Merge branch 'master' of github.com:biod/BioD

bio/bam/baseinfo.d

@@ -30,6 +30,7 @@ import bio.bam.read;
 import bio.bam.tagvalue;
 import bio.bam.iontorrent.flowcall;
 import bio.bam.md.core;
+import bio.bam.cigar;
 
 import std.range;
 import std.conv;

bio/bam/read.d

@@ -1007,7 +1007,7 @@ private:
         assert(n < 16);
         // http://graphics.stanford.edu/~seander/bithacks.html#ConditionalSetOrClearBitsWithoutBranching
         ushort mask = cast(ushort)(1 << n);
-        _flag = (_flag & ~mask) | ((-cast(int)b) & mask);
+        _flag = (_flag & ~cast(int)(mask)) | ((-cast(int)b) & mask);
     }
 
     // If _chunk is still a slice, not an array, duplicate it.

bio/core/utils/format.d

@@ -58,7 +58,7 @@ private {
         char* wstr=str;
 
         static if (isSigned!T) { 
-            ulong uvalue = (value < 0) ? -value : value;
+            ulong uvalue = (value < 0) ? -cast(int)(value) : value;
         } else {
             ulong uvalue = value;
         }

examples/calculate_gc_content_from_reference.d

@@ -1,4 +1,9 @@
-// run example: rdmd -I.. calculate_gc_content_from_reference.d
+// BioD depends on stream.d which is no longer included with phobos.
+// To run this example from this directory,
+// Clone the undead repository with
+// git clone https://github.com:dlang/undeaD.git at the appropriate location and ensure
+// it is available on your path
+// Run example: rdmd -I.. -I../location_of_undead/src calculate_gc_content_from_reference.d
 
 import bio.bam.reader;
 import bio.bam.md.reconstruct : dna;

examples/create_bam_from_scratch.d

@@ -1,9 +1,15 @@
-// run example: rdmd -I.. create_bam_from_scratch.d
+// BioD depends on stream.d which is no longer included with phobos.
+// To run this example from this directory,
+// Clone the undead repository with
+// git clone https://github.com:dlang/undeaD.git at the appropriate location and ensure
+// it is available on your path
+// Run example: rdmd -I.. -I../location_of_undead/src create_bam_from_scratch.d
 
 // 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 undead.stream, std.stdio;
+import bio.bam.cigar;
 
 void main() {
     auto header = new SamHeader(); // First, create SAM header 

examples/iterate_tags.d

@@ -1,4 +1,9 @@
-// run example: rdmd -I.. iterate_tags.d
+// BioD depends on stream.d which is no longer included with phobos.
+// To run this example from this directory,
+// Clone the undead repository with
+// git clone https://github.com:dlang/undeaD.git at the appropriate location and ensure
+// it is available on your path
+// Run example: rdmd -I.. -I../location_of_undead/src iterate_tags.d
 
 import bio.bam.reader, bio.bam.tagvalue;
 import std.stdio, std.datetime;

examples/make_pileup.d

@@ -1,4 +1,9 @@
-// run example: rdmd -I.. make_pileup.d
+// BioD depends on stream.d which is no longer included with phobos.
+// To run this example from this directory,
+// Clone the undead repository with
+// git clone https://github.com:dlang/undeaD.git at the appropriate location and ensure
+// it is available on your path
+// Run example: rdmd -I.. -I../location_of_undead/src make_pileup.d
 
 import bio.bam.reader;
 import bio.bam.pileup;

examples/print_base_info.d

@@ -1,4 +1,9 @@
-// run example: rdmd -I.. print_base_info.d
+// BioD depends on stream.d which is no longer included with phobos.
+// To run this example from this directory,
+// Clone the undead repository with
+// git clone https://github.com:dlang/undeaD.git at the appropriate location and ensure
+// it is available on your path
+// Run example: rdmd -I.. -I../location_of_undead/src print_base_info.d
 
 import bio.bam.reader;
 import bio.bam.baseinfo;

examples/read_bam_file.d

@@ -1,4 +1,9 @@
-// run example: rdmd -I.. example1.d
+// BioD depends on stream.d which is no longer included with phobos.
+// To run this example from this directory,
+// Clone the undead repository with
+// git clone https://github.com:dlang/undeaD.git at the appropriate location and ensure
+// it is available on your path
+// Run example: rdmd -I.. -I../location_of_undead/src read_bam_file.d
 
 import bio.bam.reader;
 import bio.bam.pileup;

examples/transverse_multiple_bam_files.d

@@ -1,4 +1,9 @@
-// run example: rdmd -I.. transverse_multiple_bam_files.d
+// BioD depends on stream.d which is no longer included with phobos.
+// To run this example from this directory,
+// Clone the undead repository with
+// git clone https://github.com:dlang/undeaD.git at the appropriate location and ensure
+// it is available on your path
+// Run example: rdmd -I.. -I../location_of_undead/src transverse_multiple_bam_files.d
 
 import bio.bam.multireader;
 import bio.bam.read : compareCoordinates;