multichrom work for SLiM and VCF output, and readFromVCF()

Author: bhaller

QtSLiM/help/SLiMHelpClasses.html

@@ -118,6 +118,14 @@ development head (in the master branch):
 			Haplosome method outputMS(): check that all haplosomes belong to a single chromosome, output MS based on that
 			Subpopulation method outputMSSample(): add a [Niso<Chromosome>$ chromosome = NULL] parameter to identify the chromosome to sample with
 			Haplosome method readFromMS(): check that all haplosomes belong to a single chromosome, input MS based on that
+		fix built-in SLiM-format partial input/output methods for multiple chromosomes:
+			Haplosome method output(): check that all haplosomes belong to a single chromosome; output the chromosome symbol in the header if multi-chrom
+			Subpopulation method outputSample(): check that all haplosomes belong to a single chromosome
+		fix built-in VCF input/output methods for multiple chromosomes:
+			Haplosome method outputVCF(): check that all haplosomes belong to a single chromosome; pairs haplosomes as appropriate
+			Subpopulation method outputVCFSample(): check that all haplosomes belong to a single chromosome; use chromosome symbols for the CHROM column
+			add [l$ groupAsIndividuals = T] parameter; if F, each haplosome is emitted as a haploid call rather than forming diploids, regardless of the chromosome's ploidy
+			Haplosome_Class::ExecuteMethod_readFromVCF(): require VCF data that is single-chromosome, as with output
 
 
 version 4.3 (Eidos version 3.3):

SLiMgui/SLiMHelpClasses.rtf

@@ -98,6 +98,53 @@ Chromosome::Chromosome(Species &p_species, ChromosomeType p_type, int64_t p_id,
 	color_sub_ = "#3333FF";
 	if (!color_sub_.empty())
 		Eidos_GetColorComponents(color_sub_, &color_sub_red_, &color_sub_green_, &color_sub_blue_);
+	
+	// depending on the type of chromosome, cache some properties for quick reference
+	// FIXME MULTICHROM: add more properties here, like:
+	//
+	//		DefaultsToZeroRecombination()
+	//		IsSexChromosome()
+	//		TypeString()	("A" for type kA_DiploidAutosome, etc.)
+	//		...lots more, scan the code...
+	switch (type_)
+	{
+		case ChromosomeType::kA_DiploidAutosome:				// type "A"
+			intrinsic_ploidy_ = 2;
+			break;
+		case ChromosomeType::kH_HaploidAutosome:				// type "H"
+			intrinsic_ploidy_ = 1;
+			break;
+		case ChromosomeType::kX_XSexChromosome:					// type "X"
+			intrinsic_ploidy_ = 2;
+			break;
+		case ChromosomeType::kY_YSexChromosome:					// type "Y"
+			intrinsic_ploidy_ = 1;
+			break;
+		case ChromosomeType::kZ_ZSexChromosome:					// type "Z"
+			intrinsic_ploidy_ = 2;
+			break;
+		case ChromosomeType::kW_WSexChromosome:					// type "W"
+			intrinsic_ploidy_ = 1;
+			break;
+		case ChromosomeType::kHF_HaploidFemaleInherited:		// type "HF"
+			intrinsic_ploidy_ = 1;
+			break;
+		case ChromosomeType::kFL_HaploidFemaleLine:				// type "FL"
+			intrinsic_ploidy_ = 1;
+			break;
+		case ChromosomeType::kHM_HaploidMaleInherited:			// type "HM"
+			intrinsic_ploidy_ = 1;
+			break;
+		case ChromosomeType::kML_HaploidMaleLine:				// type "ML"
+			intrinsic_ploidy_ = 1;
+			break;
+		case ChromosomeType::kHNull_HaploidAutosomeWithNull:	// type "H-"
+			intrinsic_ploidy_ = 2;
+			break;
+		case ChromosomeType::kNullY_YSexChromosomeWithNull:		// type "-Y"
+			intrinsic_ploidy_ = 2;
+			break;
+	}
 }
 
 Chromosome::~Chromosome(void)

VERSIONS

@@ -67,6 +67,9 @@ class Chromosome : public EidosDictionaryRetained
 	slim_chromosome_index_t index_;
 	ChromosomeType type_;
 
+	// cached properties of the chromosome that depend upon its type
+	int intrinsic_ploidy_;									// 1 or 2; the number of haplosomes kept for the chromosome
+	
 	// This vector contains all the genomic elements for this chromosome.  It is in sorted order once initialization is complete.
 	std::vector<GenomicElement *> genomic_elements_;		// OWNED POINTERS: genomic elements belong to the chromosome
 
@@ -289,15 +292,18 @@ class Chromosome : public EidosDictionaryRetained
 	explicit Chromosome(Species &p_species, ChromosomeType p_type, int64_t p_id, std::string p_symbol, slim_chromosome_index_t p_index, int p_preferred_mutcount);
 	~Chromosome(void);
 
-	inline __attribute__((always_inline)) int64_t ID(void)	{ return id_; }
-	inline __attribute__((always_inline)) const std::string &Symbol(void)	{ return symbol_; }
-	inline __attribute__((always_inline)) slim_chromosome_index_t Index(void) { return index_; }
-	inline __attribute__((always_inline)) ChromosomeType Type(void) { return type_; }
-	inline __attribute__((always_inline)) const std::string &Name(void) { return name_; }
+	inline __attribute__((always_inline)) int64_t ID(void) const	{ return id_; }
+	inline __attribute__((always_inline)) const std::string &Symbol(void) const	{ return symbol_; }
+	inline __attribute__((always_inline)) slim_chromosome_index_t Index(void) const { return index_; }
+	inline __attribute__((always_inline)) ChromosomeType Type(void) const { return type_; }
+	inline __attribute__((always_inline)) const std::string &Name(void) const { return name_; }
 	inline __attribute__((always_inline)) void SetName(const std::string &p_name) { name_ = p_name; }
 
+	inline __attribute__((always_inline)) int IntrinsicPloidy(void) const { return intrinsic_ploidy_; }
+	
 	inline __attribute__((always_inline)) std::vector<GenomicElement *> &GenomicElements(void)			{ return genomic_elements_; }
-	inline __attribute__((always_inline)) NucleotideArray *AncestralSequence(void)						{ return ancestral_seq_buffer_; }
+	inline __attribute__((always_inline)) const std::vector<GenomicElement *> &GenomicElements(void) const			{ return genomic_elements_; }
+	inline __attribute__((always_inline)) NucleotideArray *AncestralSequence(void) const						{ return ancestral_seq_buffer_; }
 
 	// initialize the random lookup tables used by Chromosome to draw mutation and recombination events
 	void CreateNucleotideMutationRateMap(void);