# HG changeset patch
# User iuc
# Date 1563198207 14400
# Node ID a41d96fc0b2013b1bd02b3afd83b3b41a74f792d

planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba

diff -r 000000000000 -r a41d96fc0b20 genrich.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/genrich.xml	Mon Jul 15 09:43:27 2019 -0400
@@ -0,0 +1,373 @@
+<tool id="genrich" name="Genrich" version="0.5">
+    <description>Detecting sites of genomic enrichment</description>
+    <requirements>
+        <requirement type="package" version="0.5">genrich</requirement>
+        <requirement type="package" version="1.9">samtools</requirement>
+    </requirements>
+
+    <version_command>Genrich --version</version_command>
+
+    <command detect_errors="exit_code"><![CDATA[
+
+#set $file_stderr = 'genrich_stderr'
+
+Genrich
+
+###########
+## Input ##
+###########
+
+## Treatment File(s)
+#if str($treatment.t_multi_select) == "Yes":
+    -t ${ ' '.join( [ "'%s'" %  $x for $x in $treatment.input_treatment_file] ) }
+#else
+    -t '$treatment.input_treatment_file'
+#end if
+
+## Control File(s)
+#if str($control.c_select) == "Yes":
+    #if str($control.c_multiple.c_multi_select) == "Yes":
+        -c ${ ' '.join( [ "'%s'" %  $x for $x in $control.c_multiple.input_control_file] ) }
+    #else
+        -c '$control.c_multiple.input_control_file'
+    #end if
+#end if
+
+####################
+## Filter Options ##
+####################
+
+#if $filter_options.duplicates:
+    '$filter_options.duplicates' '${out_dups}'
+#end if
+
+#if $filter_options.exclude_chr:
+    -e '$filter_options.exclude_chr'
+#end if
+
+#if str($cond_exclude.exclude_select) == "Yes":
+    -E $cond_exclude.erf
+#end if
+
+-m $filter_options.min_mapq
+-s $filter_options.alignment_score
+$filter_options.unpaired
+
+#if $filter_options.alignment_lengths:
+    -w $filter_options.alignment_lengths
+#end if
+
+$filter_options.alignment_lengths2
+
+##################
+## ATAC Options ##
+##################
+
+$atac_options.atac
+-d $atac_options.expand_sites
+
+#########################
+## Peakcalling Options ##
+#########################
+
+-q $peakcalling_options.max_q
+
+#if $peakcalling_options.max_p:
+    -p $peakcalling_options.max_p
+#end if
+
+-a $peakcalling_options.min_auc
+-l $peakcalling_options.min_peak_length
+-g $peakcalling_options.max_dist
+
+###################
+## Other Options ##
+###################
+
+$other_options.skip_peak_calling
+-v
+
+####################
+## Output Options ##
+####################
+
+#if $output_options.bedgraph1:
+    -f '${out_bedgraph1}'
+#end if
+
+#if $output_options.bedgraph2:
+    -k '${out_bedgraph2}'
+#end if
+
+#if $output_options.bed:
+    -b '${out_bed}'
+#end if
+
+-o '${outfile}'
+
+2>&1 > $file_stderr &&
+exit_code_for_galaxy=\$? &&
+cat $file_stderr 2>&1 &&
+exit \$exit_code_for_galaxy
+
+    ]]></command>
+    <inputs>
+        <conditional name="treatment">
+            <param name="t_multi_select" type="select" label="Are you pooling Treatment Files?" help="For more information, see Help section below" >
+                <option value="No" selected="True">No</option>
+                <option value="Yes">Yes</option>
+            </param>
+            <when value="No" >
+                <param name="input_treatment_file" argument="-t" type="data" format="qname_sorted.bam" label="Treatment File(s)" />
+            </when>
+            <when value="Yes">
+                <param name="input_treatment_file" argument="-t" type="data" format="qname_sorted.bam" multiple="true" label="Treatment Files" />
+            </when>
+        </conditional>
+
+        <conditional name="control">
+            <param name="c_select" type="select" label="Do you have a Control File?" >
+                <option value="Yes">Yes</option>
+                <option value="No" selected="True">No</option>
+            </param>
+            <when value="Yes">
+                <conditional name="c_multiple">
+                    <param name="c_multi_select" type="select" label="Are you pooling Control Files?" help="For more information, see Help section below" >
+                        <option value="No" selected="True">No</option>
+                        <option value="Yes">Yes</option>
+                    </param>
+                    <when value="No" >
+                        <param name="input_control_file" argument="-c" type="data" format="qname_sorted.bam" label="Control File(s)" />
+                    </when>
+                    <when value="Yes">
+                        <param name="input_control_file" argument="-c" type="data" format="qname_sorted.bam" multiple="true" label="Control Files" />
+                    </when>
+                </conditional>
+            </when>
+            <when value="No" />
+        </conditional>
+
+        <!-- Filter Options -->
+        <conditional name="cond_exclude">
+            <param name="exclude_select" type="select" label="Do you have a BED file of genomic regions to exclude?" help="Input BED file of genomic regions to exclude." >
+                <option value="No" selected="True">No</option>
+                <option value="Yes">Yes</option>
+            </param>
+            <when value="No" />
+            <when value="Yes">
+                <param name="erf" argument="-E" type="data" format="bed" label="BED File" />
+            </when>
+        </conditional>
+
+        <section name="filter_options" title="Filter Options">
+            <param name="duplicates" argument="-r" type="boolean" value="False" truevalue="-r -R" falsevalue="" label="Remove PCR duplicates" help="In this process, it analyzes reads/fragments based on their alignments, in three separate groups (proper pairs, discordant pairs, and singletons), and removes those identified as duplicates from further analysis. One novel feature is that this evaluation takes into account reads/fragments with multiple alignments."/>
+            <param name="exclude_chr" argument="-e" type="text" optional="True" label="Comma-separated list of chromosomes to exclude" help="All alignments to the given list of chromosomes (reference sequences) are excluded from peak-calling. More details can be found in the tool description.">
+            <sanitizer>
+                <valid initial="string.printable">
+                    <remove value="&apos;"/>
+                </valid>
+            </sanitizer>
+            </param>
+            <param name="min_mapq" argument="-m" type="integer" min="0" value="0" label="Minimum MAPQ to keep an alignment." help="All alignments with MAPQ less than the given value are eliminated. This is equivalent to filtering with samtools view -q. This option should not be used if the SAM/BAM lists multiple alignments for some reads/fragments. Instead, filtering should be accomplished via -s. (def. 0)" />
+            <param name="alignment_score" argument="-s" type="float" min="0.0" value="0.0" label="Keep sec alns with AS >= bestAS." help="Genrich considers all secondary alignments of multimapping reads, but, by default, it keeps only the alignments whose scores are equal to the best score for the read/fragment. Setting a value such as -s 20 causes Genrich also to keep secondary alignments whose scores are within 20 of the best. (def. 0)" />
+            <param name="unpaired" argument="-y" type="boolean" value="False" truevalue="-y" falsevalue="" label="Keep unpaired alignments." help="Unpaired alignments are kept, just as they appear in the SAM/BAM. (def. false)"/>
+            <param name="alignment_lengths" argument="-w" type="integer" min="1" optional="True" value="" label="Keep unpaired alignments with a certain length." help="Unpaired alignments are kept, with their lengths changed to the given value (from their 5' ends). (def. not defined)" />
+            <param name="alignment_lengths2" argument="-x" type="boolean" value="False" truevalue="-x" falsevalue="" label="Keep unpaired alns, lengths changed to paired average." help="Unpaired alignments are kept, with their lengths changed to the average length of fragments inferred from properly paired alignments (excluding those aligning to skipped chromosomes [-e]). (def. not defined)"/>
+        </section>
+
+        <!-- ATAC Options -->
+        <section name="atac_options" title="ATAC Options">
