klmr

TATA.\{6,\}T[AG]G[CT]..A...G.\{33,\}G[AT]TC[AG]A..C.*TTTT

klmr

#!/bin/bash
set -e
set -u

failed=0

for file in *.fq.gz; do
    md5=$(gunzip -c "$file" | openssl md5 | cut -f2 -d " ")
    gold=$(grep "${file/.gz/}" md5sums.txt | cut -f2)
    if [ "$md5" != "$gold" ]; then

klmr

#ifndef TEXT_STRING_HPP
#define TEXT_STRING_HPP

#include <algorithm>
#include <cstring>
#include <iterator>
#include <memory>
#include <iosfwd>

namespace text {

klmr

#include <algorithm>
#include <iostream>
#include <string>
#include <vector>

#include <boost/container/vector.hpp>

struct TrieNode {
    boost::container::vector<TrieNode> children;
    std::vector<std::vector<std::string>::const_iterator> head;

klmr

using System;
using System.Collections.Generic;

namespace klmr {
    // Version from http://stackoverflow.com/a/75502/1968
    public class Test {
        public static bool IsAssignableToGenericType(Type givenType, Type genericType) {
            var interfaceTypes = givenType.GetInterfaces();
            
            foreach (var it in interfaceTypes)

klmr

enum class dna_strand : char {
    positive = '+',
    negative = '-'
};

std::ostream& operator <<(std::ostream& out, dna_strand strand) {
    return out << static_cast<char>(strand);
}

std::istream& operator >>(std::istream& in, dna_strand& strand) {

klmr

#!/usr/bin/env bash

set -e
set -u

input="${1-/dev/stdin}"

declare -A counts=(
    [A]=0
    [C]=0

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while (getline(in, line)) {
    if (line.compare(0, 4, "@RG\t") != 0) continue;
    size_t start = line.find("\tID:");
    if (start == string::npos) continue;
    start += 4;
    size_t end = line.find("\t", start);
    if (end == string::npos or end == start) continue;
    gids.emplace(string.begin() + start, string.begin() + end);
    // Or, in C++03:
    //gids.insert(line.substr(start, end - start));

klmr

result = x == "foo" ? foo() :
         x == "bar" ? bar() :
         x == "baz" ? baz() :
         x == "qux" ? qux();

klmr

#!/usr/bin/env bash

source ~/.config/extpaths # For samtools

set -e
set -u

n=0

for bam in $*; do