_mapping_quality (pore_c.model.PoreCContactRecord attribute)
align2_phase_set (pore_c.model.PoreCContactRecord attribute)
align2_start (pore_c.model.PoreCContactRecord attribute)
align2_strand (pore_c.model.PoreCContactRecord attribute)
align_base_qscore (pore_c.model.AlignmentRecord attribute)
align_idx (pore_c.model.AlignmentRecord attribute)
align_score (pore_c.model.AlignmentRecord attribute)
align_type (pore_c.model.AlignmentRecord attribute)
AlignmentFilterReason (class in pore_c.model)
AlignmentRecord (class in pore_c.model)
AlignmentRecord.Config (class in pore_c.model)
AlignmentType (class in pore_c.model)
apply_per_read_filters() (in module pore_c.analyses.alignments)
assign_fragment() (in module pore_c.analyses.alignments)
assign_fragments() (in module pore_c.analyses.alignments)
B
BatchedFastqWriter (class in pore_c.io)
bwa_gapscore() (in module pore_c.analyses.alignments)
C
chrom (pore_c.model.AlignmentRecord attribute)
(pore_c.model.FragmentRecord attribute)
chrom_dtype() (pore_c.catalogs.ReferenceGenomeCatalog property)
chrom_lengths() (pore_c.catalogs.ReferenceGenomeCatalog property)
chrom_order() (pore_c.catalogs.ReferenceGenomeCatalog property)
close() (pore_c.io.BatchedFastqWriter method)
(pore_c.io.FastqWriter method)
(pore_c.io.TableWriter method)
(pore_c.utils.DataFrameProgress method)
command_line_json() (in module pore_c.cli_utils)
contact_fragment_adjacent (pore_c.model.PoreCContactRecord attribute)
contact_fragment_distance (pore_c.model.PoreCContactRecord attribute)
contact_genome_distance (pore_c.model.PoreCContactRecord attribute)
contact_is_cis (pore_c.model.PoreCContactRecord attribute)
contact_is_direct (pore_c.model.PoreCContactRecord attribute)
contact_read_distance (pore_c.model.PoreCContactRecord attribute)
container (pore_c.datasources.Fastq attribute)
(pore_c.datasources.IndexedFasta attribute)
create() (pore_c.catalogs.RawReadCatalog class method)
(pore_c.catalogs.ReferenceGenomeCatalog class method)
(pore_c.catalogs.VirtualDigestCatalog class method)
create_align_graph() (in module pore_c.analyses.alignments)
create_fragment_dataframe() (in module pore_c.analyses.reference)
create_regex() (in module pore_c.analyses.reference)
create_virtual_digest() (in module pore_c.analyses.reference)
D
DaskExecEnv (class in pore_c.utils)
DataFrameProgress (class in pore_c.utils)
description (pore_c.catalogs.RawReadCatalog attribute)
(pore_c.catalogs.ReferenceGenomeCatalog attribute)
(pore_c.catalogs.VirtualDigestCatalog attribute)
(pore_c.datasources.Fastq attribute)
(pore_c.datasources.IndexedFasta attribute)
direct_cis_contacts (pore_c.model.PoreCConcatemerRecord attribute)
direct_contacts (pore_c.model.PoreCConcatemerRecord attribute)
direct_long_range_cis_contacts (pore_c.model.PoreCConcatemerRecord attribute)
direct_short_range_cis_contacts (pore_c.model.PoreCConcatemerRecord attribute)
direct_trans_contacts (pore_c.model.PoreCConcatemerRecord attribute)
E
end (pore_c.model.AlignmentRecord attribute)
(pore_c.model.FragmentRecord attribute)
expand_output_prefix() (in module pore_c.cli_utils)
export_to_cooler() (in module pore_c.analyses.contacts)
export_to_merged_no_dups() (in module pore_c.analyses.contacts)
export_to_paired_end_fastq() (in module pore_c.analyses.contacts)
export_to_pairs() (in module pore_c.analyses.contacts)
export_to_salsa_bed() (in module pore_c.analyses.contacts)
ExportDependentOption (class in pore_c.cli_utils)
F
Fastq (class in pore_c.datasources)
FastqWriter (class in pore_c.io)
fields (pore_c.model.AlignmentRecord.Config attribute)
(pore_c.model.FragmentRecord.Config attribute)
(pore_c.model.PoreCConcatemerRecord.Config attribute)
(pore_c.model.PoreCContactRecord.Config attribute)
(pore_c.model.PoreCRecord.Config attribute)
filename_matches_regex() (in module pore_c.cli_utils)
filter_exact_overlap_on_query() (in module pore_c.analyses.alignments)
filter_reason (pore_c.model.PoreCRecord attribute)
filter_records() (in module pore_c.analyses.reads)
filter_shortest_path() (in module pore_c.analyses.alignments)
filter_singleton() (in module pore_c.analyses.alignments)
find_fragment_intervals() (in module pore_c.analyses.reference)
