Index

A | B | C | D | E | F | G | H | I | J | L | M | N | O | P | R | S | T | U | V | W | X | Z

A

add() (pbcommand.models.DataStore method)
ALIGNMENT_CMP_H5 (pbcommand.models.FileTypes attribute)
ALL (pbcommand.services.JobStates attribute)
ALL() (pbcommand.models.FileTypes static method)
(pbcommand.models.ResourceTypes class method)
(pbcommand.models.TaskOptionTypes class method)
(pbcommand.services.JobTypes class method)
ALL_CHOICES() (pbcommand.models.TaskOptionTypes class method)
ALL_COMPLETED (pbcommand.services.JobStates attribute)
ALL_DATASET_TYPES() (pbcommand.models.FileTypes static method)
ALL_SIMPLE() (pbcommand.models.TaskOptionTypes class method)

B

BAM (pbcommand.models.FileTypes attribute)
BAM_ALN (pbcommand.models.FileTypes attribute)
BAM_CCS (pbcommand.models.FileTypes attribute)
BAM_CCS_ALN (pbcommand.models.FileTypes attribute)
BAM_SUB (pbcommand.models.FileTypes attribute)
BAMBAI (pbcommand.models.FileTypes attribute)
BasePacBioOption (class in pbcommand.models)
BAX (pbcommand.models.FileTypes attribute)
BAZ (pbcommand.models.FileTypes attribute)
BED (pbcommand.models.FileTypes attribute)
BIGWIG (pbcommand.models.FileTypes attribute)
BLASR_M4 (pbcommand.models.FileTypes attribute)
BOOL (pbcommand.models.TaskOptionTypes attribute)

C

CFG (pbcommand.models.FileTypes attribute)
CHOICE_FLOAT (pbcommand.models.TaskOptionTypes attribute)
CHOICE_INT (pbcommand.models.TaskOptionTypes attribute)
CHOICE_STR (pbcommand.models.TaskOptionTypes attribute)
CHUNK (pbcommand.models.FileTypes attribute)
chunk_d (pbcommand.models.PipelineChunk attribute)
CHUNK_KEY_PREFIX (pbcommand.models.PipelineChunk attribute)
chunk_keys (pbcommand.models.PipelineChunk attribute)
chunk_metadata (pbcommand.models.PipelineChunk attribute)
cmd (pbcommand.engine.ExtCmdResult attribute)
compose() (in module pbcommand.utils)
COND_RESEQ (pbcommand.models.FileTypes attribute)
Constants (class in pbcommand.utils)
CONTIG_FA (pbcommand.models.FileTypes attribute)
CONVERT_FASTA (pbcommand.services.JobTypes attribute)
create_by_pipeline_template_id() (pbcommand.services.ServiceAccessLayer method)
create_logger_resource() (pbcommand.services.ServiceAccessLayer method)
CREATED (pbcommand.services.JobStates attribute)
CSV (pbcommand.models.FileTypes attribute)

D

DataStore (class in pbcommand.models)
DataStoreFile (class in pbcommand.models)
DataStoreViewRule (class in pbcommand.models)
default (pbcommand.models.BasePacBioOption attribute)
default_name (pbcommand.models.FileType attribute)
DS_ALIGN (pbcommand.models.FileTypes attribute)
DS_ALIGN_CCS (pbcommand.models.FileTypes attribute)
DS_BARCODE (pbcommand.models.FileTypes attribute)
DS_CCS (pbcommand.models.FileTypes attribute)
DS_CONTIG (pbcommand.models.FileTypes attribute)
DS_GMAP_REF (pbcommand.models.FileTypes attribute)
DS_REF (pbcommand.models.FileTypes attribute)
DS_SUBREADS (pbcommand.models.FileTypes attribute)
DS_SUBREADS_H5 (pbcommand.models.FileTypes attribute)

E

exit_code (pbcommand.engine.ExtCmdResult attribute)
ExtCmdResult (class in pbcommand.engine)
ExternalCommandNotFoundError

