Description: restore this file
Author: Michael R. Crusoe <michael.crusoe@gmail.com>
Last-Update: 2020-04-23

--- /dev/null
+++ salmon-1.2.1+ds1/include/kseq.h
@@ -0,0 +1,291 @@
+/* The MIT License
+
+   Copyright (c) 2008, 2009, 2011 Attractive Chaos <attractor@live.co.uk>
+
+   Permission is hereby granted, free of charge, to any person obtaining
+   a copy of this software and associated documentation files (the
+   "Software"), to deal in the Software without restriction, including
+   without limitation the rights to use, copy, modify, merge, publish,
+   distribute, sublicense, and/or sell copies of the Software, and to
+   permit persons to whom the Software is furnished to do so, subject to
+   the following conditions:
+
+   The above copyright notice and this permission notice shall be
+   included in all copies or substantial portions of the Software.
+
+   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+   EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+   MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+   NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
+   BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
+   ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+   CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+   SOFTWARE.
+*/
+
+/* Last Modified: 05MAR2012 */
+
+#ifndef AC_KSEQ_H
+#define AC_KSEQ_H
+
+#include <ctype.h>
+#include <stdlib.h>
+#include <string.h>
+
+#define KS_SEP_SPACE 0 // isspace(): \t, \n, \v, \f, \r
+#define KS_SEP_TAB 1   // isspace() && !' '
+#define KS_SEP_LINE 2  // line separator: "\n" (Unix) or "\r\n" (Windows)
+#define KS_SEP_MAX 2
+
+#define __KS_TYPE(type_t)                                                      \
+  typedef struct __kstream_t {                                                 \
+    unsigned char* buf;                                                        \
+    int begin, end, is_eof;                                                    \
+    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)
+
+#define __KS_BASIC(type_t, __bufsize)                                          \
+  static inline kstream_t* ks_init(type_t f) {                                 \
+    kstream_t* ks = (kstream_t*)calloc(1, sizeof(kstream_t));                  \
+    ks->f = f;                                                                 \
+    ks->buf = (unsigned char*)malloc(__bufsize);                               \
+    return ks;                                                                 \
+  }                                                                            \
+  static inline void ks_destroy(kstream_t* ks) {                               \
+    if (ks) {                                                                  \
+      free(ks->buf);                                                           \
+      free(ks);                                                                \
+    }                                                                          \
+  }
+
+#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++];                                          \
+  }
+
+#ifndef KSTRING_T
+#define KSTRING_T kstring_t
+typedef struct __kstring_t {
+  size_t l, m;
+  char* s;
+} kstring_t;
+#endif
+
+#ifndef kroundup32
+#define kroundup32(x)                                                          \
+  (--(x), (x) |= (x) >> 1, (x) |= (x) >> 2, (x) |= (x) >> 4, (x) |= (x) >> 8,  \
+   (x) |= (x) >> 16, ++(x))
+#endif
+
+#define __KS_GETUNTIL(__read, __bufsize)                                       \
+  static int ks_getuntil2(kstream_t* ks, int delimiter, kstring_t* str,        \
+                          int* dret, int append) {                             \
+    int gotany = 0;                                                            \
+    if (dret)                                                                  \
+      *dret = 0;                                                               \
+    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) {                                          \
+        for (i = ks->begin; i < ks->end; ++i)                                  \
+          if (ks->buf[i] == '\n')                                              \
+            break;                                                             \
+      } else if (delimiter > KS_SEP_MAX) {                                     \
+        for (i = ks->begin; i < ks->end; ++i)                                  \
+          if (ks->buf[i] == delimiter)                                         \
+            break;                                                             \
+      } 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 < (size_t)(i - ks->begin + 1)) {                     \
+        str->m = str->l + (i - ks->begin) + 1;                                 \
+        kroundup32(str->m);                                                    \
+        str->s = (char*)realloc(str->s, str->m);                               \
+      }                                                                        \
+      gotany = 1;                                                              \
+      memcpy(str->s + str->l, ks->buf + ks->begin, i - ks->begin);             \
+      str->l = str->l + (i - ks->begin);                                       \
+      ks->begin = i + 1;                                                       \
+      if (i < ks->end) {                                                       \
+        if (dret)                                                              \
+          *dret = ks->buf[i];                                                  \
+        break;                                                                 \
+      }                                                                        \
+    }                                                                          \
+    if (!gotany && ks_eof(ks))                                                 \
+      return -1;                                                               \
+    if (str->s == 0) {                                                         \
+      str->m = 1;                                                              \
+      str->s = (char*)calloc(1, 1);                                            \
