fe2dff20936a2f7d3cd570360b1d6fe0e1b65cc1
braney
  Thu Feb 10 14:15:36 2022 -0800
add an option to subColumn to skip lines that don't match

diff --git src/utils/subColumn/subColumn.c src/utils/subColumn/subColumn.c
index e8888e7..832c872 100644
--- src/utils/subColumn/subColumn.c
+++ src/utils/subColumn/subColumn.c
@@ -1,156 +1,169 @@
 /* subColumn - Substitute one column in a tab-separated file.. */
 
 /* Copyright (C) 2011 The Regents of the University of California 
  * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */
 #include "common.h"
 #include "localmem.h"
 #include "linefile.h"
 #include "hash.h"
 #include "options.h"
 #include "dystring.h"
 #include "obscure.h"
 
 
 boolean isList = FALSE;
+boolean skipMiss = FALSE;
 FILE *fMiss = NULL;
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "subColumn - Substitute one column in a tab-separated file.\n"
   "usage:\n"
   "   subColumn column in.tab sub.tab out.tab\n"
   "Where:\n"
   "    column is the column number (starting with 1)\n"
   "    in.tab is a tab-separated file\n"
   "    sub.tab is a where first column is old values, second new\n"
   "    out.tab is the substituted output\n"
   "options:\n"
   "   -list - Column is a comma-separated list.  Substitute all elements in list\n"
   "   -miss=fileName - Print misses to this file instead of aborting\n"
+  "   -skipMiss -- skip missing id's instead of outputting them\n"
   );
 }
 
 static struct optionSpec options[] = {
    {"list", OPTION_BOOLEAN},
    {"miss", OPTION_STRING},
+   {"skipMiss", OPTION_BOOLEAN},
    {NULL, 0},
 };
 
 char *subCommaList(struct hash *subHash, char *in)
 /* In is a comma-separated list.  Return the list with
  * substitution done.  This routine not reentrant. */
 {
 static struct dyString *dy;
 if (dy == NULL)
     dy = dyStringNew(0);
 else
     dyStringClear(dy);
 while (in != NULL && in[0] != 0)
     {
     char *e = strchr(in, ',');
     if (e != NULL)
         *e++ = 0;
     char *s = hashMustFindVal(subHash, in);
     dyStringPrintf(dy, "%s,", s);
     in = e;
     }
 return dy->string;
 }
 
 int missCount = 0;
 
 struct hash *hashTwoColumnTsv(char *fileName)
 /* Given a two column file (key, value) return a hash. */
 {
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 struct hash *hash = hashNew(16);
 char *row[3];
 int fields = 0;
 while ((fields = lineFileChopTab(lf, row)) != 0)
     {
     lineFileExpectWords(lf, 2, fields);
     char *name = row[0];
     char *value = lmCloneString(hash->lm, row[1]);
     hashAdd(hash, name, value);
     }
 lineFileClose(&lf);
 return hash;
 }
 
 
 void subColumn(char *asciiColumn, char *inFile, char *subFile, char *outFile)
 /* subColumn - Substitute one column in a tab-separated file.. */
 {
 struct hash *subHash = hashTwoColumnTsv(subFile);
 int column = atoi(asciiColumn);
 if (column == 0)
     usage();
 else
     column -= 1;
 char *row[1024*4];
 struct lineFile *lf = lineFileOpen(inFile, TRUE);
+struct dyString *dy = newDyString(1024);
 FILE *f = mustOpen(outFile, "w");
 int rowCount;
 while ((rowCount = lineFileChopNextTab(lf, row, ArraySize(row))) > 0)
     {
     if (rowCount == ArraySize(row))
         errAbort("Too many columns (%d) line %d of  %s.", rowCount, lf->lineIx, lf->fileName);
     if (column >= rowCount)
         errAbort("Not enough columns (%d) line %d of  %s.", rowCount, lf->lineIx, lf->fileName);
     int i;
     for (i=0; i<rowCount; ++i)
 	{
 	char *s = row[i];
 	if (i == column)
 	    {
 	    if (isList)
 	        {
 		s = subCommaList(subHash, s);
 		}
 	    else
 		{
 		char *sub = hashFindVal(subHash, s);
 		if (sub == NULL)
 		    {
+		    if (fMiss || skipMiss)
+			{
                         if (fMiss)
                             {
                             fprintf(fMiss, "%s\n", s);
                             ++missCount;
                             }
+                        if (skipMiss)
+                            goto out;
+			}
 		    else
 			errAbort("%s not in %s line %d of %s", s, subFile, lf->lineIx, lf->fileName);
 		    }
 		else
 		    s = sub;
 		}
 	    }
-	fputs(s, f);
+        dyStringAppend(dy, s);
 	if (i == rowCount-1)
-	    fputc('\n', f);
+            dyStringAppendC(dy, '\n');
 	else
-	    fputc('\t', f);
+            dyStringAppendC(dy, '\t');
 	}
+    fputs(dy->string, f);
+out:
+    dyStringResize(dy, 0);
     }
 carefulClose(&f);
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 optionInit(&argc, argv, options);
 if (argc != 5)
     usage();
 isList = optionExists("list");
 char *fileName = optionVal("miss", NULL);
 if (fileName != NULL)
     fMiss = mustOpen(fileName, "w");
+skipMiss = optionExists("skipMiss");
 subColumn(argv[1], argv[2], argv[3], argv[4]);
 if (fMiss != NULL)
     {
     carefulClose(&fMiss);
     warn("missed %d\n", missCount);
     }
 return 0;
 }