subsampling read pairs

[samtools.git] / kseq.h

diff --git a/kseq.h b/kseq.h
index 2875c77577152eb9a20b41fc044288f67eb124ab..82face095919a3991b1f927bb5422ffd95f102a4 100644 (file)
--- a/kseq.h
+++ b/kseq.h
@@ -25,6 +25,12 @@
 
 /* Contact: Heng Li <lh3@sanger.ac.uk> */
 
+/*
+  2009-07-16 (lh3): in kstream_t, change "char*" to "unsigned char*"
+ */
+
+/* Last Modified: 12APR2009 */
+
 #ifndef AC_KSEQ_H
 #define AC_KSEQ_H
 
@@ -32,9 +38,13 @@
 #include <string.h>
 #include <stdlib.h>
 
+#define KS_SEP_SPACE 0 // isspace(): \t, \n, \v, \f, \r
+#define KS_SEP_TAB   1 // isspace() && !' '
+#define KS_SEP_MAX   1
+
 #define __KS_TYPE(type_t)                                              \
        typedef struct __kstream_t {                            \
-               char *buf;                                                              \
+               unsigned char *buf;                                             \
                int begin, end, is_eof;                                 \
                type_t f;                                                               \
        } kstream_t;
@@ -47,7 +57,7 @@
        {                                                                                                                               \
                kstream_t *ks = (kstream_t*)calloc(1, sizeof(kstream_t));       \
                ks->f = f;                                                                                                      \
-               ks->buf = (char*)malloc(__bufsize);                                                     \
+               ks->buf = malloc(__bufsize);                                                            \
                return ks;                                                                                                      \
        }                                                                                                                               \
        static inline void ks_destroy(kstream_t *ks)                                    \
@@ -99,13 +109,16 @@ typedef struct __kstring_t {
                                        if (ks->end == 0) break;                                                        \
                                } else break;                                                                                   \
                        }                                                                                                                       \
-                       if (delimiter) {                                                                                        \
+                       if (delimiter > KS_SEP_MAX) {                                                           \
                                for (i = ks->begin; i < ks->end; ++i)                                   \
                                        if (ks->buf[i] == delimiter) break;                                     \
-                       } else {                                                                                                        \
+                       } else if (delimiter == KS_SEP_SPACE) {                                         \
                                for (i = ks->begin; i < ks->end; ++i)                                   \
                                        if (isspace(ks->buf[i])) break;                                         \
-                       }                                                                                                                       \
+                       } else if (delimiter == KS_SEP_TAB) {                                           \
+                               for (i = ks->begin; i < ks->end; ++i)                                   \
+                                       if (isspace(ks->buf[i]) && ks->buf[i] != ' ') break; \
+                       } else i = 0; /* never come to here! */                                         \
                        if (str->m - str->l < i - ks->begin + 1) {                                      \
                                str->m = str->l + (i - ks->begin) + 1;                                  \
                                kroundup32(str->m);                                                                             \
@@ -119,6 +132,10 @@ typedef struct __kstring_t {
                                break;                                                                                                  \
                        }                                                                                                                       \
                }                                                                                                                               \
+               if (str->l == 0) {                                                                                              \
+                       str->m = 1;                                                                                                     \
+                       str->s = (char*)calloc(1, 1);                                                           \
+               }                                                                                                                               \
                str->s[str->l] = '\0';                                                                                  \
                return str->l;                                                                                                  \
        }