F

FAILED (pbcommand.services.JobStates attribute)
FASTA (pbcommand.models.FileTypes attribute)
FASTA_ADAPTER (pbcommand.models.FileTypes attribute)
FASTA_BC (pbcommand.models.FileTypes attribute)
FASTA_CONTROL (pbcommand.models.FileTypes attribute)
FASTA_REF (pbcommand.models.FileTypes attribute)
FASTQ (pbcommand.models.FileTypes attribute)
FileType (class in pbcommand.models)
FileTypes (class in pbcommand.models)
FLOAT (pbcommand.models.TaskOptionTypes attribute)
FOFN (pbcommand.models.FileTypes attribute)
from_choice_str() (pbcommand.models.TaskOptionTypes class method)
from_d() (pbcommand.services.ServiceEntryPoint static method)
(pbcommand.services.ServiceJob static method)
from_dict() (pbcommand.models.DataStoreFile static method)
(pbcommand.models.DataStoreViewRule static method)
(pbcommand.models.PipelineDataStoreViewRules static method)
from_simple_str() (pbcommand.models.TaskOptionTypes class method)
from_str() (pbcommand.models.TaskOptionTypes class method)

G

GatherToolContractTask (class in pbcommand.models)
GCHUNK (pbcommand.models.FileTypes attribute)
get_alignmentset_by_id() (pbcommand.services.ServiceAccessLayer method)
get_alignmentsets() (pbcommand.services.ServiceAccessLayer method)
get_analysis_job_by_id() (pbcommand.services.ServiceAccessLayer method)
get_analysis_job_datastore() (pbcommand.services.ServiceAccessLayer method)
get_analysis_job_entry_points() (pbcommand.services.ServiceAccessLayer method)
get_analysis_job_report_attrs() (pbcommand.services.ServiceAccessLayer method)
get_analysis_job_report_details() (pbcommand.services.ServiceAccessLayer method)
get_analysis_job_reports() (pbcommand.services.ServiceAccessLayer method)
get_analysis_job_tasks() (pbcommand.services.ServiceAccessLayer method)
get_analysis_jobs() (pbcommand.services.ServiceAccessLayer method)
get_barcodeset_by_id() (pbcommand.services.ServiceAccessLayer method)
get_barcodesets() (pbcommand.services.ServiceAccessLayer method)
get_ccsreadset_by_id() (pbcommand.services.ServiceAccessLayer method)
get_ccsreadsets() (pbcommand.services.ServiceAccessLayer method)
get_dataset_by_id() (pbcommand.services.ServiceAccessLayer method)
get_dataset_by_uuid() (pbcommand.services.ServiceAccessLayer method)
get_dataset_metadata() (in module pbcommand.utils)
get_dataset_metadata_or_none() (in module pbcommand.utils)
get_default_argparser() (in module pbcommand.cli)
get_default_argparser_with_base_opts() (in module pbcommand.cli)
get_fasta_convert_jobs() (pbcommand.services.ServiceAccessLayer method)
get_hdfsubreadset_by_id() (pbcommand.services.ServiceAccessLayer method)
get_hdfsubreadsets() (pbcommand.services.ServiceAccessLayer method)
get_import_dataset_job_datastore() (pbcommand.services.ServiceAccessLayer method)
get_import_dataset_jobs() (pbcommand.services.ServiceAccessLayer method)
get_import_job_by_id() (pbcommand.services.ServiceAccessLayer method)
get_import_job_report_attrs() (pbcommand.services.ServiceAccessLayer method)
get_import_job_report_details() (pbcommand.services.ServiceAccessLayer method)
get_import_job_reports() (pbcommand.services.ServiceAccessLayer method)
get_import_job_tasks() (pbcommand.services.ServiceAccessLayer method)
get_job_by_id() (pbcommand.services.ServiceAccessLayer method)
get_job_by_type_and_id() (pbcommand.services.ServiceAccessLayer method)
get_merge_dataset_job_datastore() (pbcommand.services.ServiceAccessLayer method)
get_merge_dataset_jobs() (pbcommand.services.ServiceAccessLayer method)
get_parsed_args_log_level() (in module pbcommand.utils)
get_pipeline_template_by_id() (pbcommand.services.ServiceAccessLayer method)
get_referenceset_by_id() (pbcommand.services.ServiceAccessLayer method)
get_referencesets() (pbcommand.services.ServiceAccessLayer method)
get_status() (pbcommand.services.ServiceAccessLayer method)
get_subreadset_by_id() (pbcommand.services.ServiceAccessLayer method)
get_subreadsets() (pbcommand.services.ServiceAccessLayer method)
GFF (pbcommand.models.FileTypes attribute)
GZIP (pbcommand.models.FileTypes attribute)

