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Merge pull request #34 from biorelated/master

update the instructions for running the example code
bio2
Pjotr Prins 5 years ago
committed by GitHub
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commit
d31400bc40
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  1. 1
      bio/bam/baseinfo.d
  2. 7
      examples/calculate_gc_content_from_reference.d
  3. 8
      examples/create_bam_from_scratch.d
  4. 7
      examples/iterate_tags.d
  5. 7
      examples/make_pileup.d
  6. 7
      examples/print_base_info.d
  7. 7
      examples/read_bam_file.d
  8. 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;

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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