Browse Source

preped relevant namespaces to the modules. rename the modules to allow consistence with the new API and directory structure?

remotes/georgeg/master
George Githinji 4 years ago
parent
commit
9d52e43423
  1. 14
      bio/std/hts/bam/abstractreader.d
  2. 4
      bio/std/hts/bam/bai/bin.d
  3. 7
      bio/std/hts/bam/baifile.d
  4. 12
      bio/std/hts/bam/baseinfo.d
  5. 18
      bio/std/hts/bam/cigar.d
  6. 10
      bio/std/hts/bam/pileup.d
  7. 16
      bio/std/hts/bam/randomaccessmanager.d
  8. 4
      bio/std/hts/sam/header.d
  9. 16
      bio/std/hts/sam/reader.d
  10. 8
      bio/std/hts/sam/utils/fastrecordparser.d
  11. 12
      bio/std/hts/sam/utils/recordparser.d
  12. 4
      bio/std/hts/snpcallers/simple.d
  13. 4
      bio/std/hts/thirdparty/msgpack.d

14
bio/std/hts/bam/abstractreader.d

@ -21,11 +21,11 @@
DEALINGS IN THE SOFTWARE.
*/
module bio.bam.abstractreader;
module bio.std.hts.bam.abstractreader;
import bio.sam.header;
import bio.bam.read;
import bio.bam.referenceinfo;
import bio.std.hts.sam.header;
import bio.std.hts.bam.read;
import bio.std.hts.bam.referenceinfo;
public import std.range;
@ -33,13 +33,13 @@ public import std.range;
/// and $(DPREF2 sam, reader, SamReader).
interface IBamSamReader {
/// SAM header
bio.sam.header.SamHeader header() @property;
bio.std.hts.sam.header.SamHeader header() @property;
/// Information about reference sequences
const(bio.bam.referenceinfo.ReferenceSequenceInfo)[] reference_sequences() @property const nothrow;
const(bio.std.hts.bam.referenceinfo.ReferenceSequenceInfo)[] reference_sequences() @property const nothrow;
/// All reads in the file
std.range.InputRange!(bio.bam.read.BamRead) allReads() @property;
std.range.InputRange!(bio.std.hts.bam.read.BamRead) allReads() @property;
/// Filename
string filename() @property const;

4
bio/std/hts/bam/bai/bin.d

@ -21,10 +21,10 @@
DEALINGS IN THE SOFTWARE.
*/
module bio.bam.bai.bin;
module bio.std.hts.bam.bai.bin;
import bio.core.bgzf.chunk;
import bio.bam.constants;
import bio.std.hts.bam.constants;
/// Distinct bin
struct Bin {

7
bio/std/hts/bam/baifile.d

@ -21,13 +21,14 @@
DEALINGS IN THE SOFTWARE.
*/
module bio.bam.baifile;
module bio.std.hts.bam.baifile;
public import bio.core.bgzf.chunk;
public import bio.bam.bai.bin;
public import bio.std.hts.bam.bai.bin;
import bio.core.bgzf.virtualoffset;
import bio.bam.constants;
import bio.std.hts.bam.constants;
//TODO Remove stream dependency!
import undead.stream;
import std.system;
import std.exception;

12
bio/std/hts/bam/baseinfo.d

@ -21,16 +21,16 @@
DEALINGS IN THE SOFTWARE.
*/
module bio.bam.baseinfo;
module bio.std.hts.bam.baseinfo;
import bio.core.base;
import bio.core.sequence;
import bio.bam.read;
import bio.bam.tagvalue;
import bio.bam.iontorrent.flowcall;
import bio.bam.md.core;
import bio.bam.cigar;
import bio.std.hts.bam.read;
import bio.std.hts.bam.tagvalue;
import bio.std.hts.bam.iontorrent.flowcall;
import bio.std.hts.bam.md.core;
import bio.std.hts.bam.cigar;
import std.range;
import std.conv;

18
bio/std/hts/bam/cigar.d

@ -22,7 +22,7 @@
*/
module bio.bam.cigar;
module bio.std.hts.bam.cigar;
import std.algorithm;
import std.range;
@ -38,19 +38,19 @@ import core.stdc.stdlib;
import bio.core.base;
import bio.core.utils.format;
import bio.bam.abstractreader;
import bio.std.hts.bam.abstractreader;
//import bio.bam.cigar;
import bio.bam.writer;
import bio.bam.tagvalue;
import bio.bam.bai.bin;
import bio.std.hts.bam.writer;
import bio.std.hts.bam.tagvalue;
import bio.std.hts.bam.bai.bin;
import bio.bam.md.core;
import bio.std.hts.bam.md.core;
import bio.bam.utils.array;
import bio.bam.utils.value;
import bio.std.hts.bam.utils.array;
import bio.std.hts.bam.utils.value;
import bio.core.utils.switchendianness;
import bio.bam.thirdparty.msgpack : Packer, unpack;
import bio.std.hts.thirdparty.msgpack : Packer, unpack;
/**
Represents single CIGAR operation

