phased-r2 bugfix: clip single negative root up to 0

2.0/pgenlibr/DESCRIPTION

@@ -1,8 +1,8 @@
 Package: pgenlibr
 Type: Package
 Title: PLINK 2 Binary (.pgen) Reader
-Version: 0.4.0
-Date: 2025-01-15
+Version: 0.4.1
+Date: 2025-0x-yy
 Authors@R: c(person(given = "Christopher",
                     family = "Chang",
                     role = c("aut", "cre"),

2.0/pgenlibr/NAMESPACE

@@ -15,6 +15,7 @@ export(GetVariantId)
 export(GetVariantPos)
 export(GetVariantsById)
 export(HardcallPhasePresent)
+export(HasSparseHardcalls)
 export(IntAlleleCodeBuf)
 export(IntBuf)
 export(NewPgen)
@@ -24,6 +25,7 @@ export(ReadAlleles)
 export(ReadHardcalls)
 export(ReadIntList)
 export(ReadList)
+export(ReadSparseHardcalls)
 export(VariantScores)
 import(Rcpp)
 importFrom(Rcpp,evalCpp)

2.0/pgenlibr/R/RcppExports.R

@@ -129,13 +129,49 @@ BoolBuf <- function(pgen) {
 #' @param variant_num Variant index (1-based).
 #' @param allele_num Allele index; 1 corresponds to REF, 2 to the first ALT
 #' allele, 3 to the second ALT allele if it exists, etc.  Optional, defaults
-#' 2.
+#' to 2.
 #' @return No return value, called for buf-filling side-effect.
 #' @export
 ReadHardcalls <- function(pgen, buf, variant_num, allele_num = 2L) {
     invisible(.Call(`_pgenlibr_ReadHardcalls`, pgen, buf, variant_num, allele_num))
 }
 
+#' Returns whether hardcalls for the variant_numth variant and given allele
+#' are represented in a sparse manner that is supported by
+#' ReadSparseHardcalls().
+#'
+#' @param pgen Object returned by NewPgen().
+#' @param variant_num Variant index (1-based).
+#' @param allele_num Allele index; 1 corresponds to REF, 2 to the first ALT
+#' allele, 3 to the second ALT allele if it exists, etc.  Optional, defaults
+#' to 2.
+#' @return True iff the (variant, allele) pair has a sparse representation
+#' that can be returned by ReadSparseHardcalls().
+#' @export
+HasSparseHardcalls <- function(pgen, variant_num, allele_num = 2L) {
+    .Call(`_pgenlibr_HasSparseHardcalls`, pgen, variant_num, allele_num)
+}
+
+#' If HasSparseHardcalls() is true, returns a sparse representation for the
+#' (variant, allele) pair.  If HasSparseHardcalls() is false, the function
+#' fails.
+#'
+#' @param pgen Object returned by NewPgen().
+#' @param variant_num Variant index (1-based).
+#' @param allele_num Allele index; 1 corresponds to REF, 2 to the first ALT
+#' allele, 3 to the second ALT allele if it exists, etc.  Optional, defaults
+#' to 2.
+#' @param return_ints Whether to make the "counts" component of the return
+#' value an IntegerVector instead of a NumericVector; defaults to false.
+#' @return Either an empty list, in which case buf is filled in the same
+#' mannerObject where "sample_ids" is an increasing sequence of positive
+#' integers listing which samples have the allele, and "counts" is a vector
+#' listing the allele counts for those samples.
+#' @export
+ReadSparseHardcalls <- function(pgen, variant_num, allele_num = 2L, return_ints = FALSE) {
+    .Call(`_pgenlibr_ReadSparseHardcalls`, pgen, variant_num, allele_num, return_ints)
+}
+
 #' Loads the variant_numth variant, and then fills buf with numeric dosages
 #' in [0, 2] indicating the dosages of the first ALT (or user-specified)
 #' allele for each sample, with missing values represented by NA.
@@ -148,7 +184,7 @@ ReadHardcalls <- function(pgen, buf, variant_num, allele_num = 2L) {
 #' @param variant_num Variant index (1-based).
 #' @param allele_num Allele index; 1 corresponds to REF, 2 to the first ALT
 #' allele, 3 to the second ALT allele if it exists, etc.  Optional, defaults
-#' 2.
+#' to 2.
 #' @return No return value, called for buf-filling side-effect.
 #' @export
 Read <- function(pgen, buf, variant_num, allele_num = 2L) {

2.0/pgenlibr/src/RcppExports.cpp

@@ -148,6 +148,33 @@ BEGIN_RCPP
     return R_NilValue;
 END_RCPP
 }
+// HasSparseHardcalls
+bool HasSparseHardcalls(List pgen, int variant_num, int allele_num);
+RcppExport SEXP _pgenlibr_HasSparseHardcalls(SEXP pgenSEXP, SEXP variant_numSEXP, SEXP allele_numSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< List >::type pgen(pgenSEXP);
+    Rcpp::traits::input_parameter< int >::type variant_num(variant_numSEXP);
+    Rcpp::traits::input_parameter< int >::type allele_num(allele_numSEXP);
+    rcpp_result_gen = Rcpp::wrap(HasSparseHardcalls(pgen, variant_num, allele_num));
+    return rcpp_result_gen;
+END_RCPP
+}
+// ReadSparseHardcalls
+List ReadSparseHardcalls(List pgen, int variant_num, int allele_num, bool return_ints);
+RcppExport SEXP _pgenlibr_ReadSparseHardcalls(SEXP pgenSEXP, SEXP variant_numSEXP, SEXP allele_numSEXP, SEXP return_intsSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< List >::type pgen(pgenSEXP);
+    Rcpp::traits::input_parameter< int >::type variant_num(variant_numSEXP);
+    Rcpp::traits::input_parameter< int >::type allele_num(allele_numSEXP);
+    Rcpp::traits::input_parameter< bool >::type return_ints(return_intsSEXP);
+    rcpp_result_gen = Rcpp::wrap(ReadSparseHardcalls(pgen, variant_num, allele_num, return_ints));
+    return rcpp_result_gen;
+END_RCPP
+}
 // Read
 void Read(List pgen, NumericVector buf, int variant_num, int allele_num);
 RcppExport SEXP _pgenlibr_Read(SEXP pgenSEXP, SEXP bufSEXP, SEXP variant_numSEXP, SEXP allele_numSEXP) {
@@ -320,6 +347,8 @@ static const R_CallMethodDef CallEntries[] = {
     {"_pgenlibr_IntAlleleCodeBuf", (DL_FUNC) &_pgenlibr_IntAlleleCodeBuf, 1},
     {"_pgenlibr_BoolBuf", (DL_FUNC) &_pgenlibr_BoolBuf, 1},
     {"_pgenlibr_ReadHardcalls", (DL_FUNC) &_pgenlibr_ReadHardcalls, 4},
+    {"_pgenlibr_HasSparseHardcalls", (DL_FUNC) &_pgenlibr_HasSparseHardcalls, 3},
+    {"_pgenlibr_ReadSparseHardcalls", (DL_FUNC) &_pgenlibr_ReadSparseHardcalls, 4},
     {"_pgenlibr_Read", (DL_FUNC) &_pgenlibr_Read, 4},
     {"_pgenlibr_ReadAlleles", (DL_FUNC) &_pgenlibr_ReadAlleles, 4},
     {"_pgenlibr_ReadIntList", (DL_FUNC) &_pgenlibr_ReadIntList, 2},