Module thresholds (WARN / ERROR)

[pdp10]

we need to define module-specific thresholds triggering potential warnings or errors.

[pdp10]

First draft of thresholds.

• GitHub branch: mod_thres
• Threshold description: Help/3\ Analysis\ Modules/
• Configuration file: Configuration/limits.txt

# BamQC configuration file

####################
# MODULE SELECTION #
####################

# For each of the modules you can choose to not run that
# module at all by setting the value below to 1 for the
# modules you want to remove.
ChromosomeReadDensity					ignore	0
FeatureCoverage						ignore	0
GenomeCoverage						ignore	0
IndelFrequencies					ignore	0
InsertLengthDistribution				ignore	0
MappingQualityDistribution				ignore	0
# deprecated
SequenceQualityDistribution				ignore	1
SNPFrequencies						ignore	0
SNPFrequenciesByType					ignore	0
SoftClipDistribution					ignore	0
# The following option turns off InsertFrequencies, 
# SNPFrequencies, SNPFrequenciesByType, 
# and some statistics in BasicStatistics
VariantCallDetection					ignore	0



##############################
# MODULE-SPECIFIC THRESHOLDS #
##############################

# BasicStatistics module
BasicStatistics_unmapped_percent_threshold	warn	50	
BasicStatistics_unmapped_percent_threshold	error	90

# ChromosomeReadDensity Module
ChromosomeReadDensity_readNumber_threshold	warn	25
ChromosomeReadDensity_readNumber_threshold	error	10

# GenomeCoverage module
GenomeCoverage_plot_type_chromosomes_threshold		ignore	50
GenomeCoverage_plot_bins_all_chromosomes   		ignore	5000		
GenomeCoverage_plot_bins_per_chromosome   		ignore	500
GenomeCoverage_uncovered_genome_percent_threshold	error	10
GenomeCoverage_uncovered_genome_percent_threshold	warn	5

# Indel/SNP modules		
VariantCallPosition_indel_seqpercent_xaxis_threshold   	ignore   	5
VariantCallPosition_indel_max_freq_threshold		warn   		5	
VariantCallPosition_indel_max_freq_threshold		error   	25
VariantCallPosition_snp_seqpercent_xaxis_threshold   	ignore   	5 		
VariantCallPosition_snp_max_freq_threshold   		warn   		5	
VariantCallPosition_snp_max_freq_threshold   		error   	25
VariantCallPosition_snp_max_freq_by_type_threshold	warn   		0.5	
VariantCallPosition_snp_max_freq_by_type_threshold	error   	2.5

# Insert Length Distribution module
InsertLengthDistribution_max_insert_size   		ignore   	10000.0
InsertLengthDistribution_bin_size   			ignore   	1.0
InsertLengthDistribution_percentage_deviation   	error   	75.0
InsertLengthDistribution_percentage_deviation   	warn   		50.0

# MappingQualityDistribution module
MappingQualityDistribution_fraction   		error  0.50
MappingQualityDistribution_fraction   		warn   0.75

# SoftClipDistribution module 
SoftClipDistribution_clip_number_threshold	error	100
SoftClipDistribution_clip_number_threshold	warn	25

# Annotation Module
AnnotationSet_annotation_cache_capacity   	ignore   50000



#################################################
# MODULES WITH CURRENTLY NO EXPLICIT THRESHOLDS #
#################################################
# FeatureCoverage module

[pdp10]

Merged to develop branch. See PR #32 .