diff -u -r -N a/src/core/io.c b/src/core/io.c
--- a/src/core/io.c	2020-08-17 15:23:43.000000000 +0900
+++ b/src/core/io.c	2020-08-24 11:45:55.000000000 +0900
@@ -87,21 +87,29 @@
   return rval ? false : true;
 }
 
-signed char gt_io_peek(GtIO *io)
+int gt_io_peek(GtIO *io)
 {
   char c;
   gt_assert(io);
-  gt_io_get_char(io, &c);
+  int e = gt_io_get_char(io, &c);
   gt_io_unget_char(io, c);
-  return c;
+  if (e == -1) {
+    return EOF;
+  } else{
+    return c;
+  }
 }
 
-signed char gt_io_next(GtIO *io)
+int gt_io_next(GtIO *io)
 {
   char c;
   gt_assert(io);
-  gt_io_get_char(io, &c);
-  return c;
+  int e = gt_io_get_char(io, &c);
+  if (e == -1) {
+    return EOF;
+  } else{
+    return c;
+  }
 }
 
 GtUword gt_io_get_line_number(const GtIO *io)
@@ -122,9 +130,9 @@
   return io->path;
 }
 
-int gt_io_expect(GtIO *io, char expected_char, GtError *err)
+int gt_io_expect(GtIO *io, int expected_char, GtError *err)
 {
-  char cc;
+  int cc;
   gt_error_check(err);
   cc = gt_io_next(io);
   if (cc != expected_char) {
diff -u -r -N a/src/core/io.h b/src/core/io.h
--- a/src/core/io.h	2020-08-17 15:23:43.000000000 +0900
+++ b/src/core/io.h	2020-08-24 11:46:21.000000000 +0900
@@ -37,12 +37,12 @@
 void          gt_io_unget_char(GtIO*, char);
 bool          gt_io_line_start(const GtIO*);
 bool          gt_io_has_char(GtIO*);
-signed char   gt_io_peek(GtIO*);
-signed char   gt_io_next(GtIO*);
+int           gt_io_peek(GtIO*);
+int           gt_io_next(GtIO*);
 GtUword       gt_io_get_line_number(const GtIO*);
 const char*   gt_io_get_filename(const GtIO*);
 GtStr*        gt_io_get_filename_str(const GtIO*);
 
-int           gt_io_expect(GtIO*, char expected_char, GtError*);
+int           gt_io_expect(GtIO*, int expected_char, GtError*);
 
 #endif
diff -u -r -N a/src/core/seq_iterator_fastq.c b/src/core/seq_iterator_fastq.c
--- a/src/core/seq_iterator_fastq.c	2020-08-17 15:57:33.000000000 +0900
+++ b/src/core/seq_iterator_fastq.c	2020-08-20 17:28:23.000000000 +0900
@@ -92,10 +92,10 @@
 
 static inline int parse_fastq_seqname(GtSeqIteratorFastQ *seqit,
                                       GtStr *buffer,
-                                      char startchar,
+                                      int startchar,
                                       GtError *err)
 {
-  char currentchar;
+  int currentchar;
   bool firstsymbol = true;
   gt_error_check(err);
   gt_assert(seqit && buffer);
@@ -127,7 +127,7 @@
                                 GtError *err)
 {
   int had_err = 0;
-  char currentchar;
+  int currentchar;
   GtStr *tmp_str = gt_str_new();
 
   gt_error_check(err);
@@ -207,7 +207,7 @@
 static inline int parse_fastq_qualities(GtSeqIteratorFastQ *seqit,
                                         GT_UNUSED GtError *err)
 {
-  char currentchar;
+  int currentchar;
   GtUword i = 0;
   gt_assert(gt_str_length(seqit->sequencebuffer) > 0);
   if ((currentchar = fastq_buf_getchar(seqit)) == EOF)
diff -u -r -N a/src/extended/bed_parser.c b/src/extended/bed_parser.c
--- a/src/extended/bed_parser.c	2020-08-17 16:16:25.000000000 +0900
+++ b/src/extended/bed_parser.c	2020-08-24 11:47:38.000000000 +0900
@@ -84,7 +84,7 @@
   gt_error_check(err);
   had_err = gt_io_expect(bed_file, BLANK_CHAR, err);
   while (!had_err) {
-    char cc = gt_io_peek(bed_file);
+    int cc = gt_io_peek(bed_file);
     if (cc == GT_CARRIAGE_RETURN) {
       gt_io_next(bed_file);
       if (gt_io_peek(bed_file) == GT_END_OF_LINE)
@@ -189,7 +189,7 @@
 
 static bool bed_separator(GtIO *bed_file)
 {
-  char cc = gt_io_peek(bed_file);
+  int cc = gt_io_peek(bed_file);
   if (cc == BLANK_CHAR || cc == TABULATOR_CHAR)
     return true;
   return false;
@@ -212,7 +212,7 @@
 
