176 lines
6.4 KiB
C++
176 lines
6.4 KiB
C++
/*
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Description: BQSR
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Copyright : All right reserved by ICT
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Author : Zhang Zhonghai
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Date : 2025/10/10
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*/
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#pragma once
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#include <string>
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#include <vector>
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using std::string;
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using std::vector;
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namespace nsbqsr {
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enum IndexFormat { BAI, CSI };
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} // namespace nsbqsr
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/* bqsr parameters */
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struct BQSRArg {
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// common parameters
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string INPUT_FILE; // input bam filename
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string OUTPUT_FILE; // output bam filename
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int NUM_THREADS = 1;
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size_t MAX_MEM = ((size_t)1) << 30; // 1G
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bool DUPLEX_IO = true; //
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/* "Whether to create an index when writing VCF or coordinate sorted BAM output.", common = true */
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bool CREATE_INDEX = true;
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nsbqsr::IndexFormat INDEX_FORMAT = nsbqsr::IndexFormat::BAI;
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/* Add PG tag to each read in a SAM or BAM (PGTagArgumentCollection)*/
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bool ADD_PG_TAG_TO_READS = true;
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//
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string CLI_STR;
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//
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string START_TIME;
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string PROGRAM_RECORD_ID = "FastBQSR";
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// reference file
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string REFERENCE_FILE;
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// known sites vcf files
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vector<string> KNOWN_SITES_VCFS;
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// end of common parameters
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// We always use the same covariates. The field is retained for compatibility with GATK3 reports.
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bool DO_NOT_USE_STANDARD_COVARIATES = false;
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//It makes no sense to run BQSR without sites. so we remove this option.
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bool RUN_WITHOUT_DBSNP = false;
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// We don't support SOLID. The field is retained for compatibility with GATK3 reports.
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string SOLID_RECAL_MODE = "SET_Q_ZERO";
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string SOLID_NOCALL_STRATEGY = "THROW_EXCEPTION";
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//@Hidden @Argument(fullName = "default-platform", optional = true,
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// doc = "If a read has no platform then default to the provided String. Valid options are illumina, 454, and solid.") public String
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string DEFAULT_PLATFORM = "";
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// @Hidden @Argument(fullName = "force-platform", optional = true,
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// doc = "If provided, the platform of EVERY read will be forced to be the provided String. Valid options are illumina, 454, and "solid.")
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string FORCE_PLATFORM = "";
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string existingRecalibrationReport = "";
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/**
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* The context covariate will use a context of this size to calculate its covariate value for base mismatches. Must be
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* between 1 and 13 (inclusive). Note that higher values will increase runtime and required java heap size.
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*/
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int MISMATCHES_CONTEXT_SIZE = 2;
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/**
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* The context covariate will use a context of this size to calculate its covariate value for base insertions and deletions.
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* Must be between 1 and 13 (inclusive). Note that higher values will increase runtime and required java heap size.
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*/
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int INDELS_CONTEXT_SIZE = 3;
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/**
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* The cycle covariate will generate an error if it encounters a cycle greater than this value.
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* This argument is ignored if the Cycle covariate is not used.
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*/
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int MAXIMUM_CYCLE_VALUE = 500;
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/**
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* A default base qualities to use as a prior (reported quality) in the mismatch covariate model. This value will replace
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* all base qualities in the read for this default value. Negative value turns it off. [default is off]
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*/
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int8_t MISMATCHES_DEFAULT_QUALITY = -1;
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/**
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* A default base qualities to use as a prior (reported quality) in the insertion covariate model. This parameter is used
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* for all reads without insertion quality scores for each base. [default is on]
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*/
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int8_t INSERTIONS_DEFAULT_QUALITY = 45;
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/**
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* A default base qualities to use as a prior (reported quality) in the mismatch covariate model. This value will replace
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* all base qualities in the read for this default value. Negative value turns it off. [default is on]
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*/
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int8_t DELETIONS_DEFAULT_QUALITY = 45;
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/**
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* Reads with low quality bases on either tail (beginning or end) will not be considered in the context. This parameter
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* defines the quality below which (inclusive) a tail is considered low quality
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*/
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int8_t LOW_QUAL_TAIL = 2;
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/**
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* BQSR generates a quantization table for quick quantization later by subsequent tools. BQSR does not quantize the base
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* qualities, this is done by the engine with the -qq or -bqsr options. This parameter tells BQSR the number of levels of
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* quantization to use to build the quantization table.
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*/
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int QUANTIZING_LEVELS = 16;
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/**
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* The tag name for the binary tag covariate (if using it)
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*/
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string BINARY_TAG_NAME = "";
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/**
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* bqsr-baq-gap-open-penalty, BQSR BAQ gap open penalty (Phred Scaled). Default value is 40. 30 is perhaps better
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* for whole genome call sets
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*/
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double BAQGOP = 40;
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/**
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* This flag tells GATK not to modify quality scores less than this value. Instead they will be written out unmodified in
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* the recalibrated BAM file. In general it's unsafe to change qualities scores below < 6, since base callers use these
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* values to indicate random or bad bases. For example, Illumina writes Q2 bases when the machine has really gone wrong.
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* This would be fine in and of itself, but when you select a subset of these reads based on their ability to align to the
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* reference and their dinucleotide effect, your Q2 bin can be elevated to Q8 or Q10, leading to issues downstream.
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*/
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int PRESERVE_QSCORES_LESS_THAN = 6;
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/**
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* enable-baq, do BAQ correction" (base alignment quality), 在GATK里hidden了，用不到了？
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*/
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bool enableBAQ = false;
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/**
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* compute-indel-bqsr-tables, compute indel BQSR tables"
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*/
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bool computeIndelBQSRTables = false;
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// --------------------------------------------------------------------------------------------------------------
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//
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// quality encoding checking arguments
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//
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// --------------------------------------------------------------------------------------------------------------
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/**
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* This flag tells GATK to use the original base qualities (that were in the data before BQSR/recalibration) which
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* are stored in the OQ tag, if they are present, rather than use the post-recalibration quality scores. If no OQ
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* tag is present for a read, the standard qual score will be used.
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*/
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bool useOriginalBaseQualities = false;
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/**
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* If reads are missing some or all base quality scores, this value will be used for all base quality scores.
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* By default this is set to -1 to disable default base quality assignment.
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*/
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int8_t defaultBaseQualities = -1;
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}; |