convert standard analysis pipelines to use bam format natively

[erange.git] / checkrmask.py

diff --git a/checkrmask.py b/checkrmask.py
index 457e4c1f9ebedb7b4daf6137f9f8b850635afb28..8ae30ee958dd10fc0d7e598b7bb25fa4b4ed17c2 100755 (executable)
--- a/checkrmask.py
+++ b/checkrmask.py
@@ -55,6 +55,27 @@ def makeParser(usage=""):
 
 def checkrmask(dbfile, filename, outFileName, goodFileName, startField=0, cachePages=500000, logfilename=None):
 
+    if os.path.isfile(dbfile):
+        checkrmaskdb(dbfile, filename, outFileName, goodFileName, startField, cachePages, logfilename)
+    else:
+        outfile = open(outFileName, "w")
+        goodfile = open(goodFileName, "w")
+        infile = open(filename)
+        print "No database - passing through"
+        if logfilename is not None:
+            writeLog(logfilename, versionString, string.join(sys.argv[1:]))
+            writeLog(logfilename, versionString, "No database - passing through")
+
+        for line in infile:
+            outfile.write("%s\tNR\tNR\t0.00\n" % line)
+            goodfile.write(line)
+
+        outfile.close()
+        goodfile.close()
+
+
+def checkrmaskdb(dbfile, filename, outFileName, goodFileName, startField=0, cachePages=500000, logfilename=None):
+
     outfile = open(outFileName, "w")
     goodfile = open(goodFileName, "w")
     if startField < 0:
@@ -63,29 +84,14 @@ def checkrmask(dbfile, filename, outFileName, goodFileName, startField=0, cacheP
     if cachePages < 250000:
         cachePages = 250000
 
-    doLog = False
     if logfilename is not None:
         writeLog(logfilename, versionString, string.join(sys.argv[1:]))
-        doLog = True
 
     infile = open(filename)
-    if os.path.isfile(dbfile):
-        db = sqlite.connect(dbfile)
-        sql = db.cursor()
-        sql.execute("PRAGMA CACHE_SIZE = %d" % cachePages)
-        sql.execute("PRAGMA temp_store = MEMORY")
-    else:
-        print "No database - passing through"
-        if doLog:
-            writeLog(logfilename, versionString, "No database - passing through")
-
-        for line in infile:
-            outfile.write("%s\tNR\tNR\t0.00\n" % line)
-            goodfile.write(line)
-
-        outfile.close()
-        goodfile.close()
-        sys.exit(0)
+    db = sqlite.connect(dbfile)
+    sql = db.cursor()
+    sql.execute("PRAGMA CACHE_SIZE = %d" % cachePages)
+    sql.execute("PRAGMA temp_store = MEMORY")
 
     featureList = []
     featureDict = {}