fixed errors in undead import paths

bio/core/bgzf/inputstream.d

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

bio/core/bgzf/outputstream.d

@@ -28,7 +28,7 @@ import bio.core.bgzf.compress;
 
 import bio.core.utils.roundbuf;
 
-import undead.stream;
+import contrib.undead.stream;
 import std.exception;
 import std.parallelism;
 import std.array;

bio/core/utils/stream.d

@@ -1,6 +1,6 @@
 module bio.core.utils.stream;
 
-public import undead.stream;
+public import contrib.undead.stream;
 import core.stdc.stdio;
 import core.stdc.errno;
 import core.stdc.string;
@@ -48,7 +48,7 @@ FileMode toFileMode(string mode) {
     return result;
 }
 
-final class File: undead.stream.File {
+final class File: contrib.undead.stream.File {
     this(string filename, string mode="rb") {
         version (Posix) {
             // Issue 8528 workaround

bio/core/utils/switchendianness.d

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

bio/std/hts/bam/bai/indexing.d

@@ -30,7 +30,7 @@ import bio.std.hts.bam.constants;
 import bio.std.hts.bam.bai.bin;
 import bio.core.bgzf.chunk;
 
-import undead.stream;
+import contrib.undead.stream;
 import std.array;
 import std.algorithm;
 import std.system;

bio/std/hts/bam/baifile.d

@@ -29,7 +29,7 @@ import bio.core.bgzf.virtualoffset;
 import bio.std.hts.bam.constants;
 
 //TODO Remove stream dependency!
-import undead.stream;
+import contrib.undead.stream;
 import std.system;
 import std.exception;
 import std.algorithm;

bio/std/hts/bam/reader.d

@@ -96,7 +96,7 @@ class BamReader : IBamSamReader {
       }
       -------------------------------------------
      */
-    this(undead.stream.Stream stream,
+    this(contrib.undead.stream.Stream stream,
          TaskPool task_pool = taskPool) {
         _source_stream = new EndianStream(stream, Endian.littleEndian);
         _task_pool = task_pool;

bio/std/hts/bam/readrange.d

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

bio/std/hts/bam/reference.d

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

bio/std/hts/bam/referenceinfo.d

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

bio/std/hts/bam/writer.d

@@ -35,7 +35,7 @@ import bio.core.utils.stream;
 
 import std.parallelism;
 import std.exception;
-import undead.stream;
+import contrib.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(undead.stream.Stream stream,
+    this(contrib.undead.stream.Stream stream,
          int compression_level=-1,
          std.parallelism.TaskPool task_pool=std.parallelism.taskPool,
          size_t buffer_size=0)

bio/std/sff/reader.d

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

bio/std/sff/readrange.d

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

bio/std/sff/writer.d

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