Merge branch 'dev'

Author: molpopgen

REVISION_HISTORY.md

@@ -33,6 +33,10 @@ However:
 
 1. Sequence/SeqRegexes.hpp -- not working.  This will not be fixed until GCC supports <regex>.  The function is now currently implemented in a non-regex manner, which is lame, but it works.
 
+## libsequence 1.8.6
+
+* Patch for Issue #7
+
 ## libsequence 1.8.5
 
 * The API for the template classSequence::PolyTableSlice has changed.  During the development of [another project](http://github.com/molpopgen/foRward), I ran into some limitations of the previous API that would require some ugly hacks to work around.  The new interface is more modern, and the new implementation will be faster for sliding windows over a physical distance.

configure

@@ -1,6 +1,6 @@
 #! /bin/sh
 # Guess values for system-dependent variables and create Makefiles.
-# Generated by GNU Autoconf 2.69 for libsequence 1.8.5.
+# Generated by GNU Autoconf 2.69 for libsequence 1.8.6.
 #
 # Report bugs to <https://github.com/molpopgen/libsequence>.
 #
@@ -590,8 +590,8 @@ MAKEFLAGS=
 # Identity of this package.
 PACKAGE_NAME='libsequence'
 PACKAGE_TARNAME='libsequence'
-PACKAGE_VERSION='1.8.5'
-PACKAGE_STRING='libsequence 1.8.5'
+PACKAGE_VERSION='1.8.6'
+PACKAGE_STRING='libsequence 1.8.6'
 PACKAGE_BUGREPORT='https://github.com/molpopgen/libsequence'
 PACKAGE_URL=''
 
@@ -1338,7 +1338,7 @@ if test "$ac_init_help" = "long"; then
   # Omit some internal or obsolete options to make the list less imposing.
   # This message is too long to be a string in the A/UX 3.1 sh.
   cat <<_ACEOF
-\`configure' configures libsequence 1.8.5 to adapt to many kinds of systems.
+\`configure' configures libsequence 1.8.6 to adapt to many kinds of systems.
 
 Usage: $0 [OPTION]... [VAR=VALUE]...
 
@@ -1408,7 +1408,7 @@ fi
 
 if test -n "$ac_init_help"; then
   case $ac_init_help in
-     short | recursive ) echo "Configuration of libsequence 1.8.5:";;
+     short | recursive ) echo "Configuration of libsequence 1.8.6:";;
    esac
   cat <<\_ACEOF
 
@@ -1521,7 +1521,7 @@ fi
 test -n "$ac_init_help" && exit $ac_status
 if $ac_init_version; then
   cat <<\_ACEOF
-libsequence configure 1.8.5
+libsequence configure 1.8.6
 generated by GNU Autoconf 2.69
 
 Copyright (C) 2012 Free Software Foundation, Inc.
@@ -2011,7 +2011,7 @@ cat >config.log <<_ACEOF
 This file contains any messages produced by compilers while
 running configure, to aid debugging if configure makes a mistake.
 
-It was created by libsequence $as_me 1.8.5, which was
+It was created by libsequence $as_me 1.8.6, which was
 generated by GNU Autoconf 2.69.  Invocation command line was
 
   $ $0 $@
@@ -2877,7 +2877,7 @@ fi
 
 # Define the identity of the package.
  PACKAGE='libsequence'
- VERSION='1.8.5'
+ VERSION='1.8.6'
 
 
 cat >>confdefs.h <<_ACEOF
@@ -16192,7 +16192,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
 # report actual input values of CONFIG_FILES etc. instead of their
 # values after options handling.
 ac_log="
-This file was extended by libsequence $as_me 1.8.5, which was
+This file was extended by libsequence $as_me 1.8.6, which was
 generated by GNU Autoconf 2.69.  Invocation command line was
 
   CONFIG_FILES    = $CONFIG_FILES
@@ -16258,7 +16258,7 @@ _ACEOF
 cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
 ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`"
 ac_cs_version="\\
-libsequence config.status 1.8.5
+libsequence config.status 1.8.6
 configured by $0, generated by GNU Autoconf 2.69,
   with options \\"\$ac_cs_config\\"
 

configure.ac

@@ -1,6 +1,6 @@
 AC_PREREQ(2.59)
 
-AC_INIT([libsequence], [1.8.5], [https://github.com/molpopgen/libsequence])
+AC_INIT([libsequence], [1.8.6], [https://github.com/molpopgen/libsequence])
 AC_CONFIG_SRCDIR([src/Seq/Seq.cc])
 AC_CONFIG_SRCDIR([test/FastaIO.cc])
 AC_CONFIG_SRCDIR([examples/msstats.cc])

doc/libsequence.doxygen

@@ -38,7 +38,7 @@ PROJECT_NAME           = libsequence
 # could be handy for archiving the generated documentation or if some version
 # control system is used.
 
-PROJECT_NUMBER         = 1.8.5
+PROJECT_NUMBER         = 1.8.6
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer a

src/Seq/fastq.cc

@@ -38,7 +38,9 @@ namespace Sequence {
       throw badFormat("Sequence::fastq::read - error: record did not begin with \'@\'");
     std::string temp;
     stream.ignore(1,'@');
-    stream >> first >> second >> std::ws;
+    std::getline(stream,first);
+    std::getline(stream,second);
+    stream >> std::ws;
     if ( char(stream.peek()) != '+' ) 
       throw badFormat("Sequence::fastq::read - error: third line did not begin with \'+\'");
     stream >> temp >> std::ws;