bcftbx library reference

• bcftbx.IlluminaData
  • Core data and run handling classes
  • Samplesheet handling
  • Utility classes and functions
  • Exception classes
• bcftbx.SolidData
  • SolidRun
  • SolidSample
  • SolidLibrary
  • SolidPrimaryData
  • Functions
• bcftbx.Experiment
  • Experiment
  • ExperimentList
  • LinkNames
• bcftbx.FASTQFile
  • FastqAttributes
  • FastqIterator
  • FastqRead
  • SequenceIdentifier
  • fastqs_are_pair()
  • get_fastq_file_handle()
  • nreads()
• bcftbx.JobRunner
  • BaseJobRunner
  • GEJobRunner
  • ResourceLock
  • SimpleJobRunner
  • SlurmRunner
  • fetch_runner()
• bcftbx.Pipeline
  • Classes
  • Functions
• bcftbx.Md5sum
  • Md5CheckReporter
  • Md5Checker
  • md5sum()
• bcftbx.platforms
  • get_run_completion_files()
  • get_sequencer_platform()
  • list_platforms()
• bcftbx.TabFile
  • Creating a TabFile
  • Accessing Data within a TabFile
  • Adding and Removing Data
  • Filtering Data
  • Sorting Data
  • Manipulating Data: whole column operations
  • Writing to File
  • Specifying Delimiters
  • TabFileIterator: iterating through a tab-delimited file
  • TabDataLine
  • TabFile
  • TabFileIterator
• bcftbx.simple_xls and bcftbx.Spreadsheet
  • simple_xls
  • Spreadsheet
• bcftbx.cmdparse
  • CommandParser
  • add_arg()
  • add_debug_option()
  • add_dry_run_option()
  • add_no_save_option()
  • add_nprocessors_option()
  • add_runner_option()
• bcftbx.qc
  • bcftbx.qc.report
• bcftbx.htmlpagewriter
  • HTMLPageWriter
  • PNGBase64Encoder
• bcftbx.utils
  • General utility classes
  • File handling utilities
  • File system wrappers and utilities
  • Symbolic link handling
  • Sample name utilities
  • File manipulations
  • Text manipulations
• bcftbx.ngsutils
  • Extracting reads from Fastq, cfasta and qual files