+            <param name="atac" argument="-j" type="boolean" value="False" truevalue="-j" falsevalue="" label="Use ATAC-seq mode." help="Use ATAC-seq mode (def. false)"/>
+            <param name="expand_sites" argument="-d" type="integer" min="0" value="100" label="Expand cut sites." help="Expand cut sites to x bp (def. 100)" />
+        </section>
+
+        <!-- Peakcalling Options -->
+        <section name="peakcalling_options" title="Peakcalling Options">
+            <param name="max_q" argument="-q" type="float" min="0.0" max="1.0" value="0.05" label="Maximum q-value." help="Maximum q-value (FDR-adjusted p-value). These parameters establish the statistical threshold below which a base is considered significantly enriched in the experimental sample(s) vs. the control/background. The significance value is automatically converted to a -log10 scale by Genrich. (def. 0.05)" />
+            <param name="max_p" argument="-p" type="float" min="0" max="1.0" optional="True" value="" label="Maximum p-value." help="When -p is selected, q-values are not calculated (reported as -1). (def. turned off)" />
+            <param name="min_auc" argument="-a" type="float" min="0" value="20.0" label="Minimum AUC for a peak." help="Minimum AUC for a peak. (def. 20.0)" />
+            <param name="min_peak_length" argument="-l" type="integer" min="0" value="0" label="Minimum length of a peak." help="With this option, any potential peak whose length is below the specified value is discarded, regardless of its significance. The default of 0 means that no peaks are eliminated on this basis. (def. 0)" />
+            <param name="max_dist" argument="-g" type="integer" min="0" value="100" label="Maximum distance between signif. sites." help="This parameter sets the maximum distance between sites that achieve significance in order for them to be linked together into the same potential peak. (def. 100)" />
+        </section>
+
+        <!-- Other Options -->
+        <section name="other_options" title="Other Options">
+            <param name="skip_peak_calling" argument="-X" type="boolean" value="False" truevalue="-X" falsevalue="" label="Skip peak-calling." help="This is a convenience option for those who are unsure of the peak-calling parameters but do not want to run the full analysis multiple times. Genrich interprets the alignment files (including identifying PCR duplicates) and produces intermediate log files, but does not perform the peak-calling step."/>
+        </section>
+
+        <!-- Output Options -->
+        <section name="output_options" title="Output Options">
+            <param name="bedgraph1" argument="-f" type="boolean" value="False" label="Bedgraph-ish p/q Values" help="Output bedgraph-ish file for p/q values."/>
+            <param name="bedgraph2" argument="-k" type="boolean" value="False" label="Bedgraph-ish Pileups" help="Output bedgraph-ish file for pileups and p-values."/>
+            <param name="bed" argument="-b" type="boolean" value="False" label="Bed File" help="Output BED file for reads/fragments/intervals."/>
+        </section>
+    </inputs>
+
+
+    <outputs>
+        <data name="outfile" format="encodepeak" label="${tool.name} on ${on_string}"/>
+
+        <data name="out_bedgraph1" format="bedgraph" from_work_dir="*.bedgraph" label="${tool.name} on ${on_string}: Bedgraph p/q">
+            <filter>(output_options['bedgraph1'] is True)</filter>
+        </data>
+        <data name="out_bedgraph2" format="bedgraph" from_work_dir="*.bedgraph" label="${tool.name} on ${on_string}: Bedgraph Pileups">
+            <filter>(output_options['bedgraph2'] is True)</filter>
+        </data>
+        <data name="out_bed" format="bed" from_work_dir="*.bed" label="${tool.name} on ${on_string}: Bed reads/fragments/intervals">
+            <filter>(output_options['bed'] is True)</filter>
+        </data>
+        <data name="out_dups" format="txt" from_work_dir="*.txt" label="${tool.name} on ${on_string}: PCR duplicates">
+            <filter>(filter_options['duplicates'] is True)</filter>
+        </data>
+    </outputs>
+    <tests>
+        <!-- ATAC Test Data -->
+        <test expect_num_outputs="4">
+            <param name="input_treatment_file" ftype="bam" value="atac_test.bam" />
+            <param name="atac" value="True" />
+            <param name="bedgraph1" value="True" />
+            <param name="bedgraph2" value="True" />
+            <param name="bed" value="True" />
+            <output name="outfile" ftype="encodepeak" file="atac_out.encodepeak" />
+            <output name="out_bedgraph1" ftype="bedgraph" file="atac_out2.bedgraph" />
+            <output name="out_bedgraph2" ftype="bedgraph" file="atac_out3.bedgraph" compare="contains" lines_diff="1" />
+            <output name="out_bed" ftype="bed" file="atac_out4.bed" />
+        </test>
+        <!-- ChIP Test Data with Control-->
+        <test expect_num_outputs="4">
+            <param name="input_treatment_file" ftype="bam" value="CTCF_PE_ChIP_chr22.bam" />
+            <param name="input_control_file" ftype="bam" value="CTCF_PE_CTRL_chr22.bam" />
+            <param name="c_select" value="Yes" />
+            <param name="bedgraph1" value="True" />
+            <param name="bedgraph2" value="True" />
+            <param name="bed" value="True" />
+            <output name="outfile" ftype="encodepeak" file="CTCF.encodepeak" />
+            <output name="out_bedgraph1" ftype="bedgraph" file="CTCF1.bedgraph" />
+            <output name="out_bedgraph2" ftype="bedgraph" file="CTCF2.bedgraph" compare="contains" lines_diff="1" />
+            <output name="out_bed" ftype="bed" file="CTCF.bed" />
+        </test>
+    </tests>
+    <help><![CDATA[
+
+.. class:: infomark
+
+**What it does**
+
+-------------------
+
+**Genrich** Genrich is a peak-caller for genomic enrichment assays (e.g. ChIP-seq, ATAC-seq). It analyzes alignment files generated following the assay and produces a file detailing peaks of significant enrichment.
+
+ATAC-seq is a method for assessing genomic regions of open chromatin. Since only the ends of the DNA fragments indicate where the transposase enzyme was able to insert into the chromatin, it may not be optimal to interpret alignments. Genrich has an alternative analysis mode for ATAC-seq in which it creates intervals centered on transposase cut sites. The remainder of the peak-calling process (calculating pileups and significance values) is identical to the default analysis mode. Note that the interval lengths (not the fragment lengths) are used to sum the total sequence information for the calculation of control/background pileup values.
+
+-------------------
+
+**Inputs**
+
+-------------------
+
+Genrich analyzes alignment files in SAM/BAM format. SAM files must have a header.
+SAM/BAM files for multiple replicates can be specified, comma-separated (or space-separated, in quotes).
+Multiple SAM/BAM files for a single replicate should be combined in advance via samtools merge.
+The SAM/BAM files must be sorted by queryname (via samtools sort -n).
+
+
+-----------
+
+**Outputs**
+
+-----------
+
+As indicated, the output file is in ENCODE narrowPeak format. Here are details of the fields:
+    * 1. chrom    Name of the chromosome
+    * 2. chromStart   Starting position of the peak (0-based)
+    * 3. chromEnd Ending position of the peak (not inclusive)
+    * 4. name peak_N, where N is the 0-based count
+    * 5. score    Average AUC (total AUC / bp) × 1000, rounded to the nearest int (max. 1000)
+    * 6. strand   . (no orientation)
+    * 7. signalValue  Total area under the curve (AUC)
+    * 8. pValue   Summit -log10(p-value)
+    * 9. qValue   Summit -log10(q-value), or -1 if not available (e.g. with -p)
+    * 10. peak    Summit position (0-based offset from chromStart): the midpoint of the peak interval with the highest significance (the longest interval in case of ties)
+
+Example:
+chr1    894446    894988    peak_10    402    .    217.824936    4.344683    1.946031    317
+chr1    895834    896167    peak_11    343    .    114.331093    4.344683    1.946031    90
+
+Optional files
+
+  -c  Input SAM/BAM file(s) for control sample(s)
+
+Alignment files for control samples (e.g. input DNA) can be specified, although this is not strictly required.
