Index

A

aggr_klass() (pomoxis.catalogue_errors.Error property) AlignPos (class in pomoxis.util) AlignSeg (class in pomoxis.catalogue_errors) analyse_counts() (in module pomoxis.assess_homopolymers)

analyse_homopolymers() (in module pomoxis.assess_homopolymers) analyze_counts() (in module pomoxis.catalogue_errors) are_adjacent() (in module pomoxis.catalogue_errors) average_score() (pomoxis.assess_homopolymers.AverageScore property) AverageScore (class in pomoxis.assess_homopolymers)

C

cat() (in module pomoxis.util) chunks() (in module pomoxis.util) classify_error() (in module pomoxis.catalogue_errors) classify_hp_indel() (in module pomoxis.catalogue_errors) classify_hp_sub() (in module pomoxis.catalogue_errors) ClassifyErrorTest (class in pomoxis.catalogue_errors) combine_complementary_relative_lengths() (in module pomoxis.assess_homopolymers)

Context (class in pomoxis.catalogue_errors) count_errors() (in module pomoxis.common_errors_from_bam) count_homopolymers() (in module pomoxis.assess_homopolymers) counts() (pomoxis.catalogue_errors.Error property) counts_factory() (in module pomoxis.assess_homopolymers) coverage_from_fastx() (in module pomoxis.util) coverage_of_region() (in module pomoxis.coverage_from_bam) coverage_summary_of_region() (in module pomoxis.coverage_from_bam)

E

end() (pomoxis.util.Region property) Error (class in pomoxis.catalogue_errors)

extract_long_reads() (in module pomoxis.util) extract_vals() (in module pomoxis.qscores_from_summary)

F

fast_convert() (in module pomoxis.util) FastxWrite (class in pomoxis.util)

filter_read() (in module pomoxis.subsample_bam) find_homopolymers() (in module pomoxis.assess_homopolymers)

G

get_aggr_counts() (in module pomoxis.catalogue_errors) get_aggr_klass() (in module pomoxis.catalogue_errors) get_errors() (in module pomoxis.catalogue_errors) (in module pomoxis.common_errors_from_bam) get_fraction_correct() (in module pomoxis.assess_homopolymers) get_longest_homopolymer() (in module pomoxis.assess_homopolymers) get_match_line_and_err_index() (in module pomoxis.catalogue_errors) get_next_aligned_base() (in module pomoxis.assess_homopolymers) get_pairs() (in module pomoxis.util)

get_prog_path() (in module pomoxis) get_qscores() (in module pomoxis.common_errors_from_bam) get_query_coords() (in module pomoxis.assess_homopolymers) get_query_region() (in module pomoxis.assess_homopolymers) get_ref_cover() (in module pomoxis.qscores_from_summary) get_relative_lengths() (in module pomoxis.assess_homopolymers) get_run() (in module pomoxis.catalogue_errors) get_seq_lens() (in module pomoxis.util) get_trimmed_pairs() (in module pomoxis.find_indels) (in module pomoxis.util)

I

intervaltrees_from_bed() (in module pomoxis.util)

is_in_hp() (in module pomoxis.catalogue_errors)

K

klass() (pomoxis.catalogue_errors.Error property)

L

load_counts() (in module pomoxis.assess_homopolymers)

M

main() (in module pomoxis.assess_homopolymers) (in module pomoxis.catalogue_errors) (in module pomoxis.common_errors_from_bam) (in module pomoxis.coverage_from_bam) (in module pomoxis.find_indels) (in module pomoxis.qscores_from_summary) (in module pomoxis.ref_seqs_from_bam) (in module pomoxis.stats_from_bam) (in module pomoxis.subsample_bam) (in module pomoxis.summary_from_stats) (in module pomoxis.trim_alignments) masked_stats_from_aligned_read() (in module pomoxis.stats_from_bam) match() (pomoxis.catalogue_errors.Error property) merge_counts() (in module pomoxis.assess_homopolymers)

module pomoxis pomoxis.assess_homopolymers pomoxis.bio pomoxis.catalogue_errors pomoxis.common_errors_from_bam pomoxis.coverage_from_bam pomoxis.find_indels pomoxis.qscores_from_summary pomoxis.ref_seqs_from_bam pomoxis.stats_from_bam pomoxis.subsample_bam pomoxis.summary_from_stats pomoxis.trim_alignments pomoxis.util

P

p_i() (pomoxis.catalogue_errors.Context property) pairs() (pomoxis.catalogue_errors.AlignSeg property) parse_regions() (in module pomoxis.util) plot_fraction_correct() (in module pomoxis.assess_homopolymers) plot_relative_lengths() (in module pomoxis.assess_homopolymers) plot_summary() (in module pomoxis.catalogue_errors) pomoxis module pomoxis.assess_homopolymers module pomoxis.bio module pomoxis.catalogue_errors module pomoxis.common_errors_from_bam module pomoxis.coverage_from_bam module

pomoxis.find_indels module pomoxis.qscores_from_summary module pomoxis.ref_seqs_from_bam module pomoxis.stats_from_bam module pomoxis.subsample_bam module pomoxis.summary_from_stats module pomoxis.trim_alignments module pomoxis.util module preprocess_error() (in module pomoxis.catalogue_errors) process_bam() (in module pomoxis.assess_homopolymers)

