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prepare for further changes

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This commit is contained in:
Heng Li
2020-06-06 21:55:41 -04:00
parent 97f6efc4da
commit afa93e4bbb
14 changed files with 459 additions and 465 deletions
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extract.cpp
+6 -8
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@@ -3,21 +3,19 @@
#include "Process_Read.h"
#include "khashl.h"
#include "kseq.h"
#include "utils.h"
typedef const char *cstr_t;
KHASHL_CSET_INIT(KH_LOCAL, strset_t, ss, cstr_t, kh_hash_str, kh_eq_str)
KHASHL_MAP_INIT(KH_LOCAL, hm64_t, h64, uint64_t, int, kh_hash_uint64, kh_eq_generic)
KSTREAM_INIT(gzFile, gzread, 65536)
#define GFA_MALLOC(ptr, len) ((ptr) = (__typeof__(ptr))malloc((len) * sizeof(*(ptr))))
#define GFA_REALLOC(ptr, len) ((ptr) = (__typeof__(ptr))realloc((ptr), (len) * sizeof(*(ptr))))
char *gfa_strdup(const char *src)
{
int32_t len;
char *dst;
len = strlen(src);
GFA_MALLOC(dst, len + 1);
MALLOC(dst, len + 1);
memcpy(dst, src, len + 1);
return dst;
}
@@ -25,7 +23,7 @@ char *gfa_strdup(const char *src)
char *gfa_strndup(const char *src, size_t n)
{
char *dst;
GFA_MALLOC(dst, n + 1);
MALLOC(dst, n + 1);
strncpy(dst, src, n);
dst[n] = 0;
return dst;
@@ -42,7 +40,7 @@ char **gv_read_list(const char *o, int *n_)
if (*p == ',' || *p == 0) {
if (n == m) {
m = m? m<<1 : 16;
GFA_REALLOC(s, m);
REALLOC(s, m);
}
s[n++] = gfa_strndup(q, p - q);
if (*p == 0) break;
@@ -63,7 +61,7 @@ char **gv_read_list(const char *o, int *n_)
for (p = str.s; *p && !isspace(*p); ++p);
if (n == m) {
m = m? m<<1 : 16;
GFA_REALLOC(s, m);
REALLOC(s, m);
}
s[n++] = gfa_strndup(str.s, p - str.s);
}
@@ -94,7 +92,7 @@ void ha_extract_print(const All_reads *rs, int n_rounds, int n, char **list)
for (j = 0; j < rs->total_reads; ++j)
if (max_len < (int)Get_NAME_LENGTH(*rs, j))
max_len = Get_NAME_LENGTH(*rs, j);
GFA_MALLOC(s, max_len + 1);
MALLOC(s, max_len + 1);
h = h64_init();
for (j = 0; j < rs->total_reads; ++j) {
strncpy(s, Get_NAME(*rs, j), Get_NAME_LENGTH(*rs, j));