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Original link: http://www.concentric.net/~Ttwang/tech/inthash.htm
Taken from: http://web.archive.org/web/20071223173210/http://www.concentric.net/~Ttwang/tech/inthash.htm
Reformatted using pandoc

Integer Hash Function

Thomas Wang, Jan 1997

last update Mar 2007

dnbaker

alias gdl="git diff $(git log -n 2 | grep commit | tail -n +2 | awk '{print $NF}')"

dnbaker

#!/bin/bash

# Script for installing tmux on systems where you don't have root access.
# tmux will be installed in $HOME/local/bin.
# It's assumed that wget and a C/C++ compiler are installed.

# exit on error
set -e

TMUX_VERSION=1.8

dnbaker

try:
    from cytoolz import frequencies
except ImportError:
    from collections import Counter as frequencies
    # Works, but it's less than 3x as fast
    # A simple pure python counter is twice as fast as Counter anyhow....
from itertools import chain

def get_qchars_counts(bampath):
    '''

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/* Assumes that both strings are of equal length.
 *
 */

int hd(char *a, char *b) {
    int ret = 0;
    while(*a) ret += (*a++ != *b++);
    return ret;
}

dnbaker

1. General Background and Overview

• Probabilistic Data Structures for Web Analytics and Data Mining : A great overview of the space of probabilistic data structures and how they are used in approximation algorithm implementation.
• Models and Issues in Data Stream Systems
• Philippe Flajolet’s contribution to streaming algorithms : A presentation by Jérémie Lumbroso that visits some of the hostorical perspectives and how it all began with Flajolet
• Approximate Frequency Counts over Data Streams by Gurmeet Singh Manku & Rajeev Motwani : One of the early papers on the subject.
• [Methods for Finding Frequent Items in Data Streams](http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.187.9800&rep

dnbaker

#ifndef FALL_THROUGH_IPOW_H
#define FALL_THROUGH_IPOW_H
#include "stdint.h"

static inline int64_t ipow(int32_t base, uint8_t exp) {
    static const uint8_t highest_bit_set[] = {
        0, 1, 2, 2, 3, 3, 3, 3,
        4, 4, 4, 4, 4, 4, 4, 4,
        5, 5, 5, 5, 5, 5, 5, 5,
        5, 5, 5, 5, 5, 5, 5, 5,

dnbaker

#ifndef KMER2STR_H
#define KMER2STR_H
#include "stdint.h"


#ifndef num2nuc
# ifndef NUM2NUC_STR
#  define NUM2NUC_STR "ACGTN"
# endif
# define num2nuc(x) NUM2NUC_STR[(uint8_t)x]

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import pysam
from itertools import chain

def get_qchars(bampath):
  return set(chain.from_iterable(set(c.qual) for
             c in pysam.AlignmentFile(bampath)))

dnbaker

/*
 * :abstract: set the base in pSeq at index i in the read to the base in bSeq at index i in the read.
 * These 8-bit integers are the points in memory returned by bam_get_seq(p) and bam_get_seq(b), respectively.
 * :param: pSeq [uint8_t *]
 * :param: bSeq [uint8_t *]
 * :param: i [int/integral type]
*/
#define set_base(pSeq, bSeq, i) (pSeq)[(i)>>1] = ((bam_seqi(bSeq, i) << (((~i) & 1) << 2)) | (((pSeq)[(i)>>1]) & (0xf0U >> (((~i) & 1) << 2))))
/*
 * :abstract: set the base at index i in the read to "N".