10
bio/std/hts/bam/pileup.d

@ -67,12 +67,12 @@
/// }
/// }
/// ---------------------------------------------------------
module bio.bam.pileup;
module bio.std.hts.bam.pileup;
import bio.bam.cigar;
import bio.bam.read;
import bio.bam.md.reconstruct;
import bio.bam.splitter;
import bio.std.hts.bam.cigar;
import bio.std.hts.bam.read;
import bio.std.hts.bam.md.reconstruct;
import bio.std.hts.bam.splitter;
import std.algorithm;
import std.range;

16
bio/std/hts/bam/randomaccessmanager.d

@ -24,14 +24,14 @@
/**
Module for random access operations on BAM file.
*/
module bio.bam.randomaccessmanager;
import bio.bam.constants;
import bio.bam.reader;
import bio.bam.read;
import bio.bam.readrange;
import bio.bam.baifile;
import bio.bam.region;
module bio.std.hts.bam.randomaccessmanager;
import bio.std.hts.bam.constants;
import bio.std.hts.bam.reader;
import bio.std.hts.bam.read;
import bio.std.hts.bam.readrange;
import bio.std.hts.bam.baifile;
import bio.std.hts.bam.region;
import bio.core.utils.algo;
import bio.core.bgzf.block;

4
bio/std/hts/sam/header.d

@ -21,9 +21,9 @@
DEALINGS IN THE SOFTWARE.
*/
module bio.sam.header;
module bio.std.hts.sam.header;
import bio.bam.thirdparty.msgpack;
import bio.std.hts.thirdparty.msgpack;
import bio.core.utils.format;
import std.algorithm;

16
bio/std/hts/sam/reader.d

@ -21,13 +21,13 @@
DEALINGS IN THE SOFTWARE.
*/
module bio.sam.reader;
import bio.bam.abstractreader;
import bio.sam.header;
import bio.bam.read;
import bio.bam.reference;
import bio.bam.referenceinfo;
module bio.std.hts.sam.reader;
//
import bio.std.hts.bam.abstractreader;
import bio.std.hts.sam.header;
import bio.std.hts.bam.read;
import bio.std.hts.bam.reference;
import bio.std.hts.bam.referenceinfo;
import bio.core.utils.outbuffer;
import bio.core.utils.range;
@ -35,7 +35,7 @@ import bio.core.utils.bylinefast;
alias ByLineFast _LineRange;
version(DigitalMars) {
import bio.sam.utils.recordparser;
import bio.std.hts.sam.utils.recordparser;
} else {
import bio.sam.utils.fastrecordparser;
}

8
bio/std/hts/sam/utils/fastrecordparser.d

@ -59,10 +59,10 @@ static const int sam_alignment_en_alignment_tag_parsing = 251;
#line 419 "sam_alignment.rl"
import bio.sam.header;
import bio.bam.cigar;
import bio.bam.read;
import bio.bam.bai.bin;
import bio.std.hts.sam.header;
import bio.std.hts.bam.cigar;
import bio.std.hts.bam.read;
import bio.std.hts.bam.bai.bin;
import bio.core.utils.outbuffer;
import bio.core.base;
import std.conv;

12
bio/std/hts/sam/utils/recordparser.d

@ -1,4 +1,4 @@
module bio.sam.utils.recordparser;
module bio.std.hts.sam.utils.recordparser;
#line 1 "sam_alignment.rl"
/*
@ -578,10 +578,10 @@ static int sam_alignment_en_alignment_tag_parsing = 251;
#line 419 "sam_alignment.rl"
import bio.sam.header;
import bio.bam.cigar;
import bio.bam.read;
import bio.bam.bai.bin;
import bio.std.hts.sam.header;
import bio.std.hts.bam.cigar;
import bio.std.hts.bam.read;
import bio.std.hts.bam.bai.bin;
import bio.core.utils.outbuffer;
import bio.core.base;
import std.conv;
@ -1441,7 +1441,7 @@ unittest {
assert(equal!approxEqual(to!(float[])(alignment["Y1"]), [13.263, -3.1415, 52.63461]));
assert(to!char(alignment["XT"]) == 'U');
import bio.bam.reference;
import bio.std.hts.bam.reference;
auto info = ReferenceSequenceInfo("20", 1234567);

4
bio/std/hts/snpcallers/simple.d

@ -1,6 +1,6 @@
module bio.bam.snpcallers.simple;
module bio.std.hts.bam.snpcallers.simple;
import bio.bam.pileup;
import bio.std.hts.bam.pileup;
import bio.core.utils.algo;
import std.algorithm;

4
bio/std/hts/thirdparty/msgpack.d

@ -1,5 +1,3 @@
// Written in the D programming language.
/**
* MessagePack serializer and deserializer implementation.
*
@ -29,7 +27,7 @@
* License: <a href="http://www.boost.org/LICENSE_1_0.txt">Boost License 1.0</a>.
* Authors: Masahiro Nakagawa
*/
module bio.bam.thirdparty.msgpack;
module bio.std.hts.thirdparty.msgpack;
import std.array;
import std.exception;

Loading…
Cancel
Save