+SAM/BAM files for multiple replicates can be listed, comma-separated (or space-separated, in quotes) and in the same order as the experimental files. Missing control files should be indicated with null.
+
+  -f  Output bedgraph-ish file for p/q values
+
+With a single replicate, this log file lists experimental/control pileup values, p- and q-values, and significance (*) for each interval.
+
+Example:
+chr1    894435    894436    33.000000    2.477916    3.183460    1.208321
+chr1    894436    894442    34.000000    2.477916    3.231466    1.241843
+chr1    894442    894446    35.000000    2.477916    3.278469    1.274561
+chr1    894446    894447    36.000000    2.477916    3.324516    1.306471    *
+chr1    894447    894450    39.000000    2.477916    3.457329    1.398035    *
+chr1    894450    894451    40.000000    2.477916    3.499948    1.427253    *
+chr1    894451    894460    41.000000    2.477916    3.541798    1.455938    *
+
+With multiple replicates, this log file lists p-values of each replicate, combined p-value, q-value, and significance for each interval.
+Note that this file (as well as the -k file, below) is called "bedgraph-ish" because it contains multiple dataValue fields, which isn't strictly allowed in the bedGraph format. However, a simple application of awk can produce the desired bedgraph files for visualization purposes (see this awk reference for a guide to printing specific fields of input records).
+When peak-calling is skipped (-X), the significance column is not produced.
+
+  -k  Output bedgraph-ish file for pileups and p-values
+
+For each replicate, sequentially, this file lists a header line (# experimental file: <name>; control file: <name>), followed by experimental/control pileups and a p-value for each interval. This is the way to examine pileup values with multiple replicates, since the -f log file does not supply them in that case.
+
+  -b  Output BED file for reads/fragments/intervals
+
+This is an unsorted BED file of the reads/fragments/intervals analyzed. The 4th column gives the read name, number of valid alignments, 'E'xperimental or 'C'ontrol, and sample number (0-based), e.g. SRR5427886.59_2_E_0.
+
+  -R  Output file for PCR duplicates (only with -r)
+
+This log file lists the header of each read/fragment classified as a PCR duplicate, followed by the alignment, the header of the read/fragment it matched, and the alignment type.
+
+Example:
+SRR5427886.5958     chr4:185201876-185201975            SRR5427886.4688    paired
+SRR5427886.1826     chr12:34372610,+;chr1:91852878,-    SRR5427886.2040    discordant
+SRR5427886.10866    chr14:53438632,+                    SRR5427886.4746    single
+
+The duplicates from multiple input files are separated by a comment line listing the next filename, such as # experimental file #0: SRR5427886.bam.
+This file can be used to filter the original SAM/BAM file, using a simple script such as getReads.py, for example.
+
+
+--------------------
+
+**More Information**
+
+--------------------
+
+See the excellent `Genrich documentation`_
+
+.. _`Genrich documentation`: https://github.com/jsh58/Genrich
+
+
+--------------------
+
+**Galaxy Wrapper Development**
+
+--------------------
+
+Author: Florian Heyl <heylf@informatik.uni-freiburg.de>
+
+
+    ]]></help>
+    <citations>
+        <citation type="bibtex">
+@misc{genrich,
+    title = {Genrich},
+    url = {https://github.com/jsh58/Genrich},
+    urldate = {2019-07-15},
+    author = {John M. Gaspar},
+    year = {2018},
+}
+        </citation>
+    </citations>
+</tool>
diff -r 000000000000 -r a41d96fc0b20 test-data/CTCF.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/CTCF.bed	Mon Jul 15 09:43:27 2019 -0400
@@ -0,0 +1,955 @@
+chr22	39268661	39268882	DG7PMJN1:313:C1579ACXX:4:1101:1327:21682_1_E_0
+chr22	47158056	47158376	DG7PMJN1:313:C1579ACXX:4:1101:1332:42537_1_E_0
+chr22	47089504	47089698	DG7PMJN1:313:C1579ACXX:4:1101:1332:87995_1_E_0
+chr22	32061696	32062004	DG7PMJN1:313:C1579ACXX:4:1101:1334:64870_1_E_0
+chr22	27129531	27129743	DG7PMJN1:313:C1579ACXX:4:1101:1335:62201_1_E_0
+chr22	36462290	36462537	DG7PMJN1:313:C1579ACXX:4:1101:1337:68808_1_E_0
+chr22	21306063	21306268	DG7PMJN1:313:C1579ACXX:4:1101:1338:175510_1_E_0
+chr22	18379432	18379662	DG7PMJN1:313:C1579ACXX:4:1101:1353:6398_1_E_0
+chr22	39492880	39493165	DG7PMJN1:313:C1579ACXX:4:1101:1353:95885_1_E_0
+chr22	31316312	31316530	DG7PMJN1:313:C1579ACXX:4:1101:1355:14336_1_E_0
+chr22	46432623	46432839	DG7PMJN1:313:C1579ACXX:4:1101:1361:86288_1_E_0
+chr22	22776990	22777208	DG7PMJN1:313:C1579ACXX:4:1101:1362:161018_1_E_0
+chr22	34319847	34320073	DG7PMJN1:313:C1579ACXX:4:1101:1366:139084_1_E_0
+chr22	39566735	39566961	DG7PMJN1:313:C1579ACXX:4:1101:1368:93380_1_E_0
+chr22	39378468	39378802	DG7PMJN1:313:C1579ACXX:4:1101:1371:153735_1_E_0
+chr22	29223458	29223749	DG7PMJN1:313:C1579ACXX:4:1101:1372:19426_1_E_0
+chr22	42494019	42494222	DG7PMJN1:313:C1579ACXX:4:1101:1373:92078_1_E_0
+chr22	50982866	50983075	DG7PMJN1:313:C1579ACXX:4:1101:1375:74927_1_E_0
+chr22	22511297	22511510	DG7PMJN1:313:C1579ACXX:4:1101:1376:42382_1_E_0
+chr22	47154865	47155113	DG7PMJN1:313:C1579ACXX:4:1101:1376:172509_1_E_0
+chr22	22193635	22193984	DG7PMJN1:313:C1579ACXX:4:1101:1378:70470_1_E_0
+chr22	28275318	28275639	DG7PMJN1:313:C1579ACXX:4:1101:1380:66504_1_E_0
+chr22	51130096	51130412	DG7PMJN1:313:C1579ACXX:4:1101:1381:101381_1_E_0
+chr22	43151700	43151988	DG7PMJN1:313:C1579ACXX:4:1101:1383:80388_1_E_0
+chr22	29550297	29550637	DG7PMJN1:313:C1579ACXX:4:1101:1384:159425_1_E_0
+chr22	45335869	45336069	DG7PMJN1:313:C1579ACXX:4:1101:1392:62140_1_E_0
+chr22	39706894	39707144	DG7PMJN1:313:C1579ACXX:4:1101:1392:148796_1_E_0
+chr22	42142707	42142909	DG7PMJN1:313:C1579ACXX:4:1101:1399:93401_1_E_0
+chr22	25348098	25348291	DG7PMJN1:313:C1579ACXX:4:1101:1402:183382_1_E_0
+chr22	22556130	22556393	DG7PMJN1:313:C1579ACXX:4:1101:1407:106599_1_E_0
+chr22	32838053	32838399	DG7PMJN1:313:C1579ACXX:4:1101:1407:121847_1_E_0
+chr22	43810586	43810909	DG7PMJN1:313:C1579ACXX:4:1101:1408:49267_1_E_0