H

H5 (pbcommand.models.FileTypes attribute)

I

I_BAI (pbcommand.models.FileTypes attribute)
I_FCI (pbcommand.models.FileTypes attribute)
I_INDEXER (pbcommand.models.FileTypes attribute)
I_PBI (pbcommand.models.FileTypes attribute)
I_SAM (pbcommand.models.FileTypes attribute)
I_SAW (pbcommand.models.FileTypes attribute)
import_dataset_barcode() (pbcommand.services.ServiceAccessLayer method)
import_dataset_hdfsubread() (pbcommand.services.ServiceAccessLayer method)
import_dataset_reference() (pbcommand.services.ServiceAccessLayer method)
import_dataset_subread() (pbcommand.services.ServiceAccessLayer method)
IMPORT_DS (pbcommand.services.JobTypes attribute)
IMPORT_DSTORE (pbcommand.services.JobTypes attribute)
import_fasta() (pbcommand.services.ServiceAccessLayer method)
INPUT_XML (pbcommand.models.FileTypes attribute)
InputFileType (class in pbcommand.models)
INT (pbcommand.models.TaskOptionTypes attribute)
is_choice() (pbcommand.models.TaskOptionTypes class method)
is_dataset() (in module pbcommand.utils)
is_tmp_resource() (pbcommand.models.ResourceTypes class method)
is_valid() (pbcommand.models.ResourceTypes class method)
is_valid_id() (pbcommand.models.FileTypes static method)

J

JOB_DEFAULT_TIMEOUT (pbcommand.services.ServiceAccessLayer attribute)
JobStates (class in pbcommand.services)
JobTypes (class in pbcommand.services)
JSON (pbcommand.models.FileTypes attribute)

L

load_from_d() (pbcommand.models.DataStore static method)
load_from_json() (pbcommand.models.DataStore static method)
(pbcommand.models.PipelineDataStoreViewRules static method)
LOG (pbcommand.models.FileTypes attribute)
LOG_FILE (pbcommand.models.ResourceTypes attribute)
log_progress_update() (pbcommand.services.ServiceAccessLayer method)
log_traceback() (in module pbcommand.utils)

M

MalformedResolvedToolContractError
MalformedToolContractError
MAX_NCHUNKS (pbcommand.models.SymbolTypes attribute)
MAX_NPROC (pbcommand.models.SymbolTypes attribute)
MERGE_DS (pbcommand.services.JobTypes attribute)
MOCK_PB_PIPE (pbcommand.services.JobTypes attribute)
MOVIE_FOFN (pbcommand.models.FileTypes attribute)

N

NCHUNKS (pbcommand.models.SymbolTypes attribute)
nfs_exists_check() (in module pbcommand.utils)
NPROC (pbcommand.models.SymbolTypes attribute)

O

OPTION_TYPE_ID (pbcommand.models.BasePacBioOption attribute)
(pbcommand.models.PacBioBooleanOption attribute)
(pbcommand.models.PacBioFloatChoiceOption attribute)
(pbcommand.models.PacBioFloatOption attribute)
(pbcommand.models.PacBioIntChoiceOption attribute)
(pbcommand.models.PacBioIntOption attribute)
(pbcommand.models.PacBioStringChoiceOption attribute)
(pbcommand.models.PacBioStringOption attribute)
OPTS (pbcommand.models.SymbolTypes attribute)
OUTPUT_DIR (pbcommand.models.ResourceTypes attribute)
OutputFileType (class in pbcommand.models)

