Merge remote-tracking branch 'upstream/master'

* upstream/master:
  fix toJSON usage for new and old compilers
  test osx build
  better .travis.yml, uses dub test and tests ldc
  fix tabs/spaces in dub.json
  fix toHash signature
  fix deprecations and some warnings
  std.c -> core.stdc
  switch to undead.stream;
  fixes lomereiter/sambamba#244

.travis.yml

@@ -1,3 +1,9 @@
 language: d
-script:
-- rdmd -unittest -d test/unittests.d
+
+os:
+  - linux
+  - osx
+
+d:
+  - dmd
+  - ldc

bio/bam/bai/indexing.d

@@ -30,12 +30,12 @@ import bio.bam.constants;
 import bio.bam.bai.bin;
 import bio.core.bgzf.chunk;
 
-import std.stream;
+import undead.stream;
 import std.array;
 import std.algorithm;
 import std.system;
 import std.exception;
-import std.c.string;
+import core.stdc.string;
 
 // Suppose we have an alignment which covers bases on a reference,
 // starting from one position and ending at another position.

bio/bam/baifile.d

@@ -28,7 +28,7 @@ public import bio.bam.bai.bin;
 import bio.core.bgzf.virtualoffset;
 import bio.bam.constants;
 
-import std.stream;
+import undead.stream;
 import std.system;
 import std.exception;
 import std.algorithm;

bio/bam/pileup.d

@@ -864,6 +864,11 @@ struct PileupChunkRange(C) {
     private bool _use_md_tag;
     private ulong _start_from;
     private ulong _end_at;
+    private int _chunk_right_end;
+
+    private int computeRightEnd(ref ElementType!C chunk) {
+        return chunk.map!(r => r.position + r.basesCovered()).reduce!max;
+    }
 
     this(C chunks, bool use_md_tag, ulong start_from, ulong end_at) {
         _chunks = chunks;
@@ -885,10 +890,9 @@ struct PileupChunkRange(C) {
                     break;
                 }
 
-                auto last_read = _current_chunk[$-1];
-                if (last_read.position + last_read.basesCovered() > start_from) {
+                _chunk_right_end = computeRightEnd(_current_chunk);
+                if (_chunk_right_end > start_from)
                     break;
-                }
             }
         }
     }
@@ -900,7 +904,7 @@ struct PileupChunkRange(C) {
     auto front() @property {
         auto end_pos = _current_chunk[$-1].position;
         if (_chunks.empty || _chunks.front[0].ref_id != _current_chunk[$-1].ref_id)
-            end_pos += _current_chunk[$-1].basesCovered();
+            end_pos = _chunk_right_end;
 
         return makePileup(chain(_prev_chunk, _current_chunk),
                           _use_md_tag,
@@ -921,6 +925,8 @@ struct PileupChunkRange(C) {
             if (_current_chunk[0].ref_id >= 0) break;
         }
 
+        _chunk_right_end = computeRightEnd(_current_chunk);
+
         // if we changed reference, nullify prev_chunk
         if (_prev_chunk.length > 0 &&
             _prev_chunk[$ - 1].ref_id == _current_chunk[0].ref_id)

bio/bam/randomaccessmanager.d

@@ -50,6 +50,7 @@ import std.traits;
 import std.exception;
 import std.container;
 import std.parallelism;
+static import std.file;
 
 debug {
     import std.stdio;

bio/bam/read.d

@@ -72,7 +72,7 @@ import std.system;
 import std.traits;
 import std.array;
 import std.bitmanip;
-import std.c.stdlib;
+import core.stdc.stdlib;
 