+chr22	42891122	42891345	DG7PMJN1:313:C1579ACXX:4:1101:1409:4177_1_E_0
+chr22	39369729	39369947	DG7PMJN1:313:C1579ACXX:4:1101:1415:139393_1_E_0
+chr22	19617529	19617717	DG7PMJN1:313:C1579ACXX:4:1101:1419:25150_1_E_0
+chr22	40328883	40329177	DG7PMJN1:313:C1579ACXX:4:1101:1423:200331_1_E_0
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+chr22	46177227	46177497	MONK:4:1101:1885:171014#ATCACG_1_C_0
+chr22	47396789	47397152	MONK:4:1101:1886:19535#ATCACG_1_C_0
+chr22	24180187	24180543	MONK:4:1101:1886:121532#ATCACG_1_C_0
+chr22	41293748	41294044	MONK:4:1101:1889:105577#ATCACG_1_C_0
+chr22	19717760	19718074	MONK:4:1101:1889:162959#ATCACG_1_C_0
+chr22	46179936	46180244	MONK:4:1101:1891:32806#ATCACG_1_C_0
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+chr22	45363719	45364012	MONK:4:1101:1895:168583#ATCACG_1_C_0
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+chr22	32179203	32179465	MONK:4:1101:1898:19814#ATCACG_1_C_0
+chr22	38699259	38699611	MONK:4:1101:1901:93544#ATCACG_1_C_0
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+chr22	36291590	36291793	MONK:4:1101:1913:197165#ATCACG_1_C_0
+chr22	19465462	19465807	MONK:4:1101:1917:34367#ATCACG_1_C_0
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+chr22	34837030	34837358	MONK:4:1101:1920:150249#ATCACG_1_C_0
+chr22	26453071	26453374	MONK:4:1101:1922:130346#ATCACG_1_C_0
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+chr22	20830229	20830574	MONK:4:1101:1926:13391#ATCACG_1_C_0
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+chr22	35901849	35902253	MONK:4:1101:1952:19211#ATCACG_1_C_0
+chr22	45352923	45353266	MONK:4:1101:1952:20001#ATCACG_1_C_0
+chr22	30702262	30702594	MONK:4:1101:1952:116627#ATCACG_1_C_0
+chr22	46059105	46059415	MONK:4:1101:1954:57819#ATCACG_1_C_0
+chr22	38903368	38903735	MONK:4:1101:1956:144084#ATCACG_1_C_0
+chr22	24472660	24472914	MONK:4:1101:1958:81629#ATCACG_1_C_0
+chr22	19360117	19360433	MONK:4:1101:1963:74990#ATCACG_1_C_0
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+chr22	17331220	17331528	MONK:4:1101:1970:71843#ATCACG_1_C_0
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+chr22	31250898	31251186	MONK:4:1101:1974:89491#ATCACG_1_C_0
+chr22	40111692	40111971	MONK:4:1101:1978:148397#ATCACG_1_C_0
+chr22	35457350	35457641	MONK:4:1101:1980:173169#ATCACG_1_C_0
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+chr22	47580463	47580834	MONK:4:1101:1987:80549#ATCACG_1_C_0
+chr22	50049313	50049602	MONK:4:1101:1988:110312#ATCACG_1_C_0
+chr22	35705660	35705972	MONK:4:1101:1989:137656#ATCACG_1_C_0
+chr22	36020858	36021181	MONK:4:1101:1992:90060#ATCACG_1_C_0
+chr22	32626046	32626344	MONK:4:1101:1993:22677#ATCACG_1_C_0
+chr22	47214755	47215042	MONK:4:1101:1994:49366#ATCACG_1_C_0
+chr22	39021453	39021720	MONK:4:1101:1999:129446#ATCACG_1_C_0
+chr22	22030286	22030701	MONK:4:1101:2000:62918#ATCACG_1_C_0
+chr22	23206691	23206983	MONK:4:1101:2011:74371#ATCACG_1_C_0
+chr22	45637193	45637471	MONK:4:1101:2012:54686#ATCACG_1_C_0
+chr22	45567139	45567424	MONK:4:1101:2013:12466#ATCACG_1_C_0
+chr22	36916836	36917107	MONK:4:1101:2016:152129#ATCACG_1_C_0
+chr22	28980427	28980742	MONK:4:1101:2016:178494#ATCACG_1_C_0
+chr22	30986190	30986489	MONK:4:1101:2018:102633#ATCACG_1_C_0
+chr22	20865150	20865397	MONK:4:1101:2019:157503#ATCACG_1_C_0
+chr22	42327577	42327962	MONK:4:1101:2023:98613#ATCACG_1_C_0
+chr22	38206106	38206381	MONK:4:1101:2031:188437#ATCACG_1_C_0
+chr22	24763500	24763803	MONK:4:1101:2035:190338#ATCACG_1_C_0
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+chr22	21265687	21266111	MONK:4:1101:2036:162467#ATCACG_1_C_0
+chr22	24796223	24796573	MONK:4:1101:2041:13081#ATCACG_1_C_0
+chr22	20903546	20903860	MONK:4:1101:2043:44900#ATCACG_1_C_0
+chr22	44947744	44948083	MONK:4:1101:2045:136863#ATCACG_1_C_0
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+chr22	44562366	44562744	MONK:4:1101:2048:196819#ATCACG_1_C_0
+chr22	24582402	24582746	MONK:4:1101:2049:58183#ATCACG_1_C_0
+chr22	26010455	26010720	MONK:4:1101:2050:5906#ATCACG_1_C_0
+chr22	45463711	45464061	MONK:4:1101:2054:61445#ATCACG_1_C_0
+chr22	39339209	39339568	MONK:4:1101:2055:47818#ATCACG_1_C_0
+chr22	37702677	37702998	MONK:4:1101:2056:18419#ATCACG_1_C_0
+chr22	37214433	37214750	MONK:4:1101:2058:70645#ATCACG_1_C_0
+chr22	28314510	28314866	MONK:4:1101:2059:89462#ATCACG_1_C_0
+chr22	37825262	37825575	MONK:4:1101:2059:196988#ATCACG_1_C_0
+chr22	18141593	18141906	MONK:4:1101:2060:13739#ATCACG_1_C_0
+chr22	39925680	39926050	MONK:4:1101:2060:57734#ATCACG_1_C_0
+chr22	30580500	30580828	MONK:4:1101:2061:170858#ATCACG_1_C_0
+chr22	23028992	23029360	MONK:4:1101:2064:103362#ATCACG_1_C_0
+chr22	23528598	23528875	MONK:4:1101:2066:182063#ATCACG_1_C_0
+chr22	44874800	44875183	MONK:4:1101:2068:7662#ATCACG_1_C_0
+chr22	39584484	39584818	MONK:4:1101:2068:77978#ATCACG_1_C_0
+chr22	33797772	33798061	MONK:4:1101:2068:100271#ATCACG_1_C_0
+chr22	35986252	35986607	MONK:4:1101:2070:23404#ATCACG_1_C_0
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+chr22	36963258	36963578	MONK:4:1101:2073:141053#ATCACG_1_C_0
+chr22	19307238	19307559	MONK:4:1101:2073:146945#ATCACG_1_C_0
+chr22	31219645	31219924	MONK:4:1101:2074:66425#ATCACG_1_C_0
+chr22	19541960	19542242	MONK:4:1101:2075:118078#ATCACG_1_C_0
+chr22	27264361	27264647	MONK:4:1101:2077:158799#ATCACG_1_C_0
+chr22	42257620	42257866	MONK:4:1101:2077:197509#ATCACG_1_C_0
+chr22	35098395	35098663	MONK:4:1101:2083:101663#ATCACG_1_C_0
+chr22	20919441	20919738	MONK:4:1101:2089:170479#ATCACG_1_C_0
+chr22	51103700	51104012	MONK:4:1101:2091:141368#ATCACG_1_C_0
+chr22	40869949	40870251	MONK:4:1101:2091:200382#ATCACG_1_C_0
+chr22	45587887	45588179	MONK:4:1101:2092:30754#ATCACG_1_C_0
+chr22	30805512	30805877	MONK:4:1101:2099:16909#ATCACG_1_C_0
+chr22	44033966	44034285	MONK:4:1101:2099:32241#ATCACG_1_C_0
+chr22	41128651	41128939	MONK:4:1101:2103:85862#ATCACG_1_C_0
+chr22	28533601	28533854	MONK:4:1101:2106:138815#ATCACG_1_C_0
+chr22	22154290	22154577	MONK:4:1101:2114:80529#ATCACG_1_C_0
+chr22	38039414	38039729	MONK:4:1101:2120:28549#ATCACG_1_C_0
+chr22	39540350	39540559	MONK:4:1101:2121:154878#ATCACG_1_C_0
