lomereiter

// How to build: 
// rdmd -O -release -inline --build-only -Ipath/to/latest/sambamba/ snpcaller.d
//
// Usage: ./snpcaller input.bam > snps.dat
// (input.bam must contain MD tags)

import bamfile;
import reconstruct;
import splitter;

lomereiter

#!/usr/bin/env bash

mkdir -p gdc47/dev
git clone --branch gdc-4.7 https://github.com/D-Programming-GDC/GDC.git gdc47/dev

cd gdc47
mkdir downloads
cd downloads
wget ftp://ftp.nluug.nl/mirror/languages/gcc/releases/gcc-4.7.1/gcc-4.7.1.tar.bz2
wget ftp://ftp.nluug.nl/mirror/languages/gcc/infrastructure/mpc-0.8.1.tar.gz

lomereiter

struct Section {
    
    this(QTabFile file, string tag) {
        ...
    }
    
    /// Allows to iterate over section lines with foreach.
    int opApply(int delegate(string) call_line) {
        ...
    }

lomereiter

/tmp/ccqX2hrB.o: In function `_D19randomaccessmanager19RandomAccessManager13getAlignmentsMFmiiZS19randomaccessmanager19RandomAccessManager13getAlignmentsM87__T6filterS7319randomaccessmanager19RandomAccessManager13getAlignmentsM13__dgliteral14Z440__T6filterTS19randomaccessmanager19RandomAccessManager13getAlignmentsM360__T5UntilS7319randomaccessmanager19RandomAccessManager13getAlignmentsM13__dgliteral16TS19randomaccessmanager19RandomAccessManager188__T27disjointChunkAlignmentRangeTS3bai5utils4algo106__T20nonOverlappingChunksTS3std5range53__T11SortedRangeTAS3bai5chunk5ChunkVAyaa5_61203c2062Z11SortedRangeZ20nonOverlappingChunks6ResultZ27disjointChunkAlignmentRangeM6ResultTvZ5UntilZ6filterMFS19randomaccessmanager19RandomAccessManager13getAlignmentsM360__T5UntilS7319randomaccessmanager19RandomAccessManager13getAlignmentsM13__dgliteral16TS19randomaccessmanager19RandomAccessManager188__T27disjointChunkAlignmentRangeTS3bai5utils4algo106__T20nonOverlappingChunksTS3std5range53__T11SortedRangeTAS3bai5chunk5ChunkVAyaa5_61

lomereiter

import std.stdio;

import core.runtime;
extern(C) void lib_init() {
    Runtime.initialize();
}

import std.conv;
import std.string;
import core.memory;

lomereiter

module bgzfrange;

import std.stream;

struct BgzfBlock {
    // field types are as in the specification
    // ushort ~ uint16_t, char ~ uint8_t, uint ~ uint32_t
    public ushort bsize;
    public char[] compressed_data = void;
    public uint crc32;

lomereiter

module cinterface;

import std.traits;
import std.string;
import std.conv;
import std.range;
import std.typetuple;
import std.algorithm;
import std.ascii;

lomereiter

test: test_c.o test_d.o
	gcc -m32 -g test_d.o test_c.o -o test.so -lphobos2 -lrt -shared -lpthread

test_c.o: test.c
	gcc -c -g -m32 test.c -o test_c.o -fPIC

test_d.o: test.d
	dmd -c -m32 -g test.d -oftest_d.o -fPIC

lomereiter

test: test_c.o test_d.o
    cc -shared -m32 test_c.o test_d.o -o test.so -lphobos2

test_c.o: test.c
    gcc -c -m32 test.c -o test_c.o

test_d.o: test.d
    dmd -c -m32 test.d -oftest_d.o

lomereiter

// It turns out that combination of std.conv.emplace and FFI::MemoryPointer.new 
// can make our life much easier (at least, for structs). 
// See example at https://gist.github.com/2337729

extern (C) void* malloc(size_t sz); 
extern (C) void free(void *p); 

class DefaultMemoryManagement {
    mixin template memoryManagement() {}
}