 /**
   Represents single CIGAR operation
@@ -1579,6 +1579,7 @@ unittest {
 
     {
     import std.typecons;
+    static import bio.bam.thirdparty.msgpack;
     auto packer = bio.bam.thirdparty.msgpack.packer(Appender!(ubyte[])());
     read.toMsgpack(packer);
     auto data = packer.stream.data;

bio/bam/reader.d

@@ -94,8 +94,8 @@ class BamReader : IBamSamReader {
       }
       -------------------------------------------
      */
-    this(std.stream.Stream stream, 
-         std.parallelism.TaskPool task_pool = std.parallelism.taskPool) {
+    this(undead.stream.Stream stream,
+         TaskPool task_pool = taskPool) {
         _source_stream = new EndianStream(stream, Endian.littleEndian);
         _task_pool = task_pool;
 

bio/bam/readrange.d

@@ -29,7 +29,7 @@ import bio.bam.reader;
 import bio.core.bgzf.inputstream;
 import bio.core.bgzf.virtualoffset;
 
-import std.stream;
+import undead.stream;
 import std.algorithm;
 import std.system;
 import std.bitmanip;

bio/bam/reference.d

@@ -47,7 +47,7 @@ import bio.bam.region;
 import bio.bam.randomaccessmanager;
 import bio.core.bgzf.virtualoffset;
 
-import std.stream;
+import undead.stream;
 import std.exception;
 import std.array;
 

bio/bam/referenceinfo.d

@@ -23,7 +23,7 @@
 */
 module bio.bam.referenceinfo;
 
-import std.stream;
+import undead.stream;
 import std.exception;
 import std.array;
 

bio/bam/snpcallers/maq.d

@@ -5,7 +5,7 @@ module bio.bam.snpcallers.maq;
  */
 
 import core.stdc.math;
-import std.math : LN2, LN10, isnan;
+import std.math : LN2, LN10, isNaN;
 import std.traits;
 import std.range;
 import std.algorithm;

bio/bam/tagvalue.d

@@ -296,7 +296,7 @@ string injectOpCast() {
     }
 
     cs ~= `(is(T == string)) {` ~
-          `  if (is_string) {`
+          `  if (is_string) {` ~
           `    return bam_typeid == 'Z' ? u.Z : u.H;`~
           `  } else if (is_integer || is_float || is_character) {`~
           `    `~injectSwitchPrimitive("string")~

bio/bam/thirdparty/msgpack.d

@@ -59,7 +59,7 @@ else
 // for Converting Endian using ntohs and ntohl;
 version(Windows)
 {
-    import std.c.windows.winsock;
+    import core.stdc.windows.winsock;
 }
 else
 {
@@ -82,7 +82,7 @@ static if (real.sizeof == double.sizeof) {
     import std.numeric;
 }
 
-version(unittest) import std.file, std.c.string;
+version(unittest) import std.file, core.stdc.string;
 
 
 @trusted:
@@ -344,7 +344,7 @@ struct PackerImpl(Stream) if (isOutputRange!(Stream, ubyte) && isOutputRange!(St
      * Params:
      *  withFieldName = serialize class / struct with field name
      */
-    this(bool withFieldName = false)
+    this(bool withFieldName)
     {
         withFieldName_ = withFieldName;
     }
@@ -3145,7 +3145,7 @@ struct Value
      *  type  = the type of value.
      */
     @safe
-    this(Type type = Type.nil)
+    this(Type type)
     {
         this.type = type;
     }
@@ -3617,7 +3617,7 @@ struct Value
                         ret ^= value.toHash();
                     }
                     return ret;
-                } catch assert(0);
+                } catch (Exception) assert(0);
         }
     }
 }
@@ -4656,7 +4656,7 @@ mixin template MessagePackable(Members...)
             if (withFieldName) {
                 packer.beginMap(this.tupleof.length);
                 foreach (i, member; this.tupleof) {
-                    pack(getFieldName!(typeof(this), i));
+                    packer.pack(getFieldName!(typeof(this), i));
                     packer.pack(member);
                 }
             } else {

bio/bam/utils/array.d

@@ -23,7 +23,7 @@
 */
 module bio.bam.utils.array;
 
