be4311c07e14feb728abc6425ee606ffaa611a58
markd
  Fri Jan 22 06:46:58 2021 -0800
merge with master

diff --git src/lib/sparseMatrix.c src/lib/sparseMatrix.c
new file mode 100644
index 0000000..aa15793
--- /dev/null
+++ src/lib/sparseMatrix.c
@@ -0,0 +1,88 @@
+#include "common.h"
+#include "linefile.h"
+#include "hash.h"
+#include "localmem.h"
+#include "obscure.h"
+#include "sparseMatrix.h"
+
+
+struct sparseRowMatrix *sparseRowMatrixNew(int xSize, int ySize)
+/* Make up a new sparseRowMatrix structure */
+{
+struct sparseRowMatrix *matrix;
+AllocVar(matrix);
+matrix->xSize = xSize;
+matrix->ySize = ySize;
+matrix->lm = lmInit(0);
+lmAllocArray(matrix->lm, matrix->rows, ySize);
+return matrix;
+}
+
+void sparseRowMatrixFree(struct sparseRowMatrix **pMatrix)
+/* Free up resources associated with sparse matrix  */
+{
+struct sparseRowMatrix *matrix = *pMatrix;
+if (matrix != NULL)
+    {
+    lmCleanup(&matrix->lm);
+    freez(pMatrix);
+    }
+}
+
+void sparseRowMatrixAdd(struct sparseRowMatrix *matrix, int x, int y, float val)
+/* Add data to our sparse matrix */
+{
+struct sparseRowVal *fv;
+lmAllocVar(matrix->lm, fv);
+fv->x = x;
+fv->val = val;
+slAddHead(&matrix->rows[y], fv);
+}
+
+void sparseRowMatrixUnpackRow(struct sparseRowMatrix *matrix, int y, double *row, int rowSize)
+/* Unpack sparse matrix into buf that should be matrix->xSize long */
+{
+if (matrix->xSize != rowSize)
+    errAbort("sparseRowMatrixUnpackRow size mismatch %d vs %d", matrix->xSize, rowSize);
+int bufSize = matrix->xSize * sizeof(double);
+zeroBytes(row, bufSize);
+struct sparseRowVal *fv;
+for (fv = matrix->rows[y]; fv != NULL; fv = fv->next)
+    row[fv->x] = fv->val;
+}
+
+static void sparseRowMatrixTsvBody(struct sparseRowMatrix *matrix, char **rowLabels, FILE *f)
+/* Write body (but not header) of matrix to tsv file */
+{
+int xSize = matrix->xSize; 
+int ySize = matrix->ySize;
+int x,y;
+double row[xSize];
+for (y=0; y<ySize; ++y)
+    {
+    sparseRowMatrixUnpackRow(matrix, y, row, xSize);
+    fprintf(f, "%s", rowLabels[y]);
+    for (x=0; x<xSize; ++x)
+	{
+	double val = row[x];
+	if (val == 0.0) 
+	    fprintf(f, "\t0");	    // so much zero in the world
+	else
+	    fprintf(f, "\t%g", row[x]);
+	}
+    fprintf(f, "\n");
+    }
+}
+
+void sparseRowMatrixSaveAsTsv(struct sparseRowMatrix *matrix, 
+    char **columnLabels, char **rowLabels, char *fileName)
+/* Save sparseRowMatrix to tab-sep-file as expanded non-sparse */
+{
+FILE *f = mustOpen(fileName, "w");
+verbose(1, "outputting %d row matrix, a dot every 100 rows\n", matrix->ySize);
+fprintf(f, "gene\t");
+writeTsvRow(f, matrix->xSize, columnLabels);
+sparseRowMatrixTsvBody(matrix, rowLabels, f);
+carefulClose(&f);
+}
+