[med-svn] [Git][med-team/gmap][upstream] New upstream version 2021-05-27+ds

[Nilesh Patra (@nilesh)]

Nilesh Patra pushed to branch upstream at Debian Med / gmap


Commits:
28407ea7 by Nilesh Patra at 2021-05-30T23:20:01+05:30
New upstream version 2021-05-27+ds
- - - - -


3 changed files:

- ChangeLog
- VERSION
- src/printbuffer.c


Changes:

=====================================
ChangeLog
=====================================
@@ -1,3 +1,12 @@
+2021-05-27  twu
+
+    * index.html: Revised for latest version
+
+    * VERSION: Updated version number
+
+    * printbuffer.c: Checking for line being NULL, which can happen with gff3
+      output
+
 2021-05-11  twu
 
     * trunk, VERSION, src, Makefile.gsnaptoo.am, cigar.c, concordance.c,


=====================================
VERSION
=====================================
@@ -1 +1 @@
-2021-05-08
\ No newline at end of file
+2021-05-27
\ No newline at end of file


=====================================
src/printbuffer.c
=====================================
@@ -155,29 +155,33 @@ print_lines (FILE *fp_output, List_T *output_list, List_T *tail) {
   ptr = &(buffer[0]);
   for (l = *output_list; l != NULL; l = List_next(l)) {
     p = line = (char *) List_head(l);
-    linelength = strlen(line);
+    if (line == NULL) {
+      /* Possible with gff3 output */
+    } else {
+      linelength = strlen(line);
 
-    while (total_linelength + linelength >= OUTPUTLEN) {
-      allowed = OUTPUTLEN - total_linelength;
-      strncpy(ptr,p,allowed);
+      while (total_linelength + linelength >= OUTPUTLEN) {
+	allowed = OUTPUTLEN - total_linelength;
+	strncpy(ptr,p,allowed);
 #ifdef USE_WRITE
-      write(fileno(fp_output),buffer,OUTPUTLEN*sizeof(char));
+	write(fileno(fp_output),buffer,OUTPUTLEN*sizeof(char));
 #else
-      fwrite(buffer,sizeof(char),OUTPUTLEN,fp_output);
+	fwrite(buffer,sizeof(char),OUTPUTLEN,fp_output);
 #endif
 
-      ptr = &(buffer[0]);
-      total_linelength = 0;
+	ptr = &(buffer[0]);
+	total_linelength = 0;
 
-      p += allowed;
-      linelength -= allowed;
-    }
+	p += allowed;
+	linelength -= allowed;
+      }
       
-    strcpy(ptr,p);
-    ptr += linelength;
-    total_linelength += linelength;
+      strcpy(ptr,p);
+      ptr += linelength;
+      total_linelength += linelength;
 
-    FREE_OUT(line);
+      FREE_OUT(line);
+    }
   }
 
   if (total_linelength > 0) {
@@ -209,16 +213,24 @@ print_lines (FILE *fp_output, List_T *output_list, List_T *tail) {
 
   total_linelength = 0;
   for (l = *output_list; l != NULL; l = List_next(l)) {
-    p = line = (char *) List_head(l);
-    total_linelength += strlen(line);
+    line = (char *) List_head(l);
+    if (line == NULL) {
+      /* Possible with gff3 output */
+    } else {
+      total_linelength += strlen(line);
+    }
   }
 
   ptr = buffer = MALLOC_OUT((total_linelength+1)*sizeof(char));
   for (l = *output_list; l != NULL; l = List_next(l)) {
     line = (char *) List_head(l);
-    strcpy(ptr,line);
-    ptr += strlen(line);
-    FREE_OUT(line);
+    if (line == NULL) {
+      /* Possible with gff3 output */
+    } else {
+      strcpy(ptr,line);
+      ptr += strlen(line);
+      FREE_OUT(line);
+    }
   }
   
 #ifdef USE_WRITE



View it on GitLab: https://salsa.debian.org/med-team/gmap/-/commit/28407ea7b7ebc0adc7d45e02d7d3043c19568553

-- 
View it on GitLab: https://salsa.debian.org/med-team/gmap/-/commit/28407ea7b7ebc0adc7d45e02d7d3043c19568553
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