seqGetData, get_list (if matrix)

Author: zhengxwen

DESCRIPTION

@@ -2,8 +2,8 @@ Package: SeqArray
 Type: Package
 Title: Data management of large-scale whole-genome sequence variant calls
         using GDS files
-Version: 1.47.8
-Date: 2025-03-31
+Version: 1.47.9
+Date: 2025-04-04
 Depends: R (>= 3.5.0), gdsfmt (>= 1.31.1)
 Imports: methods, parallel, digest, S4Vectors, IRanges, GenomicRanges,
         GenomeInfoDb, Biostrings

R/Utilities.R

@@ -11,7 +11,8 @@
 
 # R expressions called in C internally
 .lang_eval <- list(
-    new_rle = quote(new("Rle", values=values, lengths=lengths))
+    new_rle = quote(new("Rle", values=values, lengths=lengths)),
+    as_List = quote(as(object, "List"))
 )
 
 # Compressed Lists in IRanges

src/GetData.cpp

@@ -826,7 +826,10 @@ static SEXP get_list(SEXP len, SEXP val, size_t elmsize, bool is_factor)
 			}
 			vv = ZeroLen;
 		} else {
-			vv = Rf_allocVector(TYPEOF(val), nn);
+			if (elmsize <= 1)
+				vv = Rf_allocVector(TYPEOF(val), nn);
+			else
+				vv = Rf_allocMatrix(TYPEOF(val), elmsize, psel[i]);
 			if (is_factor)
 			{
 				SET_CLASS(vv, GET_CLASS(val));
@@ -866,6 +869,24 @@ static SEXP get_list(SEXP len, SEXP val, size_t elmsize, bool is_factor)
 
 // .List_IRanges_value
 extern "C" SEXP OBJ_CompressedList = NULL;
+// as(, "List")
+extern "C" SEXP LANG_AS_LIST = NULL;
+
+/// create a S4Vectors::List object
+inline static SEXP as_s4vectors_list(SEXP x)
+{
+	// LANG_AS_LIST = quote(as(object, "List"))
+	SEXP epr = PROTECT(LANG_AS_LIST);
+	// set parameters
+	SETCADR(epr, x);   // parameter: object
+	// call
+	SEXP rv = PROTECT(Rf_eval(epr, R_GlobalEnv));
+	// free
+	SETCADR(epr, R_NilValue);   // parameter: object
+	// output
+	UNPROTECT(2);
+	return rv;
+}
 
 /// convert to a compressed list in IRanges
 static SEXP get_list2(SEXP len, SEXP val, bool is_factor)
@@ -1013,8 +1034,11 @@ static SEXP get_info(CFileInfo &File, TVarMap &Var, void *param)
 			// convert to a list
 			size_t d2 = (Var.NDim < 2) ? 1 : dimcnt[1];
 			if ((P->tolist == TRUE) || (d2 != 1))
+			{
 				rv_ans = get_list(I32, val, d2, is_factor);
-			else
+				if (P->tolist == NA_INTEGER)
+					rv_ans = as_s4vectors_list(rv_ans);
+			} else
 				rv_ans = get_list2(I32, val, is_factor);
 		} else {
 			// create `list(length, data)`

src/SeqArray.cpp

@@ -1567,6 +1567,7 @@ COREARRAY_DLL_EXPORT SEXP SEQ_ProgressAdd(SEXP ref, SEXP inc)
 // ===========================================================
 
 extern SEXP LANG_NEW_RLE;
+extern SEXP LANG_AS_LIST;
 extern SEXP OBJ_CompressedList;
 
 COREARRAY_DLL_EXPORT SEXP SEQ_Pkg_Init(SEXP dim_name, SEXP proc_cnt,
@@ -1584,6 +1585,7 @@ COREARRAY_DLL_EXPORT SEXP SEQ_Pkg_Init(SEXP dim_name, SEXP proc_cnt,
 	R_Process_Index = INTEGER(proc_idx);
 	// lang_eval
 	LANG_NEW_RLE = VECTOR_ELT(lang_eval, 0);
+	LANG_AS_LIST = VECTOR_ELT(lang_eval, 1);
 	// Compressed Lists in IRanges
 	OBJ_CompressedList = list_val;
 	// return