Index

Symbols

--aligner sm-analysis command line option --ccs sm-analysis command line option --CCS-bam-file sm-analysis command line option --ipd-model sm-analysis command line option --ipdsummary sm-analysis command line option --keep-temp-dir sm-analysis command line option --mapping-quality-threshold sm-analysis command line option --mappings bam-filter command line option --min-dna-seq-length bam-filter command line option --min-relative-mapping-ratio bam-filter command line option --min-subreads-per-molecule bam-filter command line option --modification-types sm-analysis command line option --nprocs-blasr sm-analysis command line option --num-simultaneous-ipdsummarys sm-analysis command line option --num-workers-per-ipdsummary sm-analysis command line option --only-produce-methylation-report sm-analysis command line option --partition sm-analysis command line option --pbindex sm-analysis command line option --quality-threshold bam-filter command line option --use-blasr-aligner sm-analysis command line option

--verbose sm-analysis command line option -a sm-analysis command line option -C sm-analysis command line option -c sm-analysis command line option -i sm-analysis command line option -l bam-filter command line option -M sm-analysis command line option -m bam-filter command line option sm-analysis command line option -N sm-analysis command line option -n sm-analysis command line option -P sm-analysis command line option -p sm-analysis command line option -q bam-filter command line option -R bam-filter command line option -r bam-filter command line option -v sm-analysis command line option <ALIGNMENT-FILE> sm-analysis command line option <BAM-FILE> bam-filter command line option sm-analysis command line option

_

__init__() (pacbio_data_processing.cigar.Cigar method) (pacbio_data_processing.sentinel.Sentinel method)

_anti_aging() (pacbio_data_processing.sentinel.Sentinel method)

A

alignment variant

B

bam-filter command line option --mappings --min-dna-seq-length --min-relative-mapping-ratio --min-subreads-per-molecule --quality-threshold -l -m -q -r -R <BAM-FILE>

Bash

C

Cigar (class in pacbio_data_processing.cigar) Command Line Interface (CLI)

Command Line Option CPython CSV file

D

diff_ratio (pacbio_data_processing.cigar.Cigar property)

E

exit status

F

FASTA

G

GFF	Graphical User Interface (GUI)

H

high_level_handler() (in module pacbio_data_processing.errors)

I

is_file_too_old (pacbio_data_processing.sentinel.Sentinel property)

M

MD5 checksum MissingGooeyError module pacbio_data_processing pacbio_data_processing.cigar pacbio_data_processing.constants pacbio_data_processing.errors pacbio_data_processing.sam pacbio_data_processing.sentinel pacbio_data_processing.templates pacbio_data_processing.types pacbio_data_processing.ui pacbio_data_processing.ui.cl pacbio_data_processing.ui.common pacbio_data_processing.ui.options

molecule

N

number_diff_items (pacbio_data_processing.cigar.Cigar property) number_diff_types (pacbio_data_processing.cigar.Cigar property)

number_pb_diffs (pacbio_data_processing.cigar.Cigar property) number_pbs (pacbio_data_processing.cigar.Cigar property)

P

pacbio_data_processing module pacbio_data_processing.cigar module pacbio_data_processing.constants module pacbio_data_processing.errors module pacbio_data_processing.sam module pacbio_data_processing.sentinel module pacbio_data_processing.templates module

pacbio_data_processing.types module pacbio_data_processing.ui module pacbio_data_processing.ui.cl module pacbio_data_processing.ui.common module pacbio_data_processing.ui.options module parse_cl_bam_filter() (in module pacbio_data_processing.ui.cl) parse_cl_sm_analysis() (in module pacbio_data_processing.ui.cl) parse_user_input() (in module pacbio_data_processing.ui.common) PATH

R

reference

S

Sentinel (class in pacbio_data_processing.sentinel) SentinelFileFound SentinelFileNotFound sim_ratio (pacbio_data_processing.cigar.Cigar property) sm-analysis command line option --aligner --ccs --CCS-bam-file --ipd-model --ipdsummary --keep-temp-dir --mapping-quality-threshold --modification-types --nprocs-blasr --num-simultaneous-ipdsummarys --num-workers-per-ipdsummary --only-produce-methylation-report --partition --pbindex --use-blasr-aligner --verbose -a -c -C -i -M -m -N -n -p -P -v <ALIGNMENT-FILE> <BAM-FILE>

SMAMergeError SMAPipelineError subread summary report

V

variant