src/hg/makeDb/hgPar/hgPar.c 1.1

Index: src/hg/makeDb/hgPar/hgPar.c
===================================================================
RCS file: src/hg/makeDb/hgPar/hgPar.c
diff -N src/hg/makeDb/hgPar/hgPar.c
--- /dev/null	1 Jan 1970 00:00:00 -0000
+++ src/hg/makeDb/hgPar/hgPar.c	17 Feb 2010 08:54:21 -0000	1.1
@@ -0,0 +1,105 @@
+/* hgPar - create PAR track. */
+#include "common.h"
+#include "linefile.h"
+#include "options.h"
+#include "psl.h"
+#include "parSpec.h"
+#include "hdb.h"
+#include "hgRelate.h"
+#include "jksql.h"
+
+static char const rcsid[] = "$Id$";
+
+void usage()
+/* Explain usage and exit. */
+{
+errAbort(
+  "hgPar - create PAR track\n"
+  "usage:\n"
+  "   hgPar db parSpecFile parTable\n"
+  "options:\n"
+  "  -fileOutput - parTable is a file to write instead of a table\n"
+  "Format of parSpecFile are rows of the following tab-separated values:\n"
+  "   name chromA startA endA chromB startB endB\n"
+  "\n"
+  "Size of regions must be the same.  Order of chromosomes is not important/\n"
+  "Name is something like 'par1', 'par2'.  The resulting table is in PSL\n"
+  "format with a record for each chromosome\n"
+  );
+}
+
+static struct optionSpec options[] = {
+    {"fileOutput", OPTION_BOOLEAN},
+    {NULL, 0},
+};
+
+static struct psl *mkParPsl(char *qName, unsigned qSize, int qStart, int qEnd,
+                            char *tName, unsigned tSize, int tStart, int tEnd)
+/* create one of the PAR psls */
+{
+if ((qEnd - qStart) != (tEnd - tStart))
+    errAbort("size of PAR locations must be the same: %s:%d-%d and %s:%d-%d",
+             qName, qStart, qEnd, tName, tStart, tEnd);
+struct psl* psl = pslNew(qName, qSize, qStart, qEnd, tName, tSize, tStart, tEnd,
+                         "+", 1, 0);
+psl->match = qEnd - qStart;
+psl->blockCount = 1;
+psl->blockSizes[0] = qEnd - qStart;
+psl->qStarts[0] = qStart;
+psl->tStarts[0] = tStart;
+return psl;
+}
+
+static struct psl *convertParSpec(struct sqlConnection *conn, struct parSpec *parSpec)
+/* convert a parSpec object two PSLs. */
+{
+int chromASize = hChromSize(sqlGetDatabase(conn), parSpec->chromA);
+int chromBSize = hChromSize(sqlGetDatabase(conn), parSpec->chromB);
+
+return slCat(mkParPsl(parSpec->chromA, chromASize, parSpec->startA, parSpec->endA,
+                      parSpec->chromB, chromBSize, parSpec->startB, parSpec->endB),
+             mkParPsl(parSpec->chromB, chromBSize, parSpec->startB, parSpec->endB,
+                      parSpec->chromA, chromASize, parSpec->startA, parSpec->endA));
+}
+
+static void loadTable(struct psl *psls, struct sqlConnection *conn, char *parTable)
+/* create and load table */
+{
+char *sqlCmd = pslGetCreateSql(parTable, PSL_TNAMEIX,  hGetMinIndexLength(sqlGetDatabase(conn)));
+sqlRemakeTable(conn, parTable, sqlCmd);
+FILE *tabFh = hgCreateTabFile(NULL, parTable);
+struct psl *psl;
+for (psl = psls; psl != NULL; psl = psl->next)
+    pslTabOut(psl, tabFh);
+hgLoadTabFile(conn, NULL, parTable, &tabFh);
+hgUnlinkTabFile(NULL, parTable);
+}
+
+static void hgPar(char *db, char *parSpecFile, char *parTable, boolean fileOutput)
+/* hgPar - create PAR track. */
+{
+struct sqlConnection *conn = sqlConnect(db);
+struct parSpec *parSpec, *parSpecs = parSpecLoadAll(parSpecFile);
+struct psl *psls = NULL;
+
+for (parSpec = parSpecs; parSpec != NULL; parSpec = parSpec->next)
+    psls = slCat(psls, convertParSpec(conn, parSpec));
+
+slSort(&psls, pslCmpTarget);
+if (fileOutput)
+    pslWriteAll(psls, parTable, FALSE);
+else
+    loadTable(psls, conn, parTable);
+
+sqlDisconnect(&conn);
+}
+
+int main(int argc, char *argv[])
+/* Process command line. */
+{
+optionInit(&argc, argv, options);
+if (argc != 4)
+    usage();
+hgPar(argv[1], argv[2], argv[3], optionExists("fileOutput"));
+return 0;
+}