-import std.c.string;
+import core.stdc.string;
 import std.traits;
 
 /// Modifies array in-place so that $(D slice) is replaced by

bio/bam/writer.d

@@ -35,7 +35,7 @@ import bio.core.utils.stream;
 
 import std.parallelism;
 import std.exception;
-import std.stream;
+import undead.stream;
 import std.traits;
 import std.system;
 import std.algorithm;
@@ -73,7 +73,7 @@ final class BamWriter {
     ///     compression_level  = compression level, must be in range -1..9
     ///     task_pool          = task pool to use for parallel compression
     ///     buffer_size        = size of BgzfOutputStream buffer
-    this(std.stream.Stream stream,
+    this(undead.stream.Stream stream,
          int compression_level=-1,
          std.parallelism.TaskPool task_pool=std.parallelism.taskPool,
          size_t buffer_size=0)

bio/core/bgzf/inputstream.d

@@ -30,7 +30,7 @@ import bio.core.bgzf.chunk;
 import bio.bam.constants;
 import bio.core.utils.roundbuf;
 
-import std.stream;
+import undead.stream;
 import std.exception;
 import std.conv;
 import std.parallelism;

bio/core/bgzf/outputstream.d

@@ -28,13 +28,13 @@ import bio.core.bgzf.compress;
 
 import bio.core.utils.roundbuf;
 
-import std.stream;
+import undead.stream;
 import std.exception;
 import std.parallelism;
 import std.array;
 import std.algorithm : max;
 import std.typecons;
-import std.c.stdlib;
+import core.stdc.stdlib;
 
 alias void delegate(ubyte[], ubyte[]) BlockWriteHandler;
 
@@ -88,7 +88,7 @@ class BgzfOutputStream : Stream {
 
         // 1 extra block to which we can write while n_tasks are executed
         auto comp_buf_size = (2 * n_tasks + 2) * max_block_size;
-        auto p = cast(ubyte*)std.c.stdlib.malloc(comp_buf_size);
+        auto p = cast(ubyte*)core.stdc.stdlib.malloc(comp_buf_size);
         _compression_buffer = p[0 .. comp_buf_size];
         _buffer = _compression_buffer[0 .. block_size];
         _tmp = _compression_buffer[max_block_size .. max_block_size * 2];
@@ -210,7 +210,7 @@ class BgzfOutputStream : Stream {
         _stream.close();
 
         writeable = false;
-        std.c.stdlib.free(_compression_buffer.ptr);
+        core.stdc.stdlib.free(_compression_buffer.ptr);
     }
 
     /// Adds EOF block. This function is called in close() method.

bio/core/utils/bylinefast.d

@@ -6,7 +6,7 @@ module bio.core.utils.bylinefast;
 
 import std.stdio;
 import std.string: indexOf;
-import std.c.string: memmove;
+import core.stdc.string: memmove;
 
 /**
    Reads by line in an efficient way (10 times faster than File.byLine from std.stdio).

bio/core/utils/format.d

@@ -34,8 +34,9 @@
  */
 module bio.core.utils.format;
 
-import std.c.stdio;
-import std.c.stdlib;
+import core.stdc.stdio;
+import core.stdc.stdlib;
+static import core.stdc.string;
 import std.string;
 import std.traits;
 import std.array;
@@ -161,7 +162,7 @@ private {
         if (isSomeString!T)
     {
         auto str = cast(const(char)[])s;
-        std.c.string.memcpy(sink, str.ptr, str.length);
+        core.stdc.string.memcpy(sink, str.ptr, str.length);
         sink += str.length;
     }
 

bio/core/utils/outbuffer.d

@@ -93,7 +93,7 @@ class OutBuffer {
     /// Responsibility that there's enough capacity is on the user
     void putUnsafe(T)(T bytes) if (is(T == ubyte[])) {
         _heap_ptr[_heap_used .. _heap_used + bytes.length] = bytes[];
-        _heap_used += bytes.length;;
+        _heap_used += bytes.length;
     }
 
