Method List
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#add_java_params CagnutPicard::Configuration
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#add_or_replace_readgroups CagnutPicard::Base
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#add_or_replace_readgroups CagnutPicard::Util
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#add_or_replace_readgroups_params CagnutPicard::Configuration
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#add_read_group_options CagnutPicard::AddOrReplaceReadGroups
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#attributes CagnutPicard::Configuration
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#build_bam_index CagnutPicard::Base
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#build_bam_index CagnutPicard::Util
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#build_bam_index_options CagnutPicard::BuildBamIndex
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#build_bam_index_params CagnutPicard::Configuration
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#check_Picard CagnutPicard::CheckTools
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#check_picard_dict CagnutPicard::CheckTools
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#check_ref_related CagnutPicard::CheckTools
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#check_tool CagnutPicard::CheckTools
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#collect_gc_bias_metrics CagnutPicard::Util
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#collect_gc_bias_metrics CagnutPicard::Base
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#collect_gc_bias_metrics_options CagnutPicard::CollectGcBiasMetrics
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#collect_gc_bias_metrics_params CagnutPicard::Configuration
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#collect_insert_size_metrics CagnutPicard::Base
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#collect_insert_size_metrics CagnutPicard::Util
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#collect_insert_size_metrics_options CagnutPicard::CollectInsertSizeMetrics
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#collect_insert_size_metrics_params CagnutPicard::Configuration
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#collect_multiple_metrics CagnutPicard::Base
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#collect_multiple_metrics CagnutPicard::Util
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#collect_multiple_metrics_options CagnutPicard::CollectMultipleMetrics
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#collect_multiple_metrics_params CagnutPicard::Configuration
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#config CagnutPicard::Util
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config CagnutPicard
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#generate_rg_str CagnutPicard::Configuration
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#generate_script CagnutPicard::QualityScoreDistribution
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#generate_script CagnutPicard::MeanQualityByCycle
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#generate_script CagnutPicard::CollectInsertSizeMetrics
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#generate_script CagnutPicard::CollectGcBiasMetrics
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#generate_script CagnutPicard::AddOrReplaceReadGroups
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#generate_script CagnutPicard::Markdup
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#generate_script CagnutPicard::CollectMultipleMetrics
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#generate_script CagnutPicard::BuildBamIndex
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#generate_script CagnutPicard::SortSam
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#initialize CagnutPicard::QualityScoreDistribution
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#initialize CagnutPicard::AddOrReplaceReadGroups
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#initialize CagnutPicard::BuildBamIndex
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#initialize CagnutPicard::Util
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#initialize CagnutPicard::CollectMultipleMetrics
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#initialize CagnutPicard::CollectInsertSizeMetrics
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#initialize CagnutPicard::MeanQualityByCycle
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#initialize CagnutPicard::SortSam
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#initialize CagnutPicard::Markdup
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#initialize CagnutPicard::CollectGcBiasMetrics
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load CagnutPicard::Configuration
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#load CagnutPicard::Configuration
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#markdup CagnutPicard::Util
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#markdup CagnutPicard::Base
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#markduplicate_options CagnutPicard::Markdup
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#markduplicate_params CagnutPicard::Configuration
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#mean_quality_by_cycle CagnutPicard::Util
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#mean_quality_by_cycle CagnutPicard::Base
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#mean_quality_by_cycle_options CagnutPicard::MeanQualityByCycle
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#mean_quality_by_cycle_params CagnutPicard::Configuration
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#modified_java_array CagnutPicard::CollectMultipleMetrics
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#modified_java_array CagnutPicard::CollectInsertSizeMetrics
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#modified_java_array CagnutPicard::SortSam
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#modified_java_array CagnutPicard::Markdup
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#modified_java_array CagnutPicard::QualityScoreDistribution
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#modified_java_array CagnutPicard::AddOrReplaceReadGroups
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#modified_java_array CagnutPicard::BuildBamIndex
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#modified_java_array CagnutPicard::MeanQualityByCycle
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#modified_java_array CagnutPicard::CollectGcBiasMetrics
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#params_combination_hash CagnutPicard::BuildBamIndex
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#params_combination_hash CagnutPicard::SortSam
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#params_combination_hash CagnutPicard::Markdup
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#params_combination_hash CagnutPicard::AddOrReplaceReadGroups
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#params_combination_hash CagnutPicard::CollectInsertSizeMetrics
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#params_combination_hash CagnutPicard::QualityScoreDistribution
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#params_combination_hash CagnutPicard::CollectMultipleMetrics
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#params_combination_hash CagnutPicard::MeanQualityByCycle
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#params_combination_hash CagnutPicard::CollectGcBiasMetrics
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#picard CagnutPicard::Util
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#picard_qc_metrics CagnutPicard::Util
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#quailty_score_distribution_options CagnutPicard::QualityScoreDistribution
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#quailty_score_distribution_params CagnutPicard::Configuration
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#quality_score_distribution CagnutPicard::Util
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#quality_score_distribution CagnutPicard::Base
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#queuing_options CagnutPicard::BuildBamIndex
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#queuing_options CagnutPicard::SortSam
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#queuing_options CagnutPicard::Markdup
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#queuing_options CagnutPicard::MeanQualityByCycle
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#queuing_options CagnutPicard::CollectInsertSizeMetrics
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#queuing_options CagnutPicard::CollectMultipleMetrics
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#queuing_options CagnutPicard::CollectGcBiasMetrics
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#queuing_options CagnutPicard::QualityScoreDistribution
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#queuing_options CagnutPicard::AddOrReplaceReadGroups
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#rg_str_picard CagnutPicard::Configuration
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#run CagnutPicard::BuildBamIndex
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#run CagnutPicard::MeanQualityByCycle
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#run CagnutPicard::SortSam
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#run CagnutPicard::Markdup
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#run CagnutPicard::AddOrReplaceReadGroups
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#run CagnutPicard::CollectMultipleMetrics
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#run CagnutPicard::CollectGcBiasMetrics
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#run CagnutPicard::CollectInsertSizeMetrics
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#run CagnutPicard::QualityScoreDistribution
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#sort_sam CagnutPicard::Util
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#sort_sam CagnutPicard::Base
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#sort_sam_options CagnutPicard::SortSam
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#sort_sam_params CagnutPicard::Configuration