New upstream version 0.2.1

language: d

script:

- rdmd -unittest -d test/unittests.d

os:

  - linux

  - osx

d:

  - dmd

  - ldc

### BioD

# BioD [![Build Status](https://travis-ci.org/biod/BioD.svg?branch=master)](https://travis-ci.org/biod/BioD) [![DUB Package](https://img.shields.io/badge/dub-v0.1.0-red.svg)](https://code.dlang.org/packages/biod)

[BioD](https://github.com/biod/BioD) is a fast and memory efficient bioinformatics library written in the [D programming language](http://dlang.org).

BioD aims to:

* Provide a platform for writing high-performance bioinformatics applications in D. BioD achieves this by:

     - automatic parallelization of tasks where possible for example reading and writing BAM files.

  - automatic parallelization of tasks where possible for example reading and writing BAM files

  - reducing the GC overhead by avoiding unnecessary memory allocations

* Offer support for manipulating common biological data formats.

* Write clear documented and maintainable codebase.

* Offer support for manipulating common biological data formats

## Why D?

### Usage

See the [examples directory](https://github.com/biod/BioD/tree/master/examples) for examples and usage.

D is a language that suits parallel programming because of guarantees

the compiler provides. D is both a low-level language and a high-level

hybrid OOP/FP language. There is no other programming language that

matches those features. Also, D templating/generics is far easier that

that of C++ or, say, Scala.

That is not to say that D is an easy language. A powerful toolbox will

be complicated. If you want to do everything with a hammer, maybe

better choose Java instead ;).

#### BioD core

* [Artem Tarasov](https://github.com/lomereiter)

* [Pjotr Prins](https://github.com/pjotrp)

For more information about D find Andrei Alexandrecu's D book. It is a

classic. Ali Çehreli's book also is recommended.

## Current development

Our current focus is to provide a bamreader and bamwriter that is

really fast and easy to use. We believe the BAM format is here to stay

for the foreseeable future in pipelines. With D we have an good way to

write performance parsers, particularly with three typical scenarios:

1. Go through a BAM file a read at a time

2. Go through a BAM file a nucleotide at a time (pileup)

3. Go through a BAM file with a sliding window

The sliding window is a derivation of the first - a read at a time or

a nucleotide at a time.

At this point this functionality is mostly in BioD, but not in an

intuitive way. We are building up this functionality and will give

examples (WIP).

# Install

The current default is to provide the path to the checked out repo to the D-compiler. For example

in sambamba we use

    DFLAGS = -wi -I. -IBioD -g

# Usage

See the [examples directory](https://github.com/biod/BioD/tree/master/examples)

for examples and usage.

BioD is also a crucial part of the [sambamba](https://github.com/biod/sambamba) tool.

# Contributing

Simply clone the repository on github and put in a pull request.

# BioD contributors and support

See

[contributors](https://github.com/biod/BioD/graphs/contributors). For

support use the [issue tracker](https://github.com/biod/BioD/issues) or contact

* [Pjotr Prins](https://github.com/pjotrp)

* [Artem Tarasov](https://github.com/lomereiter)

* [George Githinji](https://github.com/George-Githinji)

##### License

This library is licensed under the MIT license. Please see the license file for more details

# License

##### Citation

BioD is licensed under the liberal MIT (expat) [license](./LICENSE).

## ChangeLog v0.2.1 (20181004)

+ Fix bunch of deprecation warnings

+ Fixes sort removing tags from @RG header https://github.com/biod/sambamba/issues/356

+ Fixes https://github.com/biod/BioD/issues/37

## ChangeLog v0.2.0 (20180915)

64-bit compilation should be fine on ldc 1.10

+ Added FastQ parser (thanks George Githinji @george-githinji)

+ Added rewritten Bamreader f4a6c1c55c8903e948b793adbb150704d1e267b2 (thanks Pjotr Prins @pjotrp)

+ Improved big-endian support and other bug fixes (thanks Artem Tarasov @lomereiter)

+ Include SAM/BAM AH tag (thanks Indraniel Das @indraniel)

+ D undeaD compilation fixes (thanks John Colvin @John-Colvin)

+ Meson build definition added (thanks Matthias Klumpp @ximion)

+ Update outputstream.d (thanks Brett T. Hannigan @godotgildor)

+ Moved Cigar into its own module 7994406592f277bc6950739aaf75c5f948cb7928

+ Added 'asserte' method which throws an exception on assert (failure)

+ Bug fixes:

  * #31 Bug in bio/core/utils/outbuffer.d: _heap.length is not correctly set affects reading long SAM records

  * https://github.com/biod/sambamba/issues/210 correct pseudo-bin calculation (thanks @jfarek)

  * JSON header output fixes #331

0.2.1

/*

    This file is part of BioD.

    Copyright (C) 2012-2013    Artem Tarasov <lomereiter@gmail.com>

    Copyright (C) 2012-2017    Artem Tarasov <lomereiter@gmail.com>

    Permission is hereby granted, free of charge, to any person obtaining a

    copy of this software and associated documentation files (the "Software"),

import bio.bam.bai.bin;

import bio.core.bgzf.chunk;

import std.stream;

import undead.stream;

import std.array;

import std.algorithm;

import std.system;

import std.exception;

import std.c.string;

import core.stdc.string;

// Suppose we have an alignment which covers bases on a reference,

// starting from one position and ending at another position.

        void updateMetadata(ref BamReadBlock read) {

            if (read.ref_id == -1) {

                ++_no_coord;

            } else if (read.is_unmapped) {

            } else {

                if (read.is_unmapped) {

                    ++_unmapped;

                } else {

                    ++_mapped;

                    _beg_vo = cast(ulong)read.start_virtual_offset;

                _end_vo = cast(ulong)read.end_virtual_offset;

            }

        }

        void updateLinearIndex() {

            assert(_prev_read.ref_id >= 0);