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Setting up a small-ish example

Grab 5 bams and their indexes from 1000G to represent our alignments.

mkdir data && cd data
wget ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/data/HG00096/alignment/HG00096.chrom20.ILLUMINA.bwa.GBR.low_coverage.20101123.bam
wget ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/data/HG00096/alignment/HG00096.chrom20.ILLUMINA.bwa.GBR.low_coverage.20101123.bam.bai
wget ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/data/HG00097/alignment/HG00097.chrom20.SOLID.bfast.GBR.low_coverage.20101123.bam
wget ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/data/HG00097/alignment/HG00097.chrom20.SOLID.bfast.GBR.low_coverage.20101123.bam.bai

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params.bams

// mosdepth is going to need a prefix, a bam, and its index
bams_ch = Channel
    // grab the bams and/or crams
    .fromPath(params.bams, checkIfExists: true)
    // set the first element to the basename of the file without its extension
    // the second element to the alignments (bam or cram)
    // and the third element to the index
    .map { file -> tuple(file.baseName, file, file + ("${file}".endsWith('.cram') ? '.crai' : '.bai')) }

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# setting up AMI
sudo service docker stop
sudo rm -rf /var/lib/docker

# update the image
sudo yum update -y
sudo yum install -y mdadm
sudo yum install -y wget
wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash Miniconda3-latest-Linux-x86_64.sh -b -f -p $HOME/miniconda

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brwnj

#!/usr/bin/env python
# coding=utf-8
"""
Runs bcl2fastq creating fastqs and concatenates fastqs across lanes. Intended
to be used with NextSeq data and it does not do any cleanup! Original dumped
fastqs will remain along with all of the bcl files.
"""

from __future__ import print_function

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#!/usr/bin/env python
# coding=utf-8
"""
Download the best resolution of the top <limit> video from subreddit 'videos'
to <out> directory.
"""

import multiprocessing
import os
import pafy

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import editdist

def distance(a, b):
    """
    Find best edit distance between two strings of potentially uneven length.

    >>> import editdist
    >>> distance("abc", "abc")
    0
    >>> distance("abc", "abcdef")

brwnj

#!/usr/bin/env python
# encoding: utf-8
"""
Join reads based on local alignment, taking higher quality base where mismatches
are present.
"""
import sys, string, multiprocessing
from Bio import pairwise2
from toolshed import nopen
from itertools import islice, izip, izip_longest

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#Job Array

#!/usr/bin/env bash
#BSUB -J align[1-63]
#BSUB -e align.%J.%I.err
#BSUB -o align.%J.%I.out
#BSUB -q normal
#BSUB -R "select[mem>16] rusage[mem=16] span[hosts=1]"
#BSUB -n 12

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#!/usr/bin/env python
# encoding: utf-8
"""
Add a piece or all of the index read back onto R1 (or R2).
"""
from itertools import izip
from toolshed import nopen

def readfx(fh):
    # https://github.com/lh3/readfq/blob/master/readfq.py