Table of Contents - cagnut_picard-0.3.2 Documentation
Classes and Modules
- CagnutPicard
- CagnutPicard::AddOrReplaceReadGroups
- CagnutPicard::Base
- CagnutPicard::BuildBamIndex
- CagnutPicard::CheckTools
- CagnutPicard::CollectGcBiasMetrics
- CagnutPicard::CollectInsertSizeMetrics
- CagnutPicard::CollectMultipleMetrics
- CagnutPicard::Configuration
- CagnutPicard::Markdup
- CagnutPicard::MeanQualityByCycle
- CagnutPicard::QualityScoreDistribution
- CagnutPicard::SortSam
- CagnutPicard::Util
Methods
- ::config — CagnutPicard
- ::load — CagnutPicard::Configuration
- ::new — CagnutPicard::AddOrReplaceReadGroups
- ::new — CagnutPicard::BuildBamIndex
- ::new — CagnutPicard::CollectGcBiasMetrics
- ::new — CagnutPicard::CollectInsertSizeMetrics
- ::new — CagnutPicard::CollectMultipleMetrics
- ::new — CagnutPicard::Markdup
- ::new — CagnutPicard::MeanQualityByCycle
- ::new — CagnutPicard::QualityScoreDistribution
- ::new — CagnutPicard::SortSam
- ::new — CagnutPicard::Util
- #add_java_params — CagnutPicard::Configuration
- #add_or_replace_readgroups — CagnutPicard::Base
- #add_or_replace_readgroups — CagnutPicard::Util
- #add_read_group_options — CagnutPicard::AddOrReplaceReadGroups
- #attributes — CagnutPicard::Configuration
- #build_bam_index — CagnutPicard::Base
- #build_bam_index — CagnutPicard::Util
- #build_bam_index_options — CagnutPicard::BuildBamIndex
- #check_Picard — CagnutPicard::CheckTools
- #check_picard_dict — CagnutPicard::CheckTools
- #check_ref_related — CagnutPicard::CheckTools
- #check_tool — CagnutPicard::CheckTools
- #collect_gc_bias_metrics — CagnutPicard::Base
- #collect_gc_bias_metrics — CagnutPicard::Util
- #collect_gc_bias_metrics_options — CagnutPicard::CollectGcBiasMetrics
- #collect_insert_size_metrics — CagnutPicard::Base
- #collect_insert_size_metrics — CagnutPicard::Util
- #collect_insert_size_metrics_options — CagnutPicard::CollectInsertSizeMetrics
- #collect_multiple_metrics — CagnutPicard::Base
- #collect_multiple_metrics — CagnutPicard::Util
- #collect_multiple_metrics_options — CagnutPicard::CollectMultipleMetrics
- #generate_rg_str — CagnutPicard::Configuration
- #generate_script — CagnutPicard::AddOrReplaceReadGroups
- #generate_script — CagnutPicard::BuildBamIndex
- #generate_script — CagnutPicard::CollectGcBiasMetrics
- #generate_script — CagnutPicard::CollectInsertSizeMetrics
- #generate_script — CagnutPicard::CollectMultipleMetrics
- #generate_script — CagnutPicard::Markdup
- #generate_script — CagnutPicard::MeanQualityByCycle
- #generate_script — CagnutPicard::QualityScoreDistribution
- #generate_script — CagnutPicard::SortSam
- #load — CagnutPicard::Configuration
- #markdup — CagnutPicard::Base
- #markdup — CagnutPicard::Util
- #markduplicate_options — CagnutPicard::Markdup
- #mean_quality_by_cycle — CagnutPicard::Base
- #mean_quality_by_cycle — CagnutPicard::Util
- #mean_quality_by_cycle_options — CagnutPicard::MeanQualityByCycle
- #modified_java_array — CagnutPicard::AddOrReplaceReadGroups
- #modified_java_array — CagnutPicard::BuildBamIndex
- #modified_java_array — CagnutPicard::CollectGcBiasMetrics
- #modified_java_array — CagnutPicard::CollectInsertSizeMetrics
- #modified_java_array — CagnutPicard::CollectMultipleMetrics
- #modified_java_array — CagnutPicard::Markdup
- #modified_java_array — CagnutPicard::MeanQualityByCycle
- #modified_java_array — CagnutPicard::QualityScoreDistribution
- #modified_java_array — CagnutPicard::SortSam
- #params_combination_hash — CagnutPicard::AddOrReplaceReadGroups
- #params_combination_hash — CagnutPicard::BuildBamIndex
- #params_combination_hash — CagnutPicard::CollectGcBiasMetrics
- #params_combination_hash — CagnutPicard::CollectInsertSizeMetrics
- #params_combination_hash — CagnutPicard::CollectMultipleMetrics
- #params_combination_hash — CagnutPicard::Markdup
- #params_combination_hash — CagnutPicard::MeanQualityByCycle
- #params_combination_hash — CagnutPicard::QualityScoreDistribution
- #params_combination_hash — CagnutPicard::SortSam
- #picard_qc_metrics — CagnutPicard::Util
- #quailty_score_distribution_options — CagnutPicard::QualityScoreDistribution
- #quality_score_distribution — CagnutPicard::Base
- #quality_score_distribution — CagnutPicard::Util
- #queuing_options — CagnutPicard::AddOrReplaceReadGroups
- #queuing_options — CagnutPicard::BuildBamIndex
- #queuing_options — CagnutPicard::CollectGcBiasMetrics
- #queuing_options — CagnutPicard::CollectInsertSizeMetrics
- #queuing_options — CagnutPicard::CollectMultipleMetrics
- #queuing_options — CagnutPicard::Markdup
- #queuing_options — CagnutPicard::MeanQualityByCycle
- #queuing_options — CagnutPicard::QualityScoreDistribution
- #queuing_options — CagnutPicard::SortSam
- #run — CagnutPicard::AddOrReplaceReadGroups
- #run — CagnutPicard::BuildBamIndex
- #run — CagnutPicard::CollectGcBiasMetrics
- #run — CagnutPicard::CollectInsertSizeMetrics
- #run — CagnutPicard::CollectMultipleMetrics
- #run — CagnutPicard::Markdup
- #run — CagnutPicard::MeanQualityByCycle
- #run — CagnutPicard::QualityScoreDistribution
- #run — CagnutPicard::SortSam
- #sort_sam — CagnutPicard::Base
- #sort_sam — CagnutPicard::Util
- #sort_sam_options — CagnutPicard::SortSam