find_site_positions_bins() (in module pore_c.analyses.reference)
find_site_positions_biopython() (in module pore_c.analyses.reference)
find_site_positions_regex() (in module pore_c.analyses.reference)
fragment_end (pore_c.model.PoreCRecord attribute)
fragment_id (pore_c.model.FragmentRecord attribute)
(pore_c.model.PoreCRecord attribute)
fragment_length (pore_c.model.FragmentRecord attribute)
fragment_start (pore_c.model.PoreCRecord attribute)
FragmentRecord (class in pore_c.model)
FragmentRecord.Config (class in pore_c.model)
from_aligned_segment() (pore_c.model.AlignmentRecord class method)
from_pore_c_align_pair() (pore_c.model.PoreCContactRecord class method)
G
gather_concatemer_stats() (in module pore_c.analyses.contacts)
genome_id() (pore_c.catalogs.ReferenceGenomeCatalog property)
genome_size() (pore_c.catalogs.ReferenceGenomeCatalog property)
H
handle_parse_result() (pore_c.cli_utils.ExportDependentOption method)
haplotype (pore_c.model.AlignmentRecord attribute)
haplotype_pair_type (pore_c.model.PoreCContactRecord attribute)
haplotype_phased_h_cis (pore_c.model.PoreCConcatemerRecord attribute)
haplotype_phased_h_trans (pore_c.model.PoreCConcatemerRecord attribute)
haplotype_phased_sets_differ (pore_c.model.PoreCConcatemerRecord attribute)
haplotype_semi_phased (pore_c.model.PoreCConcatemerRecord attribute)
haplotype_unphased (pore_c.model.PoreCConcatemerRecord attribute)
HaplotypePairType (class in pore_c.model)
I
IndexedFasta (class in pore_c.datasources)
indirect_cis_contacts (pore_c.model.PoreCConcatemerRecord attribute)
indirect_contacts (pore_c.model.PoreCConcatemerRecord attribute)
indirect_long_range_cis_contacts (pore_c.model.PoreCConcatemerRecord attribute)
indirect_short_range_cis_contacts (pore_c.model.PoreCConcatemerRecord attribute)
indirect_trans_contacts (pore_c.model.PoreCConcatemerRecord attribute)
init_dataframe() (pore_c.model.PoreCRecord class method)
is_contained (pore_c.model.PoreCRecord attribute)
K
kmg_bases_to_int() (in module pore_c.utils)
L
list_commands() (pore_c.cli_utils.NaturalOrderGroup method)
low_mq (pore_c.model.AlignmentFilterReason attribute)
M
mapping_quality (pore_c.model.AlignmentRecord attribute)
max_direct_contact_fragment_distance (pore_c.model.PoreCConcatemerRecord attribute)
max_direct_contact_genome_distance (pore_c.model.PoreCConcatemerRecord attribute)
max_indirect_contact_fragment_distance (pore_c.model.PoreCConcatemerRecord attribute)
max_indirect_contact_genome_distance (pore_c.model.PoreCConcatemerRecord attribute)
mean_qscore() (in module pore_c.utils)
minimap_gapscore() (in module pore_c.analyses.alignments)
module
pore_c
pore_c.analyses
pore_c.analyses.alignments
pore_c.analyses.contacts
pore_c.analyses.reads
pore_c.analyses.reference
pore_c.catalogs
pore_c.cli
pore_c.cli_utils
pore_c.config
pore_c.datasources
pore_c.io
pore_c.model
pore_c.settings
pore_c.utils
N
name (pore_c.catalogs.RawReadCatalog attribute)
(pore_c.catalogs.ReferenceGenomeCatalog attribute)
(pore_c.catalogs.VirtualDigestCatalog attribute)
(pore_c.datasources.Fastq attribute)
(pore_c.datasources.IndexedFasta attribute)
NaturalOrderGroup (class in pore_c.cli_utils)
not_on_shortest_path (pore_c.model.AlignmentFilterReason attribute)
null (pore_c.model.AlignmentFilterReason attribute)
(pore_c.model.HaplotypePairType attribute)
num_contained_fragments (pore_c.model.PoreCRecord attribute)
num_fragments (pore_c.model.PoreCConcatemerRecord attribute)
num_overlapping_fragments (pore_c.model.PoreCRecord attribute)
O
overlap_length (pore_c.model.PoreCRecord attribute)
overlap_on_read (pore_c.model.AlignmentFilterReason attribute)
P
partition_access (pore_c.datasources.Fastq attribute)
(pore_c.datasources.IndexedFasta attribute)
Pass (pore_c.model.AlignmentFilterReason attribute)
pass_filter (pore_c.model.PoreCRecord attribute)
perc_of_alignment (pore_c.model.PoreCRecord attribute)
perc_of_fragment (pore_c.model.PoreCRecord attribute)
phase_qual (pore_c.model.AlignmentRecord attribute)
phase_set (pore_c.model.AlignmentRecord attribute)
phased_h_cis (pore_c.model.HaplotypePairType attribute)
