src/hg/lib/baseMaskCommon.c 1.8

Index: src/hg/lib/baseMaskCommon.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/lib/baseMaskCommon.c,v
retrieving revision 1.7
retrieving revision 1.8
diff -b -B -U 1000000 -r1.7 -r1.8
--- src/hg/lib/baseMaskCommon.c	18 Sep 2008 03:51:57 -0000	1.7
+++ src/hg/lib/baseMaskCommon.c	24 Mar 2009 15:51:04 -0000	1.8
@@ -1,277 +1,232 @@
 #include "common.h"
 #include "jksql.h"
 #include "hdb.h"
 #include "chromInfo.h"
 #include "genomeRangeTree.h"
 #include "genomeRangeTreeFile.h"
 #include "baseMaskCommon.h"
 
 static char const rcsid[] = "$Id$";
 
-//#define MJP verbose(1,"%s[%3d]: ", __func__, __LINE__);
-
-static struct chromInfo *createChromInfoList(char *name, char *database)
-/* Load up all chromosome information. 
- * Similar to featureBits.c - maybe could be moved to library ? */
-{
-struct sqlConnection *conn = hAllocConn(database);
-struct sqlResult *sr = NULL;
-char **row;
-int loaded=0;
-struct chromInfo *ret = NULL;
-unsigned totalSize = 0;
-/* do the query */
-if (sameWord(name, "all"))
-    sr = sqlGetResult(conn, "select * from chromInfo");
-else
-    {
-    char select[256];
-    safef(select, ArraySize(select), "select * from chromInfo where chrom='%s'",
-        name);
-    sr = sqlGetResult(conn, select);
-    }
-/* read the rows and build the chromInfo list */
-while ((row = sqlNextRow(sr)) != NULL)
-    {
-    struct chromInfo *el;
-    struct chromInfo *ci;
-    AllocVar(ci);
-    el = chromInfoLoad(row);
-    ci->chrom = cloneString(el->chrom);
-    ci->size = el->size;
-    totalSize += el->size;
-    slAddHead(&ret, ci);
-    ++loaded;
-    }
-if (loaded < 1)
-    errAbort("ERROR: can not find chrom name: '%s'\n", name);
-slReverse(&ret);
-if (sameWord(name, "all"))
-    verbose(2, "#\tloaded size info for %d chroms, total size: %u\n",
-        loaded, totalSize);
-sqlFreeResult(&sr);
-hFreeConn(&conn);
-return ret;
-}
 
 static char *chromTable(char *db, char *table, char *chromDb)
 /* Get chr1_table if it exists, otherwise table. 
  * You can freeMem this when done. */
 {
 char *realTable;
 struct sqlConnection *sc = hAllocConn(chromDb);
 char *chrom = hDefaultChrom(chromDb);
 hFreeConn(&sc);
 sc = hAllocConn(db);
 if (sqlTableExists(sc, table))
     {
     realTable = cloneString(table);
     }
 else
     {
     char buf[256];
     safef(buf, sizeof(buf), "%s_%s", chrom, table);
     realTable = cloneString(buf);
     }
 hFreeConn(&sc);
 return realTable;
 }
 
 void splitDbTable(char *chromDb, char *track, char **pDb, char **pTable)
 /* split the track into db name and table name. 
  * If no db specified then this will be chromDb.
  * Cannabalizes track. 
  * *pDb points a table in *track. *pTable points at database in *track or *chromDb. */
 {
 char *words[2];
 int n = chopByChar(track, '.', words, 2);
 if (n==0)
     errAbort("error: null track name");
 else if (n==1)
     {
     *pDb = chromDb;
     *pTable = words[0];
     }
 else if (n==2)
     {
     *pDb = words[0];
     *pTable = words[1];
     }
 else
     errAbort("invalid track name %s (must be 'table' or 'db.table')\n", track);
 }
 
