src/utils/raSqlQuery/raSqlQuery.c 1.17

Index: src/utils/raSqlQuery/raSqlQuery.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/utils/raSqlQuery/raSqlQuery.c,v
retrieving revision 1.16
retrieving revision 1.17
diff -b -B -U 4 -r1.16 -r1.17
--- src/utils/raSqlQuery/raSqlQuery.c	22 Nov 2009 01:37:41 -0000	1.16
+++ src/utils/raSqlQuery/raSqlQuery.c	22 Nov 2009 02:01:30 -0000	1.17
@@ -11,8 +11,9 @@
 #include "sqlNum.h"
 #include "raRecord.h"
 #include "rql.h"
 #include "portable.h"
+#include "../../hg/inc/hdb.h"
 
 static char const rcsid[] = "$Id$";
 
 static char *clQueryFile = NULL;
@@ -24,8 +25,9 @@
 static boolean clParent = FALSE;
 static boolean clAddFile = FALSE;
 static boolean clAddDb = FALSE;
 static char *clRestrict = NULL;
+static boolean clStrict = FALSE;
 static char *clDb = NULL;
 static boolean clOverrideNeeded = FALSE;
 
 static char *clTrackDbRootDir = "~/kent/src/hg/makeDb/trackDb";
@@ -37,8 +39,11 @@
 errAbort(
   "raSqlQuery - Do a SQL-like query on a RA file.\n"
   "usage:\n"
   "   raSqlQuery raFile(s) query-options\n"
+  "or\n"
+  "   raSqlQuery -db=dbName query-options\n"
+  "Where dbName is a UCSC Genome database like hg18, sacCer1, etc.\n"
   "One of the following query-options must be specified\n"
   "   -queryFile=fileName\n"
   "   \"-query=select list,of,fields where field='this'\"\n"
   "The queryFile just has a query in it in the same form as the query option, but\n"
@@ -59,9 +64,10 @@
   "   -merge - If there are multiple raFiles, records with the same keyField will be\n"
   "          merged together with fields in later files overriding fields in earlier files\n"
   "   -addFile - Add 'file' field to say where record is defined\n"
   "   -addDb - Add 'db' field to say where record is defined\n"
-  "   -restrict=keyListFile - restrict output to only ones with keys in file, which\n"
+  "   -restrict=keyListFile - restrict output to only ones with keys in file.\n"
+  "   -strict - Used only with db option.  Only report tracks that exist in db\n"
   "   -db=hg19 - Acts on trackDb files for the given database.  Sets up list of files\n"
   "              appropriately and sets parent, merge, and override all.\n"
   "              Use db=all for all databases\n"
   "The output will be to stdout, in the form of a .ra file if the select command is used\n"
@@ -81,8 +87,9 @@
    {"noInheritField", OPTION_STRING},
    {"addFile", OPTION_BOOLEAN},
    {"addDb", OPTION_BOOLEAN},
    {"restrict", OPTION_STRING},
+   {"strict", OPTION_BOOLEAN},
    {"db", OPTION_STRING},
    {"overrideNeeded", OPTION_BOOLEAN},
    {NULL, 0},
 };
@@ -430,15 +437,18 @@
 for (ra = raList; ra != NULL; ra = ra->next)
     {
     if (rqlStatementMatch(rql, ra))
         {
+	if (!clStrict || (ra->key && hTableOrSplitExists(db, ra->key)))
+	    {
 	matchCount += 1;
 	if (doSelect)
 	    {
 	    rqlStatementOutput(rql, ra, (clAddFile ? "file" : NULL), clAddDb, out);
 	    }
 	}
     }
+    }
 if (!doSelect)
     printf("%d\n", matchCount);
 }
 
@@ -455,8 +465,9 @@
 clNoInheritField = optionVal("noInheritField", clNoInheritField);
 clAddFile = optionExists("addFile");
 clAddDb = optionExists("addDb");
 clRestrict = optionVal("restrict", NULL);
+clStrict = optionExists("strict");
 clOverrideNeeded = optionExists("overrideNeeded");
 clDb = optionVal("db", NULL);
 if (argc < 2 && !clDb)
     usage();