Adds checks for failed reads and gzip files with corrupt crc.

diff --git a/kseq.h b/kseq.h
index b2238d1d3ac922ee353964a7e73710794b68b004..2f94a64f398c219ed156a03ff01bdd0f964cc1af 100644 (file)
--- a/kseq.h
+++ b/kseq.h
@@ -44,6 +44,7 @@
                type_t f;                                                               \
        } kstream_t;
 
+#define ks_err(ks) ((ks)->end == -1)
 #define ks_eof(ks) ((ks)->is_eof && (ks)->begin >= (ks)->end)
 #define ks_rewind(ks) ((ks)->is_eof = (ks)->begin = (ks)->end = 0)
 
@@ -66,11 +67,13 @@
 #define __KS_GETC(__read, __bufsize)                                           \
        static inline int ks_getc(kstream_t *ks)                                \
        {                                                                                                               \
+               if (ks_err(ks)) return -3;                                                      \
                if (ks->is_eof && ks->begin >= ks->end) return -1;      \
                if (ks->begin >= ks->end) {                                                     \
                        ks->begin = 0;                                                                  \
                        ks->end = __read(ks->f, ks->buf, __bufsize);    \
                        if (ks->end == 0) { ks->is_eof = 1; return -1;} \
+                       if (ks->end == -1) { ks->is_eof = 1; return -3;}\
                }                                                                                                       \
                return (int)ks->buf[ks->begin++];                                       \
        }
@@ -95,11 +98,13 @@ typedef struct __kstring_t {
                str->l = append? str->l : 0;                                                                    \
                for (;;) {                                                                                                              \
                        int i;                                                                                                          \
+                       if (ks_err(ks)) return -3;                                                                      \
                        if (ks->begin >= ks->end) {                                                                     \
                                if (!ks->is_eof) {                                                                              \
                                        ks->begin = 0;                                                                          \
                                        ks->end = __read(ks->f, ks->buf, __bufsize);            \
                                        if (ks->end == 0) { ks->is_eof = 1; break; }            \
+                                       if (ks->end == -1) { ks->is_eof = 1; return -3; }       \
                                } else break;                                                                                   \
                        }                                                                                                                       \
                        if (delimiter == KS_SEP_LINE) { \
@@ -167,25 +172,26 @@ typedef struct __kstring_t {
    >=0  length of the sequence (normal)
    -1   end-of-file
    -2   truncated quality string
+   -3   error reading stream
  */
 #define __KSEQ_READ(SCOPE) \
        SCOPE int kseq_read(kseq_t *seq) \
        { \
-               int c; \
+               int c,r; \
                kstream_t *ks = seq->f; \
                if (seq->last_char == 0) { /* then jump to the next header line */ \
-                       while ((c = ks_getc(ks)) != -1 && c != '>' && c != '@'); \
-                       if (c == -1) return -1; /* end of file */ \
+                       while ((c = ks_getc(ks)) >= 0 && c != '>' && c != '@'); \
+                       if (c < 0) return c; /* end of file or error*/ \
                        seq->last_char = c; \
                } /* else: the first header char has been read in the previous call */ \
                seq->comment.l = seq->seq.l = seq->qual.l = 0; /* reset all members */ \
-               if (ks_getuntil(ks, 0, &seq->name, &c) < 0) return -1; /* normal exit: EOF */ \
+               if ((r=ks_getuntil(ks, 0, &seq->name, &c)) < 0) return r;  /* normal exit: EOF or error */ \
                if (c != '\n') ks_getuntil(ks, KS_SEP_LINE, &seq->comment, 0); /* read FASTA/Q comment */ \
                if (seq->seq.s == 0) { /* we can do this in the loop below, but that is slower */ \
                        seq->seq.m = 256; \
                        seq->seq.s = (char*)malloc(seq->seq.m); \
                } \
-               while ((c = ks_getc(ks)) != -1 && c != '>' && c != '+' && c != '@') { \
+               while ((c = ks_getc(ks)) >= 0 && c != '>' && c != '+' && c != '@') { \
                        if (c == '\n') continue; /* skip empty lines */ \
                        seq->seq.s[seq->seq.l++] = c; /* this is safe: we always have enough space for 1 char */ \
                        ks_getuntil2(ks, KS_SEP_LINE, &seq->seq, 0, 1); /* read the rest of the line */ \
@@ -202,9 +208,10 @@ typedef struct __kstring_t {
                        seq->qual.m = seq->seq.m; \
                        seq->qual.s = (char*)realloc(seq->qual.s, seq->qual.m); \
                } \
-               while ((c = ks_getc(ks)) != -1 && c != '\n'); /* skip the rest of '+' line */ \
+               while ((c = ks_getc(ks)) >= 0 && c != '\n'); /* skip the rest of '+' line */ \
                if (c == -1) return -2; /* error: no quality string */ \
-               while (ks_getuntil2(ks, KS_SEP_LINE, &seq->qual, 0, 1) >= 0 && seq->qual.l < seq->seq.l); \
+               while ((c = ks_getuntil2(ks, KS_SEP_LINE, &seq->qual, 0, 1) >= 0 && seq->qual.l < seq->seq.l)); \
+               if (c == -3) return -3; /* stream error */ \
                seq->last_char = 0;     /* we have not come to the next header line */ \
                if (seq->seq.l != seq->qual.l) return -2; /* error: qual string is of a different length */ \
                return seq->seq.l; \