jdidion

# Example of two different structures for multiprocessing code.
# The first uses queues to move chunks of data between the reader
# thread (which is the main process), the worker threads (which
# do the actual computation), and the writer thread (which writes
# the results to a file). The second using shared memory Values
# and Arrays: the reader thread reads data directly into shared 
# memory char arrays, and each worker process the data in an array 
# and writes the result back to that array; the writer thread 
# copies the data from the finished char arrays to the output file.
#

jdidion

<?xml version="1.0" encoding="utf-8"?>
<style xmlns="http://purl.org/net/xbiblio/csl" class="in-text" version="1.0" demote-non-dropping-particle="sort-only" default-locale="en-US">
  <info>
    <title>National Library of Medicine (grant proposals with PMCID/PMID) - Author, Year</title>
    <title-short>NLMAuthorYear</title-short>
    <id>http://www.zotero.org/styles/national-library-of-medicine-grant-proposals</id>
    <link href="http://www.zotero.org/styles/national-library-of-medicine-grant-proposals" rel="self"/>
    <link href="http://www.nlm.nih.gov/pubs/formats/recommendedformats1991-full.pdf" rel="documentation"/>
    <link href="http://publicaccess.nih.gov/citation_methods.htm" rel="documentation"/>
    <link href="http://grants.nih.gov/grants/funding/424/SF424_RR_Guide_General_Adobe_VerC.pdf" rel="documentation"/>

jdidion

<?xml version="1.0" encoding="utf-8"?>
<style xmlns="http://purl.org/net/xbiblio/csl" class="in-text" version="1.0" demote-non-dropping-particle="sort-only" default-locale="en-US">
  <info>
    <title>National Library of Medicine (grant proposals with PMCID/PMID) - Author, Year</title>
    <title-short>NLMAuthorYear</title-short>
    <id>http://www.zotero.org/styles/national-library-of-medicine-grant-proposals</id>
    <link href="http://www.zotero.org/styles/national-library-of-medicine-grant-proposals" rel="self"/>
    <link href="http://www.nlm.nih.gov/pubs/formats/recommendedformats1991-full.pdf" rel="documentation"/>
    <link href="http://publicaccess.nih.gov/citation_methods.htm" rel="documentation"/>
    <link href="http://grants.nih.gov/grants/funding/424/SF424_RR_Guide_General_Adobe_VerC.pdf" rel="documentation"/>

jdidion

# This list was boostrapped from the FastQC contaminants.txt.
# TODO: add missing Illumina adapters from official list at:
# http://support.illumina.com/downloads/illumina-customer-sequence-letter.html

>IlluminaSingleEndAdapter1
GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG
>IlluminaSingleEndAdapter2
CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT
>IlluminaSingleEndPCRPrimer1
AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT

jdidion

Interrogate a running command

strace -e 'trace=!read,write' -p <pid>

jdidion

# Create an UpSet plot given the counts for each intersection.
# 
# The input is a data frame with N + 1 columns, where N is the
# number of sets, and M rows, where M is the number of intersections
# between the sets. The values in columns 1:N are binary values
# indicating which sets are involved in each intersection. The
# N+1 column must have the name "count" and holds the count values
# for the intersections. You can generate a template counts data
# frame using the create_counts_df() function.
# 

jdidion

from enum import IntFlag
import functools
import itertools
import operator
from ngsindex.utils import DefaultDict
from typing import (
    Generic, Iterable, Iterator, Optional, Sequence, Sized, Tuple, Type, TypeVar, Union,
    cast
)

jdidion

foo

jdidion

```cwl
#!/usr/bin/env cwl-runner

cwlVersion: v1.2

class: CommandLineTool

inputs:
  - id: reference
    type: string

jdidion

{
    "class": "CommandLineTool",
    "inputs": [
        {
            "type": {
                "type": "record",
                "fields": [
                    {
                        "type": "File",
                        "format": "http://example.com/format1",