+chr22	20884321	20884672	MONK:4:1101:2127:115141#ATCACG_1_C_0
+chr22	24551823	24552160	MONK:4:1101:2130:172811#ATCACG_1_C_0
+chr22	18259249	18259606	MONK:4:1101:2132:95793#ATCACG_1_C_0
+chr22	25373041	25373209	MONK:4:1101:2132:128439#ATCACG_1_C_0
+chr22	32529163	32529537	MONK:4:1101:2132:137046#ATCACG_1_C_0
+chr22	38822667	38823045	MONK:4:1101:2134:94771#ATCACG_1_C_0
+chr22	26159451	26159615	MONK:4:1101:2138:27181#ATCACG_1_C_0
+chr22	34441238	34441585	MONK:4:1101:2139:139454#ATCACG_1_C_0
+chr22	45610815	45611077	MONK:4:1101:2139:183067#ATCACG_1_C_0
+chr22	39671600	39671996	MONK:4:1101:2144:33342#ATCACG_1_C_0
+chr22	45926669	45926955	MONK:4:1101:2145:111087#ATCACG_1_C_0
+chr22	42353807	42353994	MONK:4:1101:2147:150414#ATCACG_1_C_0
+chr22	24153559	24153892	MONK:4:1101:2149:92715#ATCACG_1_C_0
+chr22	18633120	18633461	MONK:4:1101:2149:117901#ATCACG_1_C_0
+chr22	28398677	28398947	MONK:4:1101:2154:12577#ATCACG_1_C_0
+chr22	21293552	21293918	MONK:4:1101:2156:25409#ATCACG_1_C_0
+chr22	41276700	41276988	MONK:4:1101:2159:7211#ATCACG_1_C_0
+chr22	48967117	48967481	MONK:4:1101:2167:87699#ATCACG_1_C_0
+chr22	35225703	35226036	MONK:4:1101:2169:189605#ATCACG_1_C_0
+chr22	26683772	26684132	MONK:4:1101:2170:100928#ATCACG_1_C_0
+chr22	43356750	43357110	MONK:4:1101:2172:94564#ATCACG_1_C_0
+chr22	42949335	42949675	MONK:4:1101:2174:117708#ATCACG_1_C_0
+chr22	48493138	48493460	MONK:4:1101:2178:193175#ATCACG_1_C_0
diff -r 000000000000 -r a41d96fc0b20 test-data/CTCF.encodepeak
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/CTCF.encodepeak	Mon Jul 15 09:43:27 2019 -0400
@@ -0,0 +1,421 @@
+chr22	16874913	16875110	peak_0	1000	.	4317.339355	28.826399	23.216457	98
+chr22	17377196	17377428	peak_1	1000	.	5084.379395	28.826399	23.216457	116
+chr22	17555930	17556245	peak_2	1000	.	6903.359863	28.826399	23.216457	157
+chr22	17652822	17653159	peak_3	1000	.	8054.507812	32.549095	25.871252	145
+chr22	17686483	17686744	peak_4	1000	.	5719.926758	28.826399	23.216457	130
+chr22	17718259	17718522	peak_5	1000	.	5763.757812	28.826399	23.216457	131
+chr22	17836468	17836780	peak_6	1000	.	6837.613770	28.826399	23.216457	156
+chr22	17847348	17847549	peak_7	1000	.	4405.000977	28.826399	23.216457	100
+chr22	17979862	17980115	peak_8	1000	.	5544.603516	28.826399	23.216457	126
+chr22	17999764	17999976	peak_9	1000	.	4646.070801	28.826399	23.216457	106
+chr22	18178995	18179198	peak_10	1000	.	4448.832031	28.826399	23.216457	101
+chr22	18225329	18225542	peak_11	1000	.	4667.986328	28.826399	23.216457	106
+chr22	18267916	18268161	peak_12	1000	.	5369.279785	28.826399	23.216457	122
+chr22	18281979	18282182	peak_13	1000	.	4448.832031	28.826399	23.216457	101
+chr22	18379432	18379662	peak_14	1000	.	5040.548340	28.826399	23.216457	115
+chr22	18548727	18548914	peak_15	1000	.	4098.185059	28.826399	23.216457	93
+chr22	18558818	18559167	peak_16	1000	.	8006.881836	32.549095	25.871252	213
+chr22	18559279	18559477	peak_17	1000	.	4339.254883	28.826399	23.216457	99
+chr22	18588889	18589127	peak_18	1000	.	5215.872070	28.826399	23.216457	119
+chr22	18632607	18632823	peak_19	1000	.	4733.732422	28.826399	23.216457	108
+chr22	18941875	18942127	peak_20	1000	.	5522.687988	28.826399	23.216457	126
+chr22	18979364	18979617	peak_21	1000	.	5544.603516	28.826399	23.216457	126
+chr22	19072523	19072736	peak_22	1000	.	4667.986328	28.826399	23.216457	106
+chr22	19073753	19074058	peak_23	1000	.	6684.205566	28.826399	23.216457	152
+chr22	19166731	19167005	peak_24	1000	.	6004.827148	28.826399	23.216457	137
+chr22	19465378	19465462	peak_25	1000	.	1840.895996	28.826399	23.216457	42
+chr22	19555413	19555614	peak_26	1000	.	4405.000977	28.826399	23.216457	100
+chr22	19617529	19617717	peak_27	1000	.	4120.100586	28.826399	23.216457	94
+chr22	19667222	19667453	peak_28	1000	.	5062.463867	28.826399	23.216457	115
+chr22	19822260	19822541	peak_29	1000	.	6158.235352	28.826399	23.216457	140
+chr22	19935205	19935418	peak_30	1000	.	4667.986328	28.826399	23.216457	106
+chr22	19941405	19941602	peak_31	1000	.	4317.339355	28.826399	23.216457	98
+chr22	19983826	19984010	peak_32	1000	.	4032.438721	28.826399	23.216457	92
+chr22	20001011	20001314	peak_33	1000	.	6640.374512	28.826399	23.216457	151
+chr22	20028009	20028299	peak_34	1000	.	6355.474121	28.826399	23.216457	145
+chr22	20141306	20141540	peak_35	1000	.	5128.209961	28.826399	23.216457	117
+chr22	20144441	20144859	peak_36	1000	.	9452.676758	32.549095	25.871252	247
+chr22	20256351	20256652	peak_37	1000	.	6596.543945	28.826399	23.216457	150
+chr22	20748305	20748648	peak_38	1000	.	7694.863281	32.549095	25.871252	156
+chr22	20763590	20763927	peak_39	1000	.	7385.499512	28.826399	23.216457	168
+chr22	20772492	20772685	peak_40	1000	.	4229.677734	28.826399	23.216457	96
+chr22	20918665	20918985	peak_41	1000	.	7964.517578	34.834431	27.013382	190
+chr22	20919272	20919441	peak_42	1000	.	3703.707275	28.826399	23.216457	84
+chr22	20978930	20979168	peak_43	1000	.	5215.872070	28.826399	23.216457	119
+chr22	21051926	21052202	peak_44	1000	.	6048.658203	28.826399	23.216457	138
+chr22	21076537	21076866	peak_45	1000	.	7210.175781	28.826399	23.216457	164
+chr22	21271214	21271433	peak_46	1000	.	4799.479004	28.826399	23.216457	109
+chr22	21306063	21306268	peak_47	1000	.	4492.662598	28.826399	23.216457	102
+chr22	21306496	21306697	peak_48	1000	.	4405.000977	28.826399	23.216457	100
+chr22	21312205	21312475	peak_49	1000	.	5917.165527	28.826399	23.216457	135
+chr22	21336175	21336473	peak_50	1000	.	6530.797363	28.826399	23.216457	149
+chr22	21375289	21375534	peak_51	1000	.	5369.279785	28.826399	23.216457	122
+chr22	21458562	21458760	peak_52	1000	.	4339.254883	28.826399	23.216457	99
+chr22	21995856	21996127	peak_53	1000	.	5939.081055	28.826399	23.216457	135
+chr22	22016503	22016802	peak_54	1000	.	6552.712891	28.826399	23.216457	149
+chr22	22080951	22081225	peak_55	1000	.	6004.827148	28.826399	23.216457	137
+chr22	22193635	22193984	peak_56	1000	.	7648.484375	28.826399	23.216457	174
+chr22	22292447	22292775	peak_57	1000	.	7866.676270	34.834431	27.013382	201
+chr22	22292934	22293127	peak_58	1000	.	4229.677734	28.826399	23.216457	96
+chr22	22307189	22307420	peak_59	1000	.	5548.291016	32.549095	25.871252	111
