--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mrfast-2.1.0.5/Reads.h	Fri Mar 09 07:35:51 2012 -0500
@@ -0,0 +1,65 @@
+/*
+ * Copyright (c) <2008 - 2012>, University of Washington, Simon Fraser University
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without modification,
+ * are permitted provided that the following conditions are met:
+ *
+ * Redistributions of source code must retain the above copyright notice, this list
+ * of conditions and the following disclaimer.
+ * - Redistributions in binary form must reproduce the above copyright notice, this
+ *   list of conditions and the following disclaimer in the documentation and/or other
+ *   materials provided with the distribution.
+ * - Neither the names of the University of Washington, Simon Fraser University, 
+ *   nor the names of its contributors may be
+ *   used to endorse or promote products derived from this software without specific
+ *   prior written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+ * "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+ * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+ * A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
+ * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+ * EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+ * PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
+ * PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+ * LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+ * NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+ * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+
+
+/*
+  Authors: 
+	Farhad Hormozdiari
+        Faraz Hach
+	Can Alkan
+  Emails: 
+	farhadh AT uw DOT edu
+	fhach AT cs DOT sfu DOT ca
+	calkan AT uw DOT edu
+ */
+
+
+#ifndef __READ__
+#define __READ__
+
+typedef struct
+{
+	char *name;
+	char *seq;
+	char *rseq;
+	char *qual;
+	char *hits;
+	int readNumber;
+	short *hashValue;
+        short *rhashValue;
+	int *hashValSampleSize;
+} Read;
+
+int readAllReads(char *fileName1, char *fileName2, int compressed, unsigned char *fastq, unsigned char pe, Read **seqList, unsigned int *seqListSize);
+void loadSamplingLocations(int **samplingLocs, int *samplingLocsSize);
+void finalizeReads(char *fileName);
+void adjustQual(Read *list, int seqCnt);
+
+#endif