[FIX] Fixed minor issues.

Author: Jochen Singer

core/include/seqan/arg_parse/arg_parse_exceptions.h

@@ -45,21 +45,8 @@ namespace seqan {
 // Class ParseError
 // ----------------------------------------------------------------------------
 
-// TODO(singer): Remove this once all test are running.
-/*
-.Internal.Class.ParseError
-..cat:Miscellaneous
-..summary:General ParseError.
-*/
-
-/*class ParseError : public RuntimeError
-{
-public:
-    ParseError(std::string const & option) :
-        RuntimeError(option)
-    {}
-};
-*/
+// Defined in core/include/seqan/stream/tokenization.h
+struct ParseError;
 
 // ----------------------------------------------------------------------------
 // Class InvalidOption

core/include/seqan/stream/chunking.h

@@ -155,22 +155,22 @@ inline void advanceChunk(String<TValue, TSpec> &str, TSize size)
 // StreamBuffer
 template <typename TValue, typename TTraits>
 inline typename Chunk<StreamBuffer<TValue, TTraits> >::Type
-getChunk(StreamBuffer<TValue, TTraits>  &buf, Input)
+getChunk(StreamBuffer<TValue, TTraits> &buf, Input)
 {
     return toRange(buf.gptr(), buf.egptr());
 }
 
 template <typename TValue, typename TTraits>
 inline typename Chunk<StreamBuffer<TValue, TTraits> >::Type
-getChunk(StreamBuffer<TValue, TTraits>  &buf, Output)
+getChunk(StreamBuffer<TValue, TTraits> &buf, Output)
 {
     return toRange(buf.pptr(), buf.epptr());
 }
 
 // StreamIterator
 template <typename TStream, typename TDirection>
 inline typename Chunk<Iter<TStream, StreamIterator<Tag<TDirection> > > >::Type
-getChunk(Iter<TStream, StreamIterator<Tag<TDirection> > >  &iter, Tag<TDirection>)
+getChunk(Iter<TStream, StreamIterator<Tag<TDirection> > > &iter, Tag<TDirection>)
 {
     typedef typename Iter<TStream, StreamIterator<Input> >::TStreamBuffer TStreamBuffer;
     SEQAN_ASSERT(iter.streamBuf != NULL);

core/include/seqan/stream/stream_base.h

@@ -80,6 +80,7 @@ namespace seqan {
 ..remarks:This flag is normally set from the outside by your build system using compiler flags.
  */
 
+// TODO(singer): remove this
 //#if SEQAN_HAS_ZLIB
 struct GZFile_;
 typedef Tag<GZFile_> GZFile;

core/include/seqan/stream/tokenization.h

@@ -356,8 +356,6 @@ inline void readUntil(TTarget &target, TFwdIterator &iter, TStopFunctor &stopFun
 // Function readOne()
 // ----------------------------------------------------------------------------
 
-//TODO(singer): implement a chunked version!
-
 template <typename TTarget, typename TFwdIterator, typename TFunctor>
 inline void readOne(TTarget & target, TFwdIterator &iter, TFunctor &functor)
 {

core/include/seqan/stream/virtual_stream.h

@@ -57,20 +57,21 @@ namespace seqan {
 // TagList CompressedFileTypes
 // --------------------------------------------------------------------------
 
+
 typedef
-//#if SEQAN_HAS_ZLIB
+#if SEQAN_HAS_ZLIB
     TagList<GZFile,
-//#endif
-//#if SEQAN_HAS_BZIP2
+#endif
+#if SEQAN_HAS_BZIP2
     TagList<BZ2File,
-//#endif
+#endif
     TagList<Nothing>
-//#if SEQAN_HAS_BZIP2
+#if SEQAN_HAS_BZIP2
     >
-//#endif
-//#if SEQAN_HAS_ZLIB
+#endif
+#if SEQAN_HAS_ZLIB
     >
-//#endif
+#endif
     CompressedFileTypes;  // if TagSelector is set to -1, the file format is auto-detected
 
 // ============================================================================
@@ -139,7 +140,6 @@ unsigned char const MagicHeader<Fastq, T>::VALUE[1] = { '@' };  // Fastq's first
 // --------------------------------------------------------------------------
 
 // TODO(weese:) rename FileFormatExtensions to FileTypeExtensions or FileExtensions
-#if SEQAN_HAS_ZLIB
 template <typename T>
 struct FileFormatExtensions<GZFile, T>
 {
@@ -151,12 +151,10 @@ char const * FileFormatExtensions<GZFile, T>::VALUE[3] = {
     ".gz",      // default output extension
     ".Z",
     ".zip" };
-#endif
 
 template <typename TTag, typename T>
 struct FileFormatExtensions;
 