+chr22	22350062	22350377	peak_60	1000	.	6903.359863	28.826399	23.216457	157
+chr22	22398372	22398581	peak_61	1000	.	4580.324707	28.826399	23.216457	104
+chr22	22413599	22413807	peak_62	1000	.	4558.409180	28.826399	23.216457	104
+chr22	22510999	22511510	peak_63	1000	.	11241.259766	32.549095	25.871252	306
+chr22	22555396	22555729	peak_64	1000	.	7297.837402	28.826399	23.216457	166
+chr22	22556130	22556393	peak_65	1000	.	5763.757812	28.826399	23.216457	131
+chr22	22559998	22560239	peak_66	1000	.	5281.618164	28.826399	23.216457	120
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+chr22	38500133	38500330	peak_264	1000	.	4317.339355	28.826399	23.216457	98
+chr22	38636474	38636725	peak_265	1000	.	5500.772461	28.826399	23.216457	125
+chr22	38658003	38658270	peak_266	1000	.	6509.808105	32.549095	25.871252	127
+chr22	38749288	38749578	peak_267	1000	.	6355.474121	28.826399	23.216457	145
+chr22	38808920	38809213	peak_268	1000	.	6421.220215	28.826399	23.216457	146
+chr22	38859147	38859459	peak_269	1000	.	6837.613770	28.826399	23.216457	156
+chr22	38899836	38900101	peak_270	1000	.	5807.588379	28.826399	23.216457	132
+chr22	38968571	38968758	peak_271	1000	.	4098.185059	28.826399	23.216457	93
+chr22	39018423	39018762	peak_272	1000	.	7429.330078	28.826399	23.216457	169
+chr22	39077605	39077836	peak_273	1000	.	5062.463867	28.826399	23.216457	115
+chr22	39095780	39095980	peak_274	1000	.	4383.085449	28.826399	23.216457	100
+chr22	39150065	39150300	peak_275	1000	.	5150.125488	28.826399	23.216457	117
+chr22	39164806	39165321	peak_276	1000	.	11451.042969	32.549095	25.871252	253
+chr22	39241440	39241642	peak_277	1000	.	4426.916504	28.826399	23.216457	101
+chr22	39264976	39265171	peak_278	1000	.	4273.508301	28.826399	23.216457	97
+chr22	39267843	39268143	peak_279	1000	.	6574.628418	28.826399	23.216457	150
+chr22	39268661	39268882	peak_280	1000	.	4843.309570	28.826399	23.216457	110
+chr22	39369729	39369947	peak_281	1000	.	4777.563477	28.826399	23.216457	109
+chr22	39377173	39377544	peak_282	1000	.	8380.173828	32.549095	25.871252	221
+chr22	39378468	39378802	peak_283	1000	.	7319.752930	28.826399	23.216457	167
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+chr22	39492880	39493165	peak_285	1000	.	6245.896973	28.826399	23.216457	142
+chr22	39513857	39514145	peak_286	1000	.	6834.637695	32.549095	25.871252	106
+chr22	39519555	39519754	peak_287	1000	.	4361.170410	28.826399	23.216457	99
+chr22	39524351	39524683	peak_288	1000	.	7275.922363	28.826399	23.216457	166
+chr22	39531267	39531483	peak_289	1000	.	4733.732422	28.826399	23.216457	108
+chr22	39565125	39565326	peak_290	1000	.	4405.000977	28.826399	23.216457	100
+chr22	39566735	39567191	peak_291	1000	.	10012.019531	32.549095	25.871252	222
+chr22	39636304	39636544	peak_292	1000	.	5259.702637	28.826399	23.216457	120
+chr22	39706894	39707207	peak_293	1000	.	7194.033203	32.549095	25.871252	187
+chr22	39712578	39712848	peak_294	1000	.	5917.165527	28.826399	23.216457	135
+chr22	39739689	39739943	peak_295	1000	.	5566.518555	28.826399	23.216457	127
+chr22	39867834	39868133	peak_296	1000	.	6552.712891	28.826399	23.216457	149
+chr22	39889452	39889682	peak_297	1000	.	5040.548340	28.826399	23.216457	115
+chr22	39891782	39892096	peak_298	1000	.	6881.444336	28.826399	23.216457	157
+chr22	39892525	39892775	peak_299	1000	.	5478.856934	28.826399	23.216457	125
+chr22	39930899	39931161	peak_300	1000	.	5741.842285	28.826399	23.216457	131
+chr22	39997095	39997350	peak_301	1000	.	5588.434082	28.826399	23.216457	127
+chr22	40161005	40161291	peak_302	1000	.	6267.812500	28.826399	23.216457	143
+chr22	40328883	40329177	peak_303	1000	.	6443.135742	28.826399	23.216457	147
+chr22	40342870	40343127	peak_304	1000	.	5632.265137	28.826399	23.216457	128
+chr22	40432556	40432864	peak_305	1000	.	6749.951660	28.826399	23.216457	154
+chr22	40574389	40574620	peak_306	1000	.	5062.463867	28.826399	23.216457	115
+chr22	40832844	40833339	peak_307	1000	.	11477.876953	34.834431	27.013382	170
+chr22	40858557	40858759	peak_308	1000	.	4426.916504	28.826399	23.216457	101
+chr22	40888949	40889190	peak_309	1000	.	5281.618164	28.826399	23.216457	120
+chr22	40900611	40900894	peak_310	1000	.	6202.066406	28.826399	23.216457	141
+chr22	41042293	41042552	peak_311	1000	.	6156.613770	32.549095	25.871252	142
+chr22	41079231	41079417	peak_312	1000	.	4076.269531	28.826399	23.216457	93
+chr22	41156217	41156497	peak_313	1000	.	6136.319824	28.826399	23.216457	140
+chr22	41182241	41182434	peak_314	1000	.	4229.677734	28.826399	23.216457	96
+chr22	41295036	41295322	peak_315	1000	.	6267.812500	28.826399	23.216457	143
+chr22	41295497	41295692	peak_316	1000	.	4273.508301	28.826399	23.216457	97
+chr22	41318779	41319077	peak_317	1000	.	7027.244629	32.549095	25.871252	198
+chr22	41681978	41682226	peak_318	1000	.	5435.026367	28.826399	23.216457	124
+chr22	41697345	41697589	peak_319	1000	.	5347.364258	28.826399	23.216457	122
+chr22	41842221	41842443	peak_320	1000	.	4865.225098	28.826399	23.216457	111
+chr22	41939828	41940079	peak_321	1000	.	5500.772461	28.826399	23.216457	125
+chr22	42062696	42062991	peak_322	1000	.	6465.051270	28.826399	23.216457	147
+chr22	42098096	42098284	peak_323	1000	.	4120.100586	28.826399	23.216457	94
+chr22	42142707	42142909	peak_324	1000	.	4426.916504	28.826399	23.216457	101
+chr22	42158977	42159285	peak_325	1000	.	6749.951660	28.826399	23.216457	154
+chr22	42159769	42159957	peak_326	1000	.	4120.100586	28.826399	23.216457	94
+chr22	42176795	42177026	peak_327	1000	.	5062.463867	28.826399	23.216457	115
+chr22	42219004	42219260	peak_328	1000	.	5610.349609	28.826399	23.216457	128
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+chr22	42315059	42315294	peak_330	1000	.	5150.125488	28.826399	23.216457	117
+chr22	42321891	42322009	peak_331	1000	.	2586.020508	28.826399	23.216457	59
+chr22	42353994	42354013	peak_332	1000	.	416.393127	28.826399	23.216457	9
+chr22	42362701	42362987	peak_333	1000	.	6267.812500	28.826399	23.216457	143
+chr22	42469869	42470057	peak_334	1000	.	4120.100586	28.826399	23.216457	94
+chr22	42486877	42487267	peak_335	1000	.	9497.490234	34.834431	27.013382	177
