--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/src/sickle.h	Wed Jul 23 18:35:10 2014 -0400
@@ -0,0 +1,101 @@
+#ifndef SICKLE_H
+#define SICKLE_H
+
+#include <limits.h>
+#include <zlib.h>
+#include "kseq.h"
+
+
+/* KSEQ_INIT() cannot be called here, because we only need the types
+   defined. Calling KSEQ_INIT() would also define functions, leading
+   to an unused function warning with GCC. So, the basic typedefs
+   kseq.h has are included here, and each file that reads needs:
+
+   __KS_GETC(gzread, BUFFER_SIZE)
+   __KS_GETUNTIL(gzread, BUFFER_SIZE)
+   __KSEQ_READ
+
+*/
+
+#define BUFFER_SIZE 4096
+__KS_TYPE(gzFile)
+__KS_BASIC(gzFile, BUFFER_SIZE)
+__KSEQ_TYPE(gzFile)
+__KSEQ_BASIC(gzFile)
+
+#ifndef PROGRAM_NAME
+#define PROGRAM_NAME "sickle"
+#endif
+
+#ifndef AUTHORS
+#define AUTHORS "Nikhil Joshi, UC Davis Bioinformatics Core\n"
+#endif
+
+#ifndef VERSION
+#define VERSION 0.0
+#endif
+
+/* Options drawn from GNU's coreutils/src/system.h */
+/* These options are defined so as to avoid conflicting with option
+values used by commands */
+enum {
+  GETOPT_HELP_CHAR = (CHAR_MIN - 2),
+  GETOPT_VERSION_CHAR = (CHAR_MIN - 3)
+};
+#define GETOPT_HELP_OPTION_DECL \
+"help", no_argument, NULL, GETOPT_HELP_CHAR
+#define GETOPT_VERSION_OPTION_DECL \
+"version", no_argument, NULL, GETOPT_VERSION_CHAR
+#define case_GETOPT_HELP_CHAR(Usage_call) \
+case GETOPT_HELP_CHAR: \
+Usage_call(EXIT_SUCCESS, NULL); \
+break;
+#define case_GETOPT_VERSION_CHAR(Program_name, Version, Authors) \
+case GETOPT_VERSION_CHAR: \
+fprintf(stdout, "%s version %0.3f\nCopyright (c) 2011 The Regents " \
+"of University of California, Davis Campus.\n" \
+"%s is free software and comes with ABSOLUTELY NO WARRANTY.\n"\
+"Distributed under the MIT License.\n\nWritten by %s\n", \
+Program_name, Version, Program_name, Authors); \
+exit(EXIT_SUCCESS); \
+break;
+/* end code drawn from system.h */
+
+typedef enum {
+  PHRED,
+  SANGER,
+  SOLEXA,
+  ILLUMINA
+} quality_type;
+
+static const char typenames[4][10] = {
+	{"Phred"},
+	{"Sanger"},
+	{"Solexa"},
+	{"Illumina"}
+};
+
+#define Q_OFFSET 0
+#define Q_MIN 1
+#define Q_MAX 2
+
+static const int quality_constants[4][3] = {
+  /* offset, min, max */
+  {0, 4, 60}, /* PHRED */
+  {33, 33, 126}, /* SANGER */
+  {64, 58, 112}, /* SOLEXA; this is an approx; the transform is non-linear */
+  {64, 64, 110} /* ILLUMINA */
+};
+
+typedef struct __cutsites_ {
+    int five_prime_cut;
+	int three_prime_cut;
+} cutsites;
+
+
+/* Function Prototypes */
+int single_main (int argc, char *argv[]);
+int paired_main (int argc, char *argv[]);
+cutsites* sliding_window (kseq_t *fqrec, int qualtype, int length_threshold, int qual_threshold, int no_fiveprime, int trunc_n, int debug);
+
+#endif /*SICKLE_H*/