-#if SEQAN_HAS_BZIP2
 template <typename T>
 struct FileFormatExtensions<BZ2File, T>
 {
@@ -167,7 +165,6 @@ template <typename T>
 char const * FileFormatExtensions<BZ2File, T>::VALUE[2] = {
     ".bz2",      // default output extension
     ".bz" };
-#endif
 
 template <typename T>
 struct FileFormatExtensions<Nothing, T>

core/include/seqan/stream/zipstream/zutil.h

@@ -220,7 +220,7 @@ void   zcfree  OF((voidpf opaque, voidpf ptr));
 #define TRY_FREE(s, p) {if (p) ZFREE(s, p);}
 
 #ifdef local
-#  undef local
+#undef local
 #endif
 
 #endif /* _Z_UTIL_H */

core/include/seqan/ucsc_io.h

@@ -31,50 +31,14 @@
 // ==========================================================================
 // Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
 // ==========================================================================
-// Define SeqAn version.
+// Facade header for module ucsc_io.
 // ==========================================================================
 
+#ifndef CORE_INCLUDE_SEQAN_UCSC_IO_H_
+#define CORE_INCLUDE_SEQAN_UCSC_IO_H_
+
 #include <seqan/ucsc_io/ucsc_record.h>
 #include <seqan/ucsc_io/ucsc_io.h>
 
-#ifndef SEQAN_VERSION_H_
-#define SEQAN_VERSION_H_
-
-/**
-.Macro.SEQAN_VERSION_MAJOR
-..cat:Versioning
-..summary:Major SeqAn revision number.
-..signature:SEQAN_VERSION_MAJOR
-..example:For SeqAn version "1.3", this value is $1$, for "2.5.4", it is $2$.
-..include:seqan/version.h
-
-.Macro.SEQAN_VERSION_MINOR
-..cat:Versioning
-..summary:Minor SeqAn revision number.
-..signature:SEQAN_VERSION_MINOR
-..example:For SeqAn version "1.3", this value is $3$, for "1.5.4", it is $5$.
-..include:seqan/version.h
-
-.Macro.SEQAN_VERSION_PATCH
-..cat:Versioning
-..summary:SeqAn patch revision number.
-..signature:SEQAN_VERSION_PATCH
-..example:For SeqAn version "1.3", this value is $0$, for "1.3.4", it is $4$.
-..include:seqan/version.h
-
-.Macro.SEQAN_VERSION_PRE_RELEASE
-..cat:Versioning
-..summary:Flag ($0$/$1$) to indicate whether this is a pre-release (i.e. SVN version).
-..signature:SEQAN_VERSION_PRE_RELEASE
-..include:seqan/version.h
-*/
-
-#define SEQAN_VERSION_MAJOR 1
-
-#define SEQAN_VERSION_MINOR 5
-
-#define SEQAN_VERSION_PATCH 0
-
-#define SEQAN_VERSION_PRE_RELEASE 1
+#endif  // CORE_INCLUDE_SEQAN_UCSC_IO_H_
 
-#endif  // SEQAN_VERSION_H_

extras/include/seqan/vcf_io/read_vcf.h

@@ -361,16 +361,10 @@ readRecord(VcfRecord & record,
     skipOne(iter);
 
     // INFO
-    readUntil(record.info, iter, IsWhitespace());
-    if (IsNewline()(value(iter)))
-    {
-        if (empty(record.info))
-            throw ParseError("Unexpected end of record.");
-        skipOne(iter);
+    readUntil(record.info, iter, OrFunctor<IsTab, IsNewline>());
+    char c = readOne(iter);
+    if (IsNewline()(c))
         return;
-    }
-    else
-        skipOne(iter);
 
     // FORMAT
     readUntil(record.format, iter, NextEntry());
@@ -390,16 +384,13 @@ readRecord(VcfRecord & record,
             else
                 break;  // Done
         }
-        if (IsNewline()(value(iter)))
-        {
-            skipOne(iter);
+
+        char c = readOne(iter);
+        if (IsNewline()(c))
             return;
-        }
-        else
-            skipOne(iter);
     }
 
-    // Skip empty lines, necessary for getting to EOF if there is an empty line at the ned of the file.
+    // Skip empty lines, necessary for getting to EOF if there is an empty line at the end of the file.
     while (!atEnd(iter) && IsNewline()(value(iter)))
         skipOne(iter);
 }