     /// ditto

bio/core/utils/stream.d

@@ -1,6 +1,6 @@
 module bio.core.utils.stream;
 
-public import std.stream;
+public import undead.stream;
 import core.stdc.stdio;
 import core.stdc.errno;
 import core.stdc.string;
@@ -15,7 +15,7 @@ version(Posix){
 version(Windows) {
     private import std.file;
     private import std.utf;
-    private import std.c.windows.windows;
+    private import core.stdc.windows.windows;
     extern (Windows) {
         DWORD GetFileType(HANDLE hFile);
     }
@@ -48,7 +48,7 @@ FileMode toFileMode(string mode) {
     return result;
 }
 
-final class File: std.stream.File {
+final class File: undead.stream.File {
     this(string filename, string mode="rb") {
         version (Posix) {
             // Issue 8528 workaround
@@ -135,7 +135,6 @@ final class File: std.stream.File {
                         if (ret <= 0) {
                             size = 0;
                             throw new ReadException("read timeout");
-                            break;
                         }
                     } else {
                         throw new ReadException(to!string(strerror(errno)));

bio/core/utils/switchendianness.d

@@ -1,5 +1,5 @@
 /**
-  (Almost) a copy-paste from std/stream.d
+  (Almost) a copy-paste from undead.stream.d
 */
 module bio.core.utils.switchendianness;
 

bio/sam/header.d

@@ -8,10 +8,10 @@
     the rights to use, copy, modify, merge, publish, distribute, sublicense,
     and/or sell copies of the Software, and to permit persons to whom the
     Software is furnished to do so, subject to the following conditions:
-    
+
     The above copyright notice and this permission notice shall be included in
     all copies or substantial portions of the Software.
-    
+
     THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
     IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
     FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
@@ -117,7 +117,7 @@ private {
     mixin template toSamMethod(string line_prefix, Field...) {
         void toSam(Sink)(auto ref Sink sink) const if (isSomeSink!Sink) {
             sink.write(line_prefix);
-            mixin(serializeFields!Field());    
+            mixin(serializeFields!Field());
         }
     }
 
@@ -132,9 +132,9 @@ private {
 
     mixin template toHashMethod(string struct_name, string id_field, Field...) {
         static if (id_field != null) {
-            hash_t toHash() const {
+            hash_t toHash() const nothrow @safe{
                 hash_t result = 1;
-                mixin(generateHashExpression!Field());    
+                mixin(generateHashExpression!Field());
                 return result;
             }
 
@@ -195,12 +195,12 @@ private {
         }
     }
 
-    mixin template HeaderLineStruct(string struct_name, 
+    mixin template HeaderLineStruct(string struct_name,
                                     string line_prefix,
                                     string id_field,
-                                    Field...) 
+                                    Field...)
     {
-         mixin(`struct `~struct_name~`{ 
+         mixin(`struct `~struct_name~`{
                     mixin structFields!Field;
                     mixin parseStaticMethod!(struct_name, Field);
                     mixin toSamMethod!(line_prefix, Field);
@@ -359,7 +359,7 @@ class HeaderLineDictionary(T) {
             _index_to_id.length = _index_to_id.length - 1;
 
             _dict.remove(id);
-            _id_to_index.remove(id); 
+            _id_to_index.remove(id);
 
             return true;
         }
@@ -484,7 +484,7 @@ class SamHeader {
                     try {
                         sorting_order = to!SortingOrder(header_line.sorting_order);
                     } catch (ConvException e) {
-                        sorting_order = SortingOrder.unknown; 
+                        sorting_order = SortingOrder.unknown;
                         // FIXME: should we do that silently?
                     }
                 } else {
@@ -536,14 +536,14 @@ class SamHeader {
 
         core.memory.GC.enable();
     }
-       
+
     /// Format version
     string format_version;
 