+chr22	42494019	42494222	peak_336	1000	.	4448.832031	28.826399	23.216457	101
+chr22	42510899	42511180	peak_337	1000	.	6158.235352	28.826399	23.216457	140
+chr22	42605868	42606193	peak_338	1000	.	7122.514160	28.826399	23.216457	162
+chr22	42660219	42660519	peak_339	1000	.	6574.628418	28.826399	23.216457	150
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+chr22	42833500	42833887	peak_341	1000	.	8656.487305	32.549095	25.871252	194
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+chr22	42891122	42891345	peak_343	1000	.	4887.140625	28.826399	23.216457	111
+chr22	42892460	42892767	peak_344	1000	.	6728.036621	28.826399	23.216457	153
+chr22	42955869	42956101	peak_345	1000	.	5084.379395	28.826399	23.216457	116
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+chr22	43130034	43130261	peak_347	1000	.	4974.802246	28.826399	23.216457	113
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+chr22	43151700	43151988	peak_349	1000	.	6311.643555	28.826399	23.216457	144
+chr22	43176187	43176475	peak_350	1000	.	6311.643555	28.826399	23.216457	144
+chr22	43216100	43216405	peak_351	1000	.	6684.205566	28.826399	23.216457	152
+chr22	43263674	43264002	peak_352	1000	.	7822.756836	32.549095	25.871252	166
+chr22	43298252	43298486	peak_353	1000	.	5128.209961	28.826399	23.216457	117
+chr22	43364252	43364508	peak_354	1000	.	5610.349609	28.826399	23.216457	128
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+chr22	43507400	43507716	peak_357	1000	.	6925.275391	28.826399	23.216457	158
+chr22	43668966	43669276	peak_358	1000	.	6793.782715	28.826399	23.216457	155
+chr22	43669701	43670019	peak_359	1000	.	6969.105957	28.826399	23.216457	159
+chr22	43701655	43701841	peak_360	1000	.	4076.269531	28.826399	23.216457	93
+chr22	43742576	43742821	peak_361	1000	.	5369.279785	28.826399	23.216457	122
+chr22	43810586	43810909	peak_362	1000	.	7078.683105	28.826399	23.216457	161
+chr22	44208868	44209209	peak_363	1000	.	7473.161133	28.826399	23.216457	170
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+chr22	44278975	44279208	peak_365	1000	.	5106.294922	28.826399	23.216457	116
+chr22	44318786	44318974	peak_366	1000	.	4120.100586	28.826399	23.216457	94
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+chr22	44481496	44481815	peak_368	1000	.	6991.021484	28.826399	23.216457	159
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+chr22	45093556	45093905	peak_371	1000	.	7648.484375	28.826399	23.216457	174
+chr22	45114870	45115120	peak_372	1000	.	5478.856934	28.826399	23.216457	125
+chr22	45216659	45216953	peak_373	1000	.	6443.135742	28.826399	23.216457	147
+chr22	45335869	45336069	peak_374	1000	.	4383.085449	28.826399	23.216457	100
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+chr22	45448587	45448795	peak_376	1000	.	4558.409180	28.826399	23.216457	104
+chr22	45605224	45605465	peak_377	1000	.	5281.618164	28.826399	23.216457	120
+chr22	45664829	45665049	peak_378	1000	.	4821.394043	28.826399	23.216457	110
+chr22	46041593	46041829	peak_379	1000	.	5172.041016	28.826399	23.216457	118
+chr22	46106477	46106774	peak_380	1000	.	6508.882324	28.826399	23.216457	148
+chr22	46183124	46183315	peak_381	1000	.	4185.846680	28.826399	23.216457	95
+chr22	46390070	46390323	peak_382	1000	.	5544.603516	28.826399	23.216457	126
+chr22	46409073	46409404	peak_383	1000	.	7254.006836	28.826399	23.216457	165
+chr22	46432623	46432904	peak_384	1000	.	6588.312500	32.549095	25.871252	135
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+chr22	46518382	46518701	peak_386	1000	.	7721.090332	32.549095	25.871252	165
+chr22	46519293	46519467	peak_387	1000	.	3813.284424	28.826399	23.216457	87
+chr22	46722697	46722886	peak_388	1000	.	4142.016113	28.826399	23.216457	94
+chr22	46751393	46751665	peak_389	1000	.	5960.996582	28.826399	23.216457	136
+chr22	46934120	46934311	peak_390	1000	.	4185.846680	28.826399	23.216457	95
+chr22	46955408	46955639	peak_391	1000	.	5062.463867	28.826399	23.216457	115
+chr22	46969895	46970107	peak_392	1000	.	4646.070801	28.826399	23.216457	106
+chr22	47019401	47019740	peak_393	1000	.	7429.330078	28.826399	23.216457	169
+chr22	47089504	47089698	peak_394	1000	.	4251.593262	28.826399	23.216457	97
+chr22	47135003	47135248	peak_395	1000	.	5369.279785	28.826399	23.216457	122
+chr22	47154865	47155113	peak_396	1000	.	5435.026367	28.826399	23.216457	124
+chr22	47158056	47158376	peak_397	1000	.	7012.937012	28.826399	23.216457	160
+chr22	47598983	47599240	peak_398	1000	.	5632.265137	28.826399	23.216457	128
+chr22	48479899	48480140	peak_399	1000	.	5281.618164	28.826399	23.216457	120
+chr22	48504405	48504629	peak_400	1000	.	4909.055664	28.826399	23.216457	112
+chr22	49401594	49401921	peak_401	1000	.	7166.345215	28.826399	23.216457	163
+chr22	49553435	49553624	peak_402	1000	.	4142.016113	28.826399	23.216457	94
+chr22	49746583	49746773	peak_403	1000	.	4163.931152	28.826399	23.216457	95
+chr22	50418074	50418305	peak_404	1000	.	5062.463867	28.826399	23.216457	115
+chr22	50468615	50468928	peak_405	1000	.	7225.890625	32.549095	25.871252	187
+chr22	50512931	50513121	peak_406	1000	.	4163.931152	28.826399	23.216457	95
+chr22	50628501	50628741	peak_407	1000	.	5259.702637	28.826399	23.216457	120
+chr22	50630995	50631224	peak_408	1000	.	5018.632812	28.826399	23.216457	114
+chr22	50645170	50645459	peak_409	1000	.	6333.558594	28.826399	23.216457	144
+chr22	50716298	50716549	peak_410	1000	.	5500.772461	28.826399	23.216457	125
+chr22	50769460	50769676	peak_411	1000	.	4733.732422	28.826399	23.216457	108
+chr22	50911511	50911831	peak_412	1000	.	7012.937012	28.826399	23.216457	160
+chr22	50936751	50936936	peak_413	1000	.	4054.354248	28.826399	23.216457	92
+chr22	50965071	50965340	peak_414	1000	.	5895.250000	28.826399	23.216457	134
+chr22	50972925	50973062	peak_415	1000	.	3002.413574	28.826399	23.216457	68
+chr22	50982866	50983075	peak_416	1000	.	4580.324707	28.826399	23.216457	104
+chr22	51058888	51059217	peak_417	1000	.	7210.175781	28.826399	23.216457	164
+chr22	51066506	51066791	peak_418	1000	.	6245.896973	28.826399	23.216457	142
+chr22	51130088	51130412	peak_419	1000	.	7676.688965	32.549095	25.871252	116