P

pacbio_args_or_contract_runner() (in module pbcommand.cli)
PacBioBooleanOption (class in pbcommand.models)
PacBioFloatChoiceOption (class in pbcommand.models)
PacBioFloatOption (class in pbcommand.models)
PacBioIntChoiceOption (class in pbcommand.models)
PacBioIntOption (class in pbcommand.models)
PacBioStringChoiceOption (class in pbcommand.models)
PacBioStringOption (class in pbcommand.models)
PB_PIPE (pbcommand.services.JobTypes attribute)
pbcommand.cli (module)
pbcommand.engine (module)
pbcommand.models (module), [1], [2], [3], [4], [5]
pbcommand.pb_io (module), [1], [2]
pbcommand.services (module)
pbcommand.utils (module)
pbparser_runner() (in module pbcommand.cli)
PICKLE (pbcommand.models.FileTypes attribute)
PipelineChunk (class in pbcommand.models)
PipelineDataStoreViewRules (class in pbcommand.models)
PLS (pbcommand.models.FileTypes attribute)

R

REF_ENTRY_XML (pbcommand.models.FileTypes attribute)
REPORT (pbcommand.models.FileTypes attribute)
RESOLVED_OPTS (pbcommand.models.SymbolTypes attribute)
ResolvedGatherToolContractTask (class in pbcommand.models)
ResolvedScatteredToolContractTask (class in pbcommand.models)
ResolvedToolContract (class in pbcommand.models)
ResolvedToolContractTask (class in pbcommand.models)
resource (pbcommand.services.ServiceEntryPoint attribute)
ResourceTypes (class in pbcommand.models)
RGN_FOFN (pbcommand.models.FileTypes attribute)
ROOT_DS (pbcommand.services.ServiceAccessLayer attribute)
ROOT_JM (pbcommand.services.ServiceAccessLayer attribute)
ROOT_JOBS (pbcommand.services.ServiceAccessLayer attribute)
ROOT_PT (pbcommand.services.ServiceAccessLayer attribute)
RS_MOVIE_XML (pbcommand.models.FileTypes attribute)
run_by_pipeline_template_id() (pbcommand.services.ServiceAccessLayer method)
run_cmd() (in module pbcommand.engine)
run_import_dataset_barcode() (pbcommand.services.ServiceAccessLayer method)
run_import_dataset_by_type() (pbcommand.services.ServiceAccessLayer method)
run_import_dataset_hdfsubread() (pbcommand.services.ServiceAccessLayer method)
run_import_dataset_reference() (pbcommand.services.ServiceAccessLayer method)
run_import_dataset_subread() (pbcommand.services.ServiceAccessLayer method)
run_import_fasta() (pbcommand.services.ServiceAccessLayer method)
run_import_local_dataset() (pbcommand.services.ServiceAccessLayer method)
run_time (pbcommand.engine.ExtCmdResult attribute)
RUNNING (pbcommand.services.JobStates attribute)
RX_CHUNK_KEY (pbcommand.models.PipelineChunk attribute)

S

SAM (pbcommand.models.FileTypes attribute)
ScatterToolContractTask (class in pbcommand.models)
SCHEMA_OPTS (pbcommand.models.SymbolTypes attribute)
SCHUNK (pbcommand.models.FileTypes attribute)
ServiceAccessLayer (class in pbcommand.services)
ServiceEntryPoint (class in pbcommand.services)
ServiceJob (class in pbcommand.services)
set_chunk_key() (pbcommand.models.PipelineChunk method)
set_metadata_key() (pbcommand.models.PipelineChunk method)
setup_log() (in module pbcommand.utils)
setup_logger() (in module pbcommand.utils)
Singleton (class in pbcommand.utils)
STR (pbcommand.models.TaskOptionTypes attribute)
STS_H5 (pbcommand.models.FileTypes attribute)
STS_XML (pbcommand.models.FileTypes attribute)
SUBMITTED (pbcommand.services.JobStates attribute)
SUCCESSFUL (pbcommand.services.JobStates attribute)
SymbolTypes (class in pbcommand.models)