phased_h_trans (pore_c.model.HaplotypePairType attribute)
phased_sets_differ (pore_c.model.HaplotypePairType attribute)
pipeable_sam_input() (in module pore_c.cli_utils)
pipeable_sam_output() (in module pore_c.cli_utils)
pore_c
module
pore_c.analyses
module
pore_c.analyses.alignments
module
pore_c.analyses.contacts
module
pore_c.analyses.reads
module
pore_c.analyses.reference
module
pore_c.catalogs
module
pore_c.cli
module
pore_c.cli_utils
module
pore_c.config
module
pore_c.datasources
module
pore_c.io
module
pore_c.model
module
pore_c.settings
module
pore_c.utils
module
PoreCConcatemerRecord (class in pore_c.model)
PoreCConcatemerRecord.Config (class in pore_c.model)
PoreCContactRecord (class in pore_c.model)
PoreCContactRecord.Config (class in pore_c.model)
PoreCRecord (class in pore_c.model)
PoreCRecord.Config (class in pore_c.model)
prepare_fastq() (in module pore_c.analyses.reads)
primary (pore_c.model.AlignmentType attribute)
R
RawReadCatalog (class in pore_c.catalogs)
read_chunked() (pore_c.datasources.Fastq method)
(pore_c.datasources.IndexedFasta method)
read_end (pore_c.model.AlignmentRecord attribute)
read_idx (pore_c.model.AlignmentRecord attribute)
(pore_c.model.PoreCConcatemerRecord attribute)
(pore_c.model.PoreCContactRecord attribute)
read_length (pore_c.model.AlignmentRecord attribute)
(pore_c.model.PoreCConcatemerRecord attribute)
(pore_c.model.PoreCContactRecord attribute)
read_length_stats() (in module pore_c.analyses.reads)
read_name (pore_c.model.AlignmentRecord attribute)
(pore_c.model.PoreCConcatemerRecord attribute)
(pore_c.model.PoreCContactRecord attribute)
read_order (pore_c.model.PoreCConcatemerRecord attribute)
read_start (pore_c.model.AlignmentRecord attribute)
ReadFilterProgress (class in pore_c.analyses.reads)
ReferenceGenomeCatalog (class in pore_c.catalogs)
replace_degenerate() (in module pore_c.analyses.reference)
revcomp() (in module pore_c.analyses.reference)
S
save() (pore_c.utils.DataFrameProgress method)
scatter() (pore_c.utils.DaskExecEnv method)
secondary (pore_c.model.AlignmentType attribute)
semi_phased (pore_c.model.HaplotypePairType attribute)
setup_logging() (in module pore_c.settings)
short_overlap (pore_c.model.AlignmentFilterReason attribute)
singleton (pore_c.model.AlignmentFilterReason attribute)
start (pore_c.model.AlignmentRecord attribute)
(pore_c.model.FragmentRecord attribute)
strand (pore_c.model.AlignmentRecord attribute)
summarize() (pore_c.analyses.reads.ReadFilterProgress static method)
summarize_concatemer_table() (in module pore_c.analyses.contacts)
supplementary (pore_c.model.AlignmentType attribute)
T
TableWriter (class in pore_c.io)
to_contacts() (in module pore_c.analyses.alignments)
to_dask() (pore_c.datasources.IndexedFasta method)
to_dataframe() (pore_c.model.AlignmentRecord class method)
to_intervals() (in module pore_c.analyses.reference)
total_cis_contacts (pore_c.model.PoreCConcatemerRecord attribute)
total_contacts (pore_c.model.PoreCConcatemerRecord attribute)
total_long_range_cis_contacts (pore_c.model.PoreCConcatemerRecord attribute)
total_short_range_cis_contacts (pore_c.model.PoreCConcatemerRecord attribute)
total_trans_contacts (pore_c.model.PoreCConcatemerRecord attribute)
trans (pore_c.model.HaplotypePairType attribute)
U
unmapped (pore_c.model.AlignmentFilterReason attribute)
(pore_c.model.AlignmentType attribute)
unphased (pore_c.model.HaplotypePairType attribute)
update_data() (pore_c.analyses.reads.ReadFilterProgress method)
(pore_c.utils.DataFrameProgress method)
update_dataframe_with_haplotypes() (pore_c.model.AlignmentRecord static method)
update_progress_bar() (pore_c.analyses.reads.ReadFilterProgress method)
(pore_c.utils.DataFrameProgress method)
use_enum_values (pore_c.model.AlignmentRecord.Config attribute)
(pore_c.model.FragmentRecord.Config attribute)
(pore_c.model.PoreCConcatemerRecord.Config attribute)
(pore_c.model.PoreCContactRecord.Config attribute)
(pore_c.model.PoreCRecord.Config attribute)
V
version (pore_c.datasources.Fastq attribute)
(pore_c.datasources.IndexedFasta attribute)
VirtualDigestCatalog (class in pore_c.catalogs)
W
write() (pore_c.io.TableWriter method)