 static time_t fileUpdateTime(char *file)
 /* Return the file modification time or -1 if file does not exist */
 {
 struct stat statBuf;
 statBuf.st_mtime = -1;
 if (fileExists(file))
     if (stat(file,&statBuf)==-1)
         errnoAbort("could not stat file %s\n", file);
 return statBuf.st_mtime;
 }
 
 static time_t chromTableUpdateTime(char *db, char *table, char *chromDb)
 /* Find the last update time for table in db.
  * If the table doesnt exist, find a chromosome or scaffold) name from chromDb and 
  * check if the table is split by chromosome.
  * Errors out if time is not a positive integer.
  * Returns the table update time. */
 {
 /* get either table or chr1_table (or scaffold123_table)*/
 char *realTable = chromTable(db, table, chromDb);
 time_t time = 0;
 /* connect to database and get last update time for table if it exists */
 struct sqlConnection *sc = hAllocConn(db);
 if (sqlTableExists(sc, realTable))
     time = sqlTableUpdateTime(sc, realTable);
 else
     errAbort("cant find table %s or %s in %s database (using chromosomes from %s)\n", table, realTable, db, chromDb);
 if (time <= 0)
     errAbort("invalid table update time (%d)\n", (int)time);
 freeMem(realTable);
 hFreeConn(&sc);
 return time;
 }
 
 static char *cacheFile(char *cacheDir, char *db, char *table, char *suffix)
 /* Create cache file name as {cacheDir}/{db}/{table}{suffix}
  * Errors out if directory cacheDir does not exist.
  * Creates directory cacheDir/db/ if this does not exist.
  * Return cache file name. Return value needs to be freeMem'd */
 {
 char *file;
 /* generate bama file name and cache directories if necessary */
 int n = strlen(cacheDir)+1+strlen(db)+1+strlen(table)+strlen(suffix)+1;
 if (!fileExists(cacheDir)) /* if cache dir does not exist, abort */
     errAbort("cache directory [%s] does not exist \n", cacheDir);
 AllocArray(file, n);
 safef(file, n, "%s/%s/",cacheDir,db);
 if (!fileExists(file)) /* if cacheDir/db/ does not exist, make it */
     makeDirs(file);
 safecat(file, n, table);
 safecat(file, n, suffix);
 return file;
 }
 
 static void makeTempFile(char *file)
 /* Make a temp file using the template file name.
  * File name should contain XXXXXX as the suffix.
  * An empty temporary file is created and the input file name
  * is modified to contain the name of the temp file created.
  * The temp file is closed and safe to be overwritten.
  * Errors out if the temp file could not be created. */
 {
 int fd = mkstemp(file);
 if (fd==-1)
     errAbort("could not create temp file %s\n", file);
 if (close(fd) != 0)
     errnoAbort("could not close temp file %s\n", file);
 }
 
 static int formatTime(char *buf, int bufSize, char *prefix, time_t time, char *suffix)
 /* Format time as YYYY-MM-DD HH:MM:SS into buffer 'buf' 
  * of size 'bufSize'.
  * Prepends 'prefix' and appends 'suffix' to the formatted time. 
  * Returns the number of bytes written to buf. */
 {
     struct tm  *ts = localtime(&time);
     char timeBuf[80];
     if (!strftime(timeBuf, sizeof(timeBuf), "%Y-%m-%d %H:%M:%S", ts))
         errAbort("error formatting time in strftime \n");
     return safef(buf, bufSize, "%s%s%s", prefix, timeBuf, suffix);
 }
 
 static void writeCacheLog(char *file, char *db, char *table, time_t newCacheTime, time_t tableTime, time_t oldCacheTime)
 /* Append db.table and the new cache time, table update time, and
  * old cache time (if any) to the log file.
  * Closes the file. */
 {
 char buf[1024], timeBuf[1024];
 safef(buf, sizeof(buf), "%s.%s: ", db, table);
 formatTime(timeBuf, sizeof(timeBuf), "newCache=[", newCacheTime, "] ");
 safecat(buf, sizeof(buf), timeBuf);
 formatTime(timeBuf, sizeof(timeBuf), "tableUpdateTime=[", tableTime, "] ");
 safecat(buf, sizeof(buf), timeBuf);
 if (oldCacheTime<=0)
     safef(timeBuf, sizeof(timeBuf), "oldCache=[]\n");
 else
     formatTime(timeBuf, sizeof(timeBuf), "oldCache=[", oldCacheTime, "]\n");
 safecat(buf, sizeof(buf), timeBuf);
 FILE *f = mustOpen(file, "a");
 mustWrite(f, buf, strlen(buf));
 carefulClose(&f);
 }
 