T

TASK_TYPE (pbcommand.models.SymbolTypes attribute)
TASK_TYPE_ID (pbcommand.models.GatherToolContractTask attribute)
(pbcommand.models.ResolvedGatherToolContractTask attribute)
(pbcommand.models.ResolvedScatteredToolContractTask attribute)
(pbcommand.models.ResolvedToolContractTask attribute)
(pbcommand.models.ScatterToolContractTask attribute)
(pbcommand.models.ToolContractTask attribute)
TaskOptionTypes (class in pbcommand.models)
TMP_DIR (pbcommand.models.ResourceTypes attribute)
TMP_FILE (pbcommand.models.ResourceTypes attribute)
tmpdir_resources (pbcommand.models.ResolvedToolContractTask attribute)
tmpfile_resources (pbcommand.models.ResolvedToolContractTask attribute)
to_d() (pbcommand.services.ServiceEntryPoint method)
to_dict() (pbcommand.models.BasePacBioOption method)
(pbcommand.models.DataStore method)
(pbcommand.models.DataStoreFile method)
(pbcommand.models.DataStoreViewRule method)
(pbcommand.models.InputFileType method)
(pbcommand.models.OutputFileType method)
(pbcommand.models.PipelineChunk method)
(pbcommand.models.PipelineDataStoreViewRules method)
(pbcommand.models.ResolvedGatherToolContractTask method)
(pbcommand.models.ResolvedScatteredToolContractTask method)
(pbcommand.models.ResolvedToolContract method)
(pbcommand.models.ResolvedToolContractTask method)
(pbcommand.models.ScatterToolContractTask method)
(pbcommand.models.ToolContract method)
(pbcommand.models.ToolContractTask method)
(pbcommand.models.ToolDriver method)
to_summary() (pbcommand.services.ServiceAccessLayer method)
ToolContract (class in pbcommand.models)
ToolContractTask (class in pbcommand.models)
ToolDriver (class in pbcommand.models)
TRC (pbcommand.models.FileTypes attribute)
TXT (pbcommand.models.FileTypes attribute)

U

uri (pbcommand.services.ServiceAccessLayer attribute)

V

validate_core_type() (pbcommand.models.BasePacBioOption class method)
(pbcommand.models.PacBioBooleanOption class method)
(pbcommand.models.PacBioFloatChoiceOption class method)
(pbcommand.models.PacBioFloatOption class method)
(pbcommand.models.PacBioIntChoiceOption class method)
(pbcommand.models.PacBioIntOption class method)
(pbcommand.models.PacBioStringChoiceOption class method)
(pbcommand.models.PacBioStringOption class method)
validate_core_type_with_choices() (pbcommand.models.PacBioFloatChoiceOption class method)
(pbcommand.models.PacBioIntChoiceOption class method)
(pbcommand.models.PacBioStringChoiceOption class method)
validate_option() (pbcommand.models.BasePacBioOption method)
VCF (pbcommand.models.FileTypes attribute)
version (pbcommand.models.DataStore attribute)

W

walker() (in module pbcommand.utils)
was_successful() (pbcommand.services.ServiceJob method)
which() (in module pbcommand.utils)
which_or_raise() (in module pbcommand.utils)
write_json() (pbcommand.models.DataStore method)
(pbcommand.models.PipelineDataStoreViewRules method)
write_resolved_tool_contract() (in module pbcommand.pb_io), [1]
write_tool_contract() (in module pbcommand.pb_io), [1]
write_update_json() (pbcommand.models.DataStore method)
WRITER_SCHEMA_VERSION (pbcommand.models.ToolContract attribute)

X

XML (pbcommand.models.FileTypes attribute)

Z

ZIP (pbcommand.models.FileTypes attribute)