group to utils library

zwdzwd · Dec 19, 2016 · 10d466c · 10d466c
1 parent facd372
commit 10d466c
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diff --git a/encode.h b/encode.h
diff --git a/stats.h b/stats.h
@@ -0,0 +1,43 @@
+#ifndef _WZ_STATS_H_
+#define _WZ_STATS_H_
+
+#include <math.h>
+#include <stdlib.h>
+#include <stdio.h>
+
+#define MAXIT 100
+#define EPS 3.0e-7
+#define FPMIN 1.0e-30
+
+typedef enum{HOMOREF = 0, HET = 1, HOMOVAR = 2} Genotype;
+
+double binom_pval(int s, int n, double p);
+
+double pval2qual(double pval);
+
+double varcall_pval(int kr, int kv, double error, double mu, double contam);
+
+double genotype_lnlik(Genotype genotype, int kr, int kv, double error, double contam);
+
+double somatic_lnlik(int kr, int kv, double error);
+
+double fisher_exact(int n11, int n12, int n21, int n22, double *_left, double *_right, double *two);
+
+/* double ln_beta_incdiff_kernel(double p1, double p2, int a, int b); */
+double inconsist_score(int kr_tumor, int kv_tumor, int kr_normal, int kv_normal, double mu, double error);
+
+double ln_sum2(double ln1, double ln2);
+
+double ln_sum3(double ln1, double ln2, double ln3);
+
+double ln_substract(double ln1, double ln2);
+
+double ln_binom_kernel(double p, int a, int b);
+
+double ln_beta_incdiff_kernel(double p1, double p2, int a, int b);
+
+double somatic_posterior(int kr_t, int kv_t, int kr_n, int kv_n, double error, double mu, double mu_somatic, double contam);
+
+double beta_binomial(int k, int n, double a, double b);
+
+#endif
diff --git a/wqueue.h b/wqueue.h
@@ -0,0 +1,90 @@
+#ifndef _WQUEUE_H_
+#define _WQUEUE_H_
+
+#include <pthread.h>
+#include <stdint.h>
+#include <stdlib.h>
+
+/* 
+   by [email protected]
+
+   block get when empty
+   block put when full
+
+   example usage:
+
+*/
+
+#define DEFINE_WQUEUE(name, _wqueue_elem_t)                             \
+  typedef struct {                                                      \
+    uint32_t size;                                                      \
+    _wqueue_elem_t *data;                                               \
+    uint32_t head, tail;                                                \
+    int full, empty;                                                    \
+    pthread_mutex_t mut;                                                \
+    pthread_cond_t not_full, not_empty;                                 \
+  } wqueue_##name##_t;                                                  \
+  static inline wqueue_##name##_t *wqueue_init_##name(uint32_t size) {	\
+    wqueue_##name##_t *q = calloc(1, sizeof(wqueue_##name##_t));        \
+      q->empty = 1;                                                     \
+      q->size = size;                                                   \
+      q->data = calloc(size, sizeof(_wqueue_elem_t));                   \
+      pthread_mutex_init(&q->mut, NULL);                                \
+      pthread_cond_init(&q->not_full, NULL);                            \
+      pthread_cond_init(&q->not_empty, NULL);                           \
+      return q;                                                         \
+  }                                                                     \
+  static inline void wqueue_destroy_##name(wqueue_##name##_t *q) {      \
+    free(q->data);                                                      \
+    pthread_mutex_destroy(&q->mut);                                     \
+    pthread_cond_destroy(&q->not_full);                                 \
+    pthread_cond_destroy(&q->not_empty);                                \
+    free(q);                                                            \
+  }                                                                     \
+  static inline void wqueue_get_##name(wqueue_##name##_t *q,            \
+                                       _wqueue_elem_t *e) {             \
+    pthread_mutex_lock(&q->mut);                                        \
+    while(q->empty) pthread_cond_wait(&q->not_empty, &q->mut);          \
+    *e = q->data[q->head++];                                            \
+    if (q->head == q->size) q->head = 0;                                \
+    if (q->head == q->tail) q->empty = 1;                               \
+    q->full = 0;                                                        \
+    pthread_mutex_unlock(&q->mut);                                      \
+    pthread_cond_signal(&q->not_full);                                  \
+  }                                                                     \
+  static inline void wqueue_put_##name(wqueue_##name##_t *q,            \
+                                       _wqueue_elem_t *e) {             \
+    pthread_mutex_lock(&q->mut);                                        \
+    while(q->full) pthread_cond_wait(&q->not_full, &q->mut);            \
+    q->data[q->tail++] = *e;                                            \
+    if (q->tail == q->size) q->tail = 0;                                \
+    if (q->head == q->tail) q->full = 1;                                \
+    q->empty = 0;                                                       \
+    pthread_mutex_unlock(&q->mut);                                      \
+    pthread_cond_signal(&q->not_empty);                                 \
+  }                                                                     \
+  static inline void wqueue_put2_##name(wqueue_##name##_t *q,           \
+                                        _wqueue_elem_t e) {             \
+    pthread_mutex_lock(&q->mut);                                        \
+    while(q->full) pthread_cond_wait(&q->not_full, &q->mut);            \
+    q->data[q->tail++] = e;                                             \
+    if (q->tail == q->size) q->tail = 0;                                \
+    if (q->head == q->tail) q->full = 1;                                \
+    q->empty = 0;                                                       \
+    pthread_mutex_unlock(&q->mut);                                      \
+    pthread_cond_signal(&q->not_empty);                                 \
+  }
+
+#define wqueue_t(name) wqueue_##name##_t
+
+#define wqueue_init(name, size) wqueue_init_##name(size)
+
+#define wqueue_destroy(name, q) wqueue_destroy_##name(q)
+
+#define wqueue_get(name, q, e) wqueue_get_##name(q, e)
+
+#define wqueue_put(name, q, e) wqueue_put_##name(q, e)
+
+#define wqueue_put2(name, q, e) wqueue_put2_##name(q, e)
+
+#endif
diff --git a/wstr.h b/wstr.h
@@ -0,0 +1,51 @@
+
+#ifndef _WZ_STR_H_
+#define _WZ_STR_H_
+
+#include <stdio.h>
+#include <stdarg.h>
+#include <ctype.h>
+#include "kstring.h"
+
+#define kstring_init(s) kstring_t (s); (s).s=0; (s).m=(s).l=0;
+
+#define _WZ_STRLEN 100
+
+static inline char*
+wasprintf(const char *fmt, ...) {
+
+  char *s = malloc(_WZ_STRLEN);	/* default length */
+
+  va_list args;
+  va_start(args, fmt);
+  int l = vsnprintf(s, _WZ_STRLEN, fmt, args); /* if fail, l is the number characters that would've been written */
+  if (l >= _WZ_STRLEN) {
+    s = realloc(s, l+1);
+    va_start(args, fmt);
+    vsnprintf(s, l+1, fmt, args);
+  }
+  va_end(args);
+
+  return s;
+}
+
+static inline int strcount_char(char *s, char c) {
+  int i, n=0;
+  for (i=0; s[i]; ++i)
+    if (s[i] == c)
+      ++n;
+  return n;
+}
+
+static inline void ensure_number(char *s) {
+  int i;
+  for (i=0;s[i];++i) {
+    if (!isdigit(s[i]) && s[i]!='.') {
+      fprintf(stderr, "[%s:%d] Trying to convert nondigit string to number: %s\n", __func__, __LINE__, s);
+      fflush(stderr);
+      exit(1);
+    }
+  }
+}
+
+#endif /* _WZ_STR_H_ */