 void trackToBaseMask(char *db, char *track, char *chromDb, char *oBama, boolean quiet)
 /* Create a baseMask file oBama representing the 'track' in database 'db'.
  * If quiet = false, outputs number of based on overlap of chromosome ranges. */
 {
 struct bed *b, *bList;
 struct genomeRangeTree *tree = genomeRangeTreeNew();
 //struct slName *chrom, *chromList = hAllChromNamesDb(db);
 struct chromInfo *ci, *ciList = createChromInfoList("all", chromDb);
 struct sqlConnection *conn = hAllocConn(db);
 struct rbTree *rt;
 double totalSize = 0, treeSize = 0, nodes = 0;
 /* loop over all chromosomes adding to range tree */
 for (ci = ciList ; ci ; ci = ci->next)
     {
     totalSize += ci->size;
     rt = NULL;
     if ( (bList = hGetBedRange(db, track, ci->chrom, 0, 0, NULL)) )
 	{
 	rt = genomeRangeTreeFindOrAddRangeTree(tree, ci->chrom);
         for ( b = bList ; b ; b = b->next )
 	    {
 	    bedIntoRangeTree(b, rt);
 	    }
 	nodes += rt->n;
         bedFreeList(&bList);
 	}
     if (!quiet && rt)
 	treeSize += rangeTreeOverlapTotalSize(rt);
     }
 if (!quiet)
     fprintf(stderr,"%1.0f bases in %1.0f ranges in %d chromosomes of %1.0f (%4.3f%%) bases in genome\n",
 	treeSize, nodes, tree->hash->elCount, totalSize, 100.0*treeSize/totalSize);
 if (oBama)
     genomeRangeTreeWrite(tree, oBama); /* write the tree out */
 genomeRangeTreeFree(&tree);
 slFreeList(&ciList);
 hFreeConn(&conn);
 }
 
 char *baseMaskCacheTrack(char *cacheDir, char *chromDb, char *db, char *table, boolean quiet, boolean logUpdateTimes)
 /* Return the file name of the cached baseMask for the specified table and db.
  * The chromInfo table is read from chromDb database.
  * The cached file will be saved in the file cacheDir/db/table.bama 
  * If logUpdateTimes is true then the table and cache update times will be
  * appended to cacheDir/db/table.bama.log
  * The bama file is written as a temp file then moved to the final name as 
  * an atomic operation. 
  * Return value must be freed with freeMem(). */
 {
 char *file = cacheFile(cacheDir, db, table, ".bama");
 time_t cacheTime = fileUpdateTime(file);
 time_t tableTime = chromTableUpdateTime(db, table, chromDb);
 if (cacheTime > tableTime)
     return file; /* cache is up to date */
 /* otherwise create a new temp bama file and the rename it to the real one */
 char *tmpFile = cacheFile(cacheDir, db, table, ".XXXXXX");
 makeTempFile(tmpFile);
 trackToBaseMask(db, table, chromDb, tmpFile, TRUE);
 if (rename(tmpFile, file))
     errnoAbort("could not rename temp file %s -> %s\n", tmpFile, file);
 freeMem(tmpFile);
 if (logUpdateTimes)
     {
     char *logFile=cacheFile(cacheDir, db, table, ".bama.log");
     time_t now = time(NULL);
     writeCacheLog(logFile, db, table, now, tableTime, cacheTime);
     freeMem(logFile);
     }
 return file;
 }