 static int track_rest(GtBEDParser *bed_parser, GtIO *bed_file, GtError *err)
 {
-  char cc;
+  int cc;
   int had_err = 0;
   gt_error_check(err);
   bed_parser->offset = 0; /* reset offset for new track line */
diff -u -r -N a/src/extended/match_iterator_blast.c b/src/extended/match_iterator_blast.c
--- a/src/extended/match_iterator_blast.c	2020-08-17 16:28:49.000000000 +0900
+++ b/src/extended/match_iterator_blast.c	2020-08-20 17:46:58.000000000 +0900
@@ -104,12 +104,15 @@
       had_err = -1;
     }
   } else {
+    int intbuf;
     while (true) {
-      while ((buffer[i] = gt_file_xfgetc(mib->pvt->gtmatchfilep)) != '\n') {
-        if (buffer[i] == EOF)
+      while ((intbuf = gt_file_xfgetc(mib->pvt->gtmatchfilep)) != '\n') {
+        if (intbuf == EOF)
           return GT_MATCHER_STATUS_END;
+        buffer[i] = intbuf;
         i++;
       }
+      buffer[i] = '\n';
       buffer[i+1] = '\0';
       if (buffer[0] == '#') {
         mib->pvt->curpos++;
diff -u -r -N a/src/extended/match_iterator_open.c b/src/extended/match_iterator_open.c
--- a/src/extended/match_iterator_open.c	2020-08-17 16:28:49.000000000 +0900
+++ b/src/extended/match_iterator_open.c	2020-08-20 17:46:40.000000000 +0900
@@ -95,12 +95,15 @@
       had_err = -1;
     }
   } else {
+    int intbuf;
     while (true) {
-      while ((buffer[i] = gt_file_xfgetc(mpi->pvt->gtmatchfilep)) != '\n') {
-        if (buffer[i] == EOF)
+      while ((intbuf = gt_file_xfgetc(mpi->pvt->gtmatchfilep)) != '\n') {
+        if (intbuf == EOF)
           return GT_MATCHER_STATUS_END;
+        buffer[i] = intbuf;
         i++;
       }
+      buffer[i] = '\n';
       buffer[i+1] = '\0';
       if (buffer[0] == '#') {
         mpi->pvt->curpos++;
diff -u -r -N a/src/extended/obo_parse_tree.c b/src/extended/obo_parse_tree.c
--- a/src/extended/obo_parse_tree.c	2020-08-17 17:06:46.000000000 +0900
+++ b/src/extended/obo_parse_tree.c	2020-08-24 11:48:09.000000000 +0900
@@ -181,7 +181,7 @@
 
 static bool ignored_char(GtIO *obo_file)
 {
-  char cc = gt_io_peek(obo_file);
+  int cc = gt_io_peek(obo_file);
   if ((cc == OBO_BLANK_CHAR) || (cc == OBO_COMMENT_CHAR) ||
       (cc == GT_CARRIAGE_RETURN) || (cc == GT_END_OF_LINE))
     return true;
@@ -218,7 +218,7 @@
   gt_error_check(err);
   had_err = gt_io_expect(obo_file, OBO_BLANK_CHAR, err);
   while (!had_err) {
-    char cc = gt_io_peek(obo_file);
+    int cc = gt_io_peek(obo_file);
     if (cc == OBO_COMMENT_CHAR)
       return comment_line(obo_file, err);
     else if (cc == GT_CARRIAGE_RETURN) {
diff -u -r -N a/src/extended/xrf_abbr_parse_tree.c b/src/extended/xrf_abbr_parse_tree.c
--- a/src/extended/xrf_abbr_parse_tree.c	2020-08-17 17:17:38.000000000 +0900
+++ b/src/extended/xrf_abbr_parse_tree.c	2020-08-24 11:48:48.000000000 +0900
@@ -163,7 +163,7 @@
 
 static bool gt_xrf_abbr_parse_tree_ignored_char(GtIO *xrf_abbr_file)
 {
-  char cc = gt_io_peek(xrf_abbr_file);
+  int cc = gt_io_peek(xrf_abbr_file);
   if ((cc == XRF_BLANK_CHAR) || (cc == XRF_COMMENT_CHAR) ||
       (cc == GT_CARRIAGE_RETURN) || (cc == GT_END_OF_LINE))
     return true;
@@ -203,7 +203,7 @@
   gt_log_log("blank");
   had_err = gt_io_expect(xrf_abbr_file, XRF_BLANK_CHAR, err);
   while (!had_err) {
-    char cc = gt_io_peek(xrf_abbr_file);
+    int cc = gt_io_peek(xrf_abbr_file);
     if (cc == XRF_COMMENT_CHAR)
       return gt_xrf_abbr_parse_tree_comment_line(xrf_abbr_file, err);
     else if (cc == GT_CARRIAGE_RETURN) {
diff -u -r -N a/src/ltr/pdom_model_set.c b/src/ltr/pdom_model_set.c
--- a/src/ltr/pdom_model_set.c	2020-08-17 17:31:47.000000000 +0900
+++ b/src/ltr/pdom_model_set.c	2020-08-20 17:28:23.000000000 +0900
@@ -65,7 +65,8 @@
 {
   GtStr *concat_dbnames, *cmdline, *indexfilename = NULL;
   GtUword i;
-  char *md5_hash, ch;
+  char *md5_hash;
+  int ch;
   const char *tmpdir;
   int had_err = 0, rval;
   FILE *dest;