Changeset 3836

Timestamp:

Aug 8, 2019, 4:11:37 AM (4 years ago)

Author:

Peter

Message:

fixes #928

Location:

branches/0.16-stable

Files:

• NEWS (modified) (1 diff)
• test/Makefile.am (modified) (1 diff)
• yat/omic/GFF2.cc (modified) (2 diffs)

branches/0.16-stable/NEWS

@@ -8 +8 @@
   - utility::Aligner::Cigar::begin(void) and ::end(void) are now
     implemented (see bug #929)
+ - Fixed bug in GFF2 parser when attribute field had space after a
+   semicolon (bug #928)
 
   A complete list of closed tickets can be found here [[br]]

branches/0.16-stable/test/Makefile.am

@@ -123 +123 @@
 
 # tests not passing through yet
-XFAIL_TESTS = test/gff.test
+XFAIL_TESTS =
 
 DISTRIBUTED_TESTS = \

branches/0.16-stable/yat/omic/GFF2.cc

@@ -24 +24 @@
 #include "GFF2.h"
 
+#include <cassert>
 #include <string>
 #include <map>
@@ -34 +35 @@
                            const std::string& str) const
   {
-    size_t i = str.find(' ');
-    std::string key = str.substr(0,i);
-    ++i;
+    size_t offset = str.find_first_not_of(' ');
+    size_t i = str.find_first_of(' ', offset);
+    assert(i >= offset);
+    std::string key = str.substr(offset, i-offset);
+    // trim spaces
+    i = str.find_first_not_of(' ', i+1);
     // trim off embracing '"'
     if (str[i]=='"')
       ++i;
-    size_t n = str.size() - i;
-    if (str[str.size()-1]=='"')
+    // skip trailing spaces
+    size_t n = str.find_last_not_of(' ');
+    // skip training '"'
+    if (str[n] == '"')
       --n;
-    m[key] = str.substr(i,n);
+    // str[n] now points to last char we want to include
+    m[key] = str.substr(i,n-i+1);
   }