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fixed errors in undead import paths

sambamba
George Githinji 4 years ago
parent
commit
b96a421ba3
  1. 2
      bio/core/bgzf/inputstream.d
  2. 2
      bio/core/bgzf/outputstream.d
  3. 4
      bio/core/utils/stream.d
  4. 2
      bio/core/utils/switchendianness.d
  5. 2
      bio/std/hts/bam/bai/indexing.d
  6. 2
      bio/std/hts/bam/baifile.d
  7. 2
      bio/std/hts/bam/reader.d
  8. 2
      bio/std/hts/bam/readrange.d
  9. 2
      bio/std/hts/bam/reference.d
  10. 2
      bio/std/hts/bam/referenceinfo.d
  11. 4
      bio/std/hts/bam/writer.d
  12. 2
      bio/std/sff/reader.d
  13. 2
      bio/std/sff/readrange.d
  14. 2
      bio/std/sff/writer.d

2
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;

2
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;

4
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

2
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;

2
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;

2
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;

2
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;

2
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;

2
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;

2
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;

4
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)

2
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;

2
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;

2
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

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