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

bio2
Pjotr Prins 5 years ago
parent
commit
5e56b2bb45
  1. 1
      bio/bam/baseinfo.d
  2. 2
      bio/bam/read.d
  3. 2
      bio/core/utils/format.d
  4. 7
      examples/calculate_gc_content_from_reference.d
  5. 8
      examples/create_bam_from_scratch.d
  6. 7
      examples/iterate_tags.d
  7. 7
      examples/make_pileup.d
  8. 7
      examples/print_base_info.d
  9. 7
      examples/read_bam_file.d
  10. 7
      examples/transverse_multiple_bam_files.d

1
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;

2
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.

2
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;
}

7
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;

8
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

7
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;

7
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;

7
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;

7
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;

7
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;

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