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.