+    } else if (delimiter == KS_SEP_LINE && str->l > 1 &&                       \
+               str->s[str->l - 1] == '\r')                                     \
+      --str->l;                                                                \
+    str->s[str->l] = '\0';                                                     \
+    return str->l;                                                             \
+  }                                                                            \
+  static inline int ks_getuntil(kstream_t* ks, int delimiter, kstring_t* str,  \
+                                int* dret) {                                   \
+    return ks_getuntil2(ks, delimiter, str, dret, 0);                          \
+  }
+
+#define KSTREAM_INIT(type_t, __read, __bufsize)                                \
+  __KS_TYPE(type_t)                                                            \
+  __KS_BASIC(type_t, __bufsize)                                                \
+  __KS_GETC(__read, __bufsize)                                                 \
+  __KS_GETUNTIL(__read, __bufsize)
+
+#define kseq_rewind(ks)                                                        \
+  ((ks)->last_char = (ks)->f->is_eof = (ks)->f->begin = (ks)->f->end = 0)
+
+#define __KSEQ_BASIC(SCOPE, type_t)                                            \
+  SCOPE kseq_t* kseq_init(type_t fd) {                                         \
+    kseq_t* s = (kseq_t*)calloc(1, sizeof(kseq_t));                            \
+    s->f = ks_init(fd);                                                        \
+    return s;                                                                  \
+  }                                                                            \
+  SCOPE void kseq_destroy(kseq_t* ks) {                                        \
+    if (!ks)                                                                   \
+      return;                                                                  \
+    free(ks->name.s);                                                          \
+    free(ks->comment.s);                                                       \
+    free(ks->seq.s);                                                           \
+    free(ks->qual.s);                                                          \
+    ks_destroy(ks->f);                                                         \
+    free(ks);                                                                  \
+  }
+
+/* Return value:
+   >=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, r;                                                                  \
+    kstream_t* ks = seq->f;                                                    \
+    if (seq->last_char == 0) { /* then jump to the next header line */         \
+      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 ((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)) >= 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 */                         \
+    }                                                                          \
+    if (c == '>' || c == '@')                                                  \
+      seq->last_char = c; /* the first header char has been read */            \
+    if (seq->seq.l + 1 >=                                                      \
+        seq->seq                                                               \
+            .m) { /* seq->seq.s[seq->seq.l] below may be out of boundary */    \
+      seq->seq.m = seq->seq.l + 2;                                             \
+      kroundup32(seq->seq.m); /* rounded to the next closest 2^k */            \
+      seq->seq.s = (char*)realloc(seq->seq.s, seq->seq.m);                     \
+    }                                                                          \
+    seq->seq.s[seq->seq.l] = 0; /* null terminated string */                   \
+    if (c != '+')                                                              \
+      return seq->seq.l; /* FASTA */                                           \
+    if (seq->qual.m <                                                          \
+        seq->seq.m) { /* allocate memory for qual in case insufficient */      \
+      seq->qual.m = seq->seq.m;                                                \
+      seq->qual.s = (char*)realloc(seq->qual.s, seq->qual.m);                  \
+    }                                                                          \
+    while ((c = ks_getc(ks)) >= 0 && c != '\n')                                \
+      ; /* skip the rest of '+' line */                                        \
+    if (c == -1)                                                               \
+      return -2; /* error: no quality string */                                \
+    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;                                                         \
+  }
+
+#define __KSEQ_TYPE(type_t)                                                    \
+  typedef struct {                                                             \
+    kstring_t name, comment, seq, qual;                                        \
+    int last_char;                                                             \
+    kstream_t* f;                                                              \
+  } kseq_t;
+
+#define KSEQ_INIT2(SCOPE, type_t, __read)                                      \
+  KSTREAM_INIT(type_t, __read, 16384)                                          \
+  __KSEQ_TYPE(type_t)                                                          \
+  __KSEQ_BASIC(SCOPE, type_t)                                                  \
+  __KSEQ_READ(SCOPE)
+
+#define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read)
+
+#define KSEQ_DECLARE(type_t)                                                   \
+  __KS_TYPE(type_t)                                                            \
+  __KSEQ_TYPE(type_t)                                                          \
+  extern kseq_t* kseq_init(type_t fd);                                         \
+  void kseq_destroy(kseq_t* ks);                                               \
+  int kseq_read(kseq_t* seq);
+
+#endif
