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def _macs2(workflow, conf):
    # merge all treatments into one
    merge_bams_treat = ShellCommand(
        "{tool} merge {output[merged]} {param[bams]}",
        tool="samtools",
        input=[target + ".bam" for target in conf.treatment_targets],
        output={"merged": conf.prefix + "_treatment.bam"})
    merge_bams_treat.param = {"bams": " ".join(merge_bams_treat.input)}

    if len(conf.treatment_targets) > 1:

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def _macs2(workflow, conf):
    # merge all treatments into one
    merge_bams_treat = ShellCommand(
        "{tool} merge {output[merged]} {param[bams]}",
        tool="samtools",
        input=[target + ".bam" for target in conf.treatment_targets],
        output={"merged": conf.prefix + "_treatment.bam"})
    merge_bams_treat.param = {"bams": " ".join(merge_bams_treat.input)}

    if len(conf.treatment_targets) > 1:

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def _bowtie(workflow, conf):
    for target in conf.sample_targets:
        bowtie = attach_back(workflow,
            ShellCommand(
                "{tool} -p {param[threads]} -S -m {param[max_align]} \
                {param[genome_index]} {input[fastq]} {output[sam]} 2> {output[bowtie_summary]}",
                input={"genome_dir": os.path.dirname(conf.get_path("lib", "genome_index")),
                       "fastq": target + ".fastq"},
                output={"sam": target + ".sam",
                        "bowtie_summary": target + "_bowtie_summary.txt", },

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CLASS1  = ["BMAL1-ZT10_rep1", "BMAL1-ZT10_rep2"]
CLASS1_PATHS = ["/mnt/Storage/data/exam_data/BMAL1/BMAL1-ZT10_rep1.bam", "/mnt/Storage/data/exam_data/BMAL1/BMAL1-ZT10_rep2.bam"]

CLASS2  = ["BMAL1-ZT22_rep1"]
CLASS2_PATHS = ["/mnt/Storage/data/exam_data/BMAL1/BMAL1-ZT22_rep1.bam"]

GTF = "/mnt/Storage/data/RefGene/mm9.gtf"


SAMPLES = CLASS1 + CLASS2

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def update_one_sample(gsmid, parse_fields=['other_ids', 'paper', 'name', 'species', 'description', 'antibody', 'factor',
                                           'cell type', 'cell line', 'tissue', 'strain']):
    """Given a gsmid, tries to create a new sample--auto-filling in the
    meta fields


    If overwrite is True and there is the sample that has the same gsmid, this function will overwrite that sample

    NOTE: will try to save the sample!!

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#!/bin/bash
sudo date 03050001

# Replace the following line with any application you need to run
open /Applications/Merriam-Webster\ 4.0/Merriam-Webster\ Dictionary.app

# sleep 60

# Set back to the current time using apple service (network needed)
sudo ntpdate -u time.apple.com

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def parseFactorByAntibody(geoPost):
    targetFlds = ["CHIP_ANTIBODY", "ANTIBODY", "CHIP", "ANTIBODY_SOURCE", "ANTIBODY_ANTIBODYDESCRIPTION",
                  "ANTIBODY_TARGETDESCRIPTION"]
    #1. try to get the values
    for t in targetFlds:
        tmp = getFromPost(geoPost, t).strip()
        if not tmp:
            continue
        tmp = tmp.upper().replace("ANTI-", " ").replace("ANTI", " ").strip()
        if len(tmp) < 10 and tmp != "":

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def _peaks_parse(input):
    total = 0
    fc20n = 0
    fc10n = 0
    peaks_info = {}
    with open(input) as peaks_xls:
        for line in peaks_xls:
            if line.startswith('# tags after filtering in treatment'):
                # tags after filtering in treatment: 13438948
                peaks_info["uniloc"] = int(line.strip().split(":")[1])

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def create_workflow(args, conf):
    """
    :type conf:ChiLinConfig 
    """
    root_workflow = Workflow("Main")
    ShellCommand("prepare","mkdir -p {output}",output = conf.target_dir).attach_to(root_workflow)

    groom_workflow = attach(root_workflow, Workflow("Groom"))
    rawQC_workflow = attach(root_workflow, Workflow("RawQC"))
    map_workflow = attach(root_workflow, Workflow("ReadsMapping"))

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#include <stdio.h>
#include <stdlib.h>
#define SHIFT 4
#define MSK 0x0F
#define UNT 1
#define N 300000000
#define print(X) for (i=1;i<1+N;i++) {printf("%d\t%d\n",i,(X)[i]);}


unsigned char aln[1+N];