Q

qb() (pomoxis.catalogue_errors.Context property) qbase() (pomoxis.util.AlignPos property) qname() (pomoxis.catalogue_errors.AlignSeg property) (pomoxis.catalogue_errors.Error property)

qp() (pomoxis.catalogue_errors.Error property) qpos() (pomoxis.util.AlignPos property) qscore() (in module pomoxis.catalogue_errors) (in module pomoxis.summary_from_stats) qscore_from_summary() (in module pomoxis.qscores_from_summary)

R

rb() (pomoxis.catalogue_errors.Context property) rbase() (pomoxis.util.AlignPos property) read() (pomoxis.catalogue_errors.Error property) ref() (pomoxis.catalogue_errors.Error property) ref_name() (pomoxis.util.Region property) Region (class in pomoxis.util) reverse_bed() (in module pomoxis.util)

reverse_complement() (in module pomoxis.bio) rle() (in module pomoxis.catalogue_errors) rlen() (pomoxis.catalogue_errors.AlignSeg property) rname() (pomoxis.catalogue_errors.AlignSeg property) (pomoxis.catalogue_errors.Error property) rp() (pomoxis.catalogue_errors.Error property) rpos() (pomoxis.util.AlignPos property) run_prog() (in module pomoxis)

S

save_counts() (in module pomoxis.assess_homopolymers) scuff_ref() (in module pomoxis.common_errors_from_bam) SeqLen (class in pomoxis.util) setUp() (pomoxis.catalogue_errors.ClassifyErrorTest method) shotgun_library() (in module pomoxis.bio) show_prog_path() (in module pomoxis) simple_klass() (in module pomoxis.catalogue_errors)

split_fastx() (in module pomoxis.util) split_fastx_cmdline() (in module pomoxis.util) start() (pomoxis.util.Region property) stats_from_aligned_read() (in module pomoxis.stats_from_bam) subsample_region_proportionally() (in module pomoxis.subsample_bam) subsample_region_uniformly() (in module pomoxis.subsample_bam) summarise_stats() (in module pomoxis.summary_from_stats)

T

tag_bam() (in module pomoxis.util) test_complex_HP_del() (pomoxis.catalogue_errors.ClassifyErrorTest method) test_fwd_repeat_ins() (pomoxis.catalogue_errors.ClassifyErrorTest method) test_HP_complete_sub() (pomoxis.catalogue_errors.ClassifyErrorTest method) test_HP_complex_sub() (pomoxis.catalogue_errors.ClassifyErrorTest method) test_hp_del_2_0() (pomoxis.catalogue_errors.ClassifyErrorTest method) test_hp_del_6_5() (pomoxis.catalogue_errors.ClassifyErrorTest method) test_HP_del_join() (pomoxis.catalogue_errors.ClassifyErrorTest method) test_HP_del_join2() (pomoxis.catalogue_errors.ClassifyErrorTest method) test_HP_del_join3() (pomoxis.catalogue_errors.ClassifyErrorTest method) test_HP_del_join4() (pomoxis.catalogue_errors.ClassifyErrorTest method) test_HP_flk_sub_ext() (pomoxis.catalogue_errors.ClassifyErrorTest method) test_HP_flk_sub_trc() (pomoxis.catalogue_errors.ClassifyErrorTest method) test_hp_ins() (pomoxis.catalogue_errors.ClassifyErrorTest method) test_HP_ins_split() (pomoxis.catalogue_errors.ClassifyErrorTest method) test_HP_ins_split2() (pomoxis.catalogue_errors.ClassifyErrorTest method)

test_HP_ins_split3() (pomoxis.catalogue_errors.ClassifyErrorTest method) test_HP_ins_split4() (pomoxis.catalogue_errors.ClassifyErrorTest method) test_HP_ins_split5() (pomoxis.catalogue_errors.ClassifyErrorTest method) test_HP_ins_split6() (pomoxis.catalogue_errors.ClassifyErrorTest method) test_HP_messy_sub() (pomoxis.catalogue_errors.ClassifyErrorTest method) test_HP_messy_sub_ext() (pomoxis.catalogue_errors.ClassifyErrorTest method) test_HP_not_complete_sub() (pomoxis.catalogue_errors.ClassifyErrorTest method) test_HP_sub_join() (pomoxis.catalogue_errors.ClassifyErrorTest method) test_HP_sub_split() (pomoxis.catalogue_errors.ClassifyErrorTest method) test_HP_sub_swap_ext() (pomoxis.catalogue_errors.ClassifyErrorTest method) test_HP_sub_swap_trc() (pomoxis.catalogue_errors.ClassifyErrorTest method) test_HP_sub_swap_trc2() (pomoxis.catalogue_errors.ClassifyErrorTest method) test_HP_swap_sub_trc() (pomoxis.catalogue_errors.ClassifyErrorTest method) test_long_multi_del() (pomoxis.catalogue_errors.ClassifyErrorTest method) test_long_multi_ins() (pomoxis.catalogue_errors.ClassifyErrorTest method) test_multi_del() (pomoxis.catalogue_errors.ClassifyErrorTest method) test_multi_ins() (pomoxis.catalogue_errors.ClassifyErrorTest method)

W

write() (pomoxis.util.FastxWrite method)

Y

yield_from_bed() (in module pomoxis.util)