standage

standage

standage

alias list='ls -lhp'
alias vsc='open -a /Applications/Visual\ Studio\ Code.app/'
alias msu='ssh hpcc.msu.edu'
alias cab='ssh cabernet.genomecenter.ucdavis.edu'
alias rum='ssh rum.genomecenter.ucdavis.edu'
alias gremlin='ssh gremlin2.soic.indiana.edu'
export CLICOLOR=1
export HISTSIZE=1000000
export HISTFILESIZE=1000000
export EDITOR=nano

standage

#!/usr/bin/env python
import argparse
import kevlar
import random
import sys

def resv_samp(objstream, n=100, stopafter=None, filterfunc=None):
    sample = list()
    for counter, obj in enumerate(objstream):
        if filterfunc:

standage

INDIVIDUALS = ('proband', 'mother', 'father')
KSIZES = ('27', '31', '35', '39', '43', '47', '51')

rule all:
    input:
        expand('{coverage}x_k{ksize}_kevlar_calls_like.vcf',
               coverage=('30'), ksize=KSIZES)


rule novel_reads:

standage

#include <iostream>
#include <assert.h>
#include <cmath>
#include "filter.hpp"

template<typename ElementType, typename CounterType, size_t maxcount>
filter<ElementType, CounterType, maxcount>::filter(std::vector<size_t> array_sizes)
        : _cells_occupied(array_sizes.size(), 0),
          _arrays(array_sizes.size(), std::vector<CounterType>())
{

standage

standage

def test_alignment_score_threshold():
    """Test for "report all near optimal alignments" strategy.

    """
    contigfile = data_file('aln_scr_thresh.contig.augfasta')
    contigstream = kevlar.parse_augmented_fastx(kevlar.open(contigfile, 'r'))
    contigs = list(contigstream)

    gdnafile = data_file('aln_scr_thresh.gdna.fa')
    gdnastream = kevlar.reference.load_refr_cutouts(kevlar.open(gdnafile, 'r'))

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chr_start-end score cigar

---

k=31

DEBUG 10_121624961-121625052 30 2M19I5M51I5M4I10M5I43M37I1M25D
DEBUG 10_135194344-135194435 53 1M29I8M49I9M5I71M8I2M
DEBUG 10_17783947-17784038 55 83I13M5I76M3I2M

standage

#!/usr/bin/env python

import argparse
from collections import defaultdict
import khmer
from math import log
import re
import scipy.stats
import sys