     /// Sorting order
     SortingOrder sorting_order = SortingOrder.unknown;
 
-    /// Dictionary of @SQ lines. 
+    /// Dictionary of @SQ lines.
     /// Removal is not allowed, you can only replace the whole dictionary.
     SqLineDictionary sequences() @property {
         if (_sequences is null)
@@ -624,7 +624,7 @@ class SamHeader {
             sink.write(to!string(sorting_order));
         }
         sink.write('\n');
-       
+
         for (size_t i = 0; i < sequences.length; i++) {
             auto sq_line = getSequence(i);
             sq_line.toSam(sink);
@@ -707,13 +707,16 @@ class SamHeader {
 
         JSONValue json;
         json.object = result;
-        sink.write(toJSON(&json));
+        static if (__VERSION__ < 2072)
+            sink.write(toJSON(&json));
+        else
+            sink.write(toJSON(json));
     }
 
     /// Packs message in the following format:
     /// $(BR)
     /// MsgPack array with elements
-    ///   $(OL 
+    ///   $(OL
     ///     $(LI format version - string)
     ///     $(LI sorting order - string)
     ///     $(LI @SQ lines - array of dictionaries)
@@ -789,7 +792,7 @@ unittest {
     dict["zzz"] = zzz;
     header.sequences = dict;
 
-    assert(header.text == 
+    assert(header.text ==
       "@HD\tVN:1.4\tSO:coordinate\n@SQ\tSN:yay\tLN:111\n@SQ\tSN:zzz\tLN:222\tUR:ftp://nyan.cat\n");
     assert(header.sequences == dict);
 

bio/sam/reader.d

@@ -49,7 +49,7 @@ import std.typecons;
 import std.parallelism;
 import std.process;
 import std.exception;
-import std.c.string;
+import core.stdc.string;
 
 BamRead _parseSamRecord(Tuple!(char[], SamReader, OutBuffer) t) {
     auto r = parseAlignmentLine(cast(string)t[0], t[1]._header, t[2]);

bio/sff/reader.d

@@ -29,7 +29,7 @@ import bio.sff.readrange;
 import bio.sff.constants;
 
 import bio.core.utils.stream;
-import std.stream;
+import undead.stream;
 import std.system;
 import std.range;
 import std.exception;

bio/sff/readrange.d

@@ -5,7 +5,7 @@ import bio.sff.index;
 import bio.core.utils.switchendianness;
 
 import std.algorithm;
-import std.stream;
+import undead.stream;
 import std.system;
 import std.array;
 

bio/sff/writer.d

@@ -4,7 +4,7 @@ import bio.sff.constants;
 import bio.sff.utils.roundup;
 
 import bio.core.utils.stream;
-import std.stream;
+import undead.stream;
 import std.system;
 
 /// Class for outputting SFF files

dub.json

@@ -8,5 +8,9 @@
 	"copyright": "Copyright © 2016, BioD developers",
 	"license": "MIT",
 	"sourcePaths": ["bio"],
-	"importPaths": ["bio"]
+	"importPaths": ["bio"],
+	"dependencies": {
+		"undead": "~>1.0.6"
+	},
+	"buildRequirements": ["allowWarnings"]
 }

examples/create_bam_from_scratch.d

@@ -3,7 +3,7 @@
 // this example shows how to create BAM files from scratch
 import bio.bam.read, bio.bam.referenceinfo, bio.sam.header;
 import bio.bam.reader, bio.bam.writer;
-import std.stream, std.stdio;
+import undead.stream, std.stdio;
 
 void main() {
     auto header = new SamHeader(); // First, create SAM header 

test/unittests.d

@@ -49,7 +49,7 @@ import bio.core.utils.roundbuf;
 import std.path;
 import std.range;
 import std.stdio;
-import std.stream;
+import undead.stream;
 import std.algorithm;
 import std.array;
 import std.conv;