b7250793caf3c402744e5facdeaa2dc37479f67e
kent
  Wed May 19 11:27:13 2021 -0700
Removing docs about matrix market support, which is just a dream at the moment.

diff --git src/utils/matrixClusterColumns/matrixClusterColumns.c src/utils/matrixClusterColumns/matrixClusterColumns.c
index 0e2d049..b925457 100644
--- src/utils/matrixClusterColumns/matrixClusterColumns.c
+++ src/utils/matrixClusterColumns/matrixClusterColumns.c
@@ -3,49 +3,45 @@
 #include "common.h"
 #include "linefile.h"
 #include "hash.h"
 #include "options.h"
 #include "obscure.h"
 #include "fieldedTable.h"
 #include "sqlNum.h"
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "matrixClusterColumns - Group the columns of a matrix into clusters, and output a matrix with\n"
   "the same number of rows and generally much fewer columns. Combines columns by taking mean.\n"
   "usage:\n"
-  "   matrixClusterColumns input meta.tsv cluster outMatrix.tsv outStats.tsv [cluster2 outMatrix2.tsv outStats2.tsv ... ]\n"
+  "   matrixClusterColumns inMatrix.tsv meta.tsv cluster outMatrix.tsv outStats.tsv [cluster2 outMatrix2.tsv outStats2.tsv ... ]\n"
   "where:\n"
-  "   input is a file either in tsv format or in mtx (matrix mart sorted) format\n"
+  "   inMatrix.tsv is a file in tsv format with cell labels in first row and gene labels in first column\n"
   "   meta.tsv is a table where the first row is field labels and the first column is sample ids\n"
   "   cluster is the name of the field with the cluster names\n"
   "You can produce multiple clusterings in the same pass through the input matrix by specifying\n"
   "additional cluster/outMatrix/outStats triples in the command line.\n"
   "options:\n"
-  "   -columnLabels=file.txt - a file with a line for each column, required for mtx inputs\n"
-  "   -rowLabels=file.txt - a file with a label for each row, also required for mtx inputs\n"
   "   -makeIndex=index.tsv - output index tsv file with <matrix-col1><input-file-pos><line-len>\n"
   "   -median if set ouput median rather than mean cluster value\n"
   );
 }
 
 /* Command line validation table. */
 static struct optionSpec options[] = {
-   {"columnLabels", OPTION_STRING},
-   {"rowLabels", OPTION_STRING},
    {"makeIndex", OPTION_STRING},
    {"median", OPTION_BOOLEAN},
    {NULL, 0},
 };
 
 
 void readLineArray(char *fileName, int *retCount, char ***retLines)
 /* Return an array of strings, one for each line of file.  Return # of lines in file too */
 {
 /* This is sloppy with memory but it doesn't matter since we won't free it. */
 struct slName *el, *list = readAllLines(fileName);
 if (list == NULL)
     errAbort("%s is empty", fileName);
 int count = slCount(list);
 char **lines;