3.6. reports.py - produce various metrics and reportsΒΆ

Reports

usage: reports.py subcommand
Sub-commands:
consolidate_bamstats

Undocumented

usage: reports.py consolidate_bamstats [-h] inFiles [inFiles ...] outFile
Positional arguments:
inFiles Input report files.
outFile Output report file.
consolidate_fastqc

Undocumented

usage: reports.py consolidate_fastqc [-h] inDirs [inDirs ...] outFile
Positional arguments:
inDirs Input FASTQC directories.
outFile Output report file.
coverage_summary

Undocumented

usage: reports.py coverage_summary [-h] [--runFile RUNFILE]
                                   [--bamstatsDir BAMSTATSDIR]
                                   coverageDir coverageSuffix outFile
Positional arguments:
coverageDir Input coverage report directory.
coverageSuffix Suffix of all coverage files.
outFile Output report file.
Options:
--runFile Link in plate info from seq runs.
--bamstatsDir Link in read info from BAM alignments.
consolidate_coverage

Undocumented

usage: reports.py consolidate_coverage [-h] inFiles [inFiles ...] adj outFile
Positional arguments:
inFiles Input coverage files.
adj Report adjective.
outFile Output report file.
consolidate_spike_count

Undocumented

usage: reports.py consolidate_spike_count [-h] inFiles [inFiles ...] outFile
Positional arguments:
inFiles Input coverage files.
outFile Output report file.