+chr22	51213606	51213856	peak_420	1000	.	5478.856934	28.826399	23.216457	125
diff -r 000000000000 -r a41d96fc0b20 test-data/CTCF1.bedgraph
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/CTCF1.bedgraph	Mon Jul 15 09:43:27 2019 -0400
@@ -0,0 +1,1935 @@
+chr	start	end	experimental	control	-log(p)	-log(q)	signif
+chr1	0	249250621	0.000000	0.000039	0.000000	0.000000
+chr2	0	243199373	0.000000	0.000039	0.000000	0.000000
+chr3	0	198022430	0.000000	0.000039	0.000000	0.000000
+chr4	0	191154276	0.000000	0.000039	0.000000	0.000000
+chr5	0	180915260	0.000000	0.000039	0.000000	0.000000
+chr6	0	171115067	0.000000	0.000039	0.000000	0.000000
+chr7	0	159138663	0.000000	0.000039	0.000000	0.000000
+chr8	0	146364022	0.000000	0.000039	0.000000	0.000000
+chr9	0	141213431	0.000000	0.000039	0.000000	0.000000
+chr10	0	135534747	0.000000	0.000039	0.000000	0.000000
+chr11	0	135006516	0.000000	0.000039	0.000000	0.000000
+chr12	0	133851895	0.000000	0.000039	0.000000	0.000000
+chr13	0	115169878	0.000000	0.000039	0.000000	0.000000
+chr14	0	107349540	0.000000	0.000039	0.000000	0.000000
+chr15	0	102531392	0.000000	0.000039	0.000000	0.000000
+chr16	0	90354753	0.000000	0.000039	0.000000	0.000000
+chr17	0	81195210	0.000000	0.000039	0.000000	0.000000
+chr18	0	78077248	0.000000	0.000039	0.000000	0.000000
+chr19	0	59128983	0.000000	0.000039	0.000000	0.000000
+chr20	0	63025520	0.000000	0.000039	0.000000	0.000000
+chr21	0	48129895	0.000000	0.000039	0.000000	0.000000
+chr22	0	16874913	0.000000	0.000039	0.000000	0.000000
+chr22	16874913	16875110	1.000000	0.000039	28.826399	23.216457	*
+chr22	16875110	17213301	0.000000	0.000039	0.000000	0.000000
+chr22	17213301	17213528	0.000000	0.793817	0.000000	0.000000
+chr22	17213528	17305939	0.000000	0.000039	0.000000	0.000000
+chr22	17305939	17306331	0.000000	0.793817	0.000000	0.000000
+chr22	17306331	17331220	0.000000	0.000039	0.000000	0.000000
+chr22	17331220	17331528	0.000000	0.793817	0.000000	0.000000
+chr22	17331528	17333158	0.000000	0.000039	0.000000	0.000000
+chr22	17333158	17333474	0.000000	0.793817	0.000000	0.000000
+chr22	17333474	17374212	0.000000	0.000039	0.000000	0.000000
+chr22	17374212	17374535	0.000000	0.793817	0.000000	0.000000
+chr22	17374535	17377196	0.000000	0.000039	0.000000	0.000000
+chr22	17377196	17377428	1.000000	0.000039	28.826399	23.216457	*
+chr22	17377428	17529435	0.000000	0.000039	0.000000	0.000000
+chr22	17529435	17529809	0.000000	0.793817	0.000000	0.000000
+chr22	17529809	17555930	0.000000	0.000039	0.000000	0.000000
+chr22	17555930	17556245	1.000000	0.000039	28.826399	23.216457	*
+chr22	17556245	17574927	0.000000	0.000039	0.000000	0.000000
+chr22	17574927	17575208	0.000000	0.793817	0.000000	0.000000
+chr22	17575208	17652822	0.000000	0.000039	0.000000	0.000000
+chr22	17652822	17652841	1.000000	0.000039	28.826399	23.216457	*
+chr22	17652841	17653093	2.000000	0.000039	32.549095	25.871252	*
+chr22	17653093	17653159	1.000000	0.000039	28.826399	23.216457	*
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+chr22	47082149	47089504	0.000000	0.000039	0.000000	0.000000
+chr22	47089504	47089698	1.000000	0.000039	28.826399	23.216457	*
+chr22	47089698	47135003	0.000000	0.000039	0.000000	0.000000
+chr22	47135003	47135248	1.000000	0.000039	28.826399	23.216457	*
+chr22	47135248	47154865	0.000000	0.000039	0.000000	0.000000
+chr22	47154865	47155113	1.000000	0.000039	28.826399	23.216457	*
+chr22	47155113	47158056	0.000000	0.000039	0.000000	0.000000
+chr22	47158056	47158376	1.000000	0.000039	28.826399	23.216457	*
+chr22	47158376	47214755	0.000000	0.000039	0.000000	0.000000
+chr22	47214755	47215042	0.000000	0.793817	0.000000	0.000000
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+chr22	47315892	47316206	0.000000	0.793817	0.000000	0.000000
+chr22	47316206	47393504	0.000000	0.000039	0.000000	0.000000
+chr22	47393504	47393812	0.000000	0.793817	0.000000	0.000000
+chr22	47393812	47396789	0.000000	0.000039	0.000000	0.000000
+chr22	47396789	47397152	0.000000	0.793817	0.000000	0.000000
+chr22	47397152	47580463	0.000000	0.000039	0.000000	0.000000
+chr22	47580463	47580834	0.000000	0.793817	0.000000	0.000000
+chr22	47580834	47598983	0.000000	0.000039	0.000000	0.000000
+chr22	47598983	47599240	1.000000	0.000039	28.826399	23.216457	*
+chr22	47599240	47624590	0.000000	0.000039	0.000000	0.000000
+chr22	47624590	47624857	0.000000	0.793817	0.000000	0.000000
+chr22	47624857	47672779	0.000000	0.000039	0.000000	0.000000
+chr22	47672779	47673081	0.000000	0.793817	0.000000	0.000000
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+chr22	47924600	47924902	0.000000	0.793817	0.000000	0.000000
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+chr22	48020580	48020954	0.000000	0.793817	0.000000	0.000000
+chr22	48020954	48042565	0.000000	0.000039	0.000000	0.000000
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+chr22	48227644	48228004	0.000000	0.793817	0.000000	0.000000
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+chr22	48479899	48480140	1.000000	0.000039	28.826399	23.216457	*
+chr22	48480140	48493138	0.000000	0.000039	0.000000	0.000000
+chr22	48493138	48493460	0.000000	0.793817	0.000000	0.000000
+chr22	48493460	48504405	0.000000	0.000039	0.000000	0.000000
+chr22	48504405	48504629	1.000000	0.000039	28.826399	23.216457	*
+chr22	48504629	48565208	0.000000	0.000039	0.000000	0.000000
+chr22	48565208	48565487	0.000000	0.793817	0.000000	0.000000
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+chr22	48578160	48578448	0.000000	0.793817	0.000000	0.000000
+chr22	48578448	48625177	0.000000	0.000039	0.000000	0.000000
+chr22	48625177	48625522	0.000000	0.793817	0.000000	0.000000
+chr22	48625522	48840344	0.000000	0.000039	0.000000	0.000000
+chr22	48840344	48840641	0.000000	0.793817	0.000000	0.000000
+chr22	48840641	48957410	0.000000	0.000039	0.000000	0.000000
+chr22	48957410	48957651	0.000000	0.793817	0.000000	0.000000
+chr22	48957651	48967117	0.000000	0.000039	0.000000	0.000000
+chr22	48967117	48967481	0.000000	0.793817	0.000000	0.000000
+chr22	48967481	49401594	0.000000	0.000039	0.000000	0.000000
+chr22	49401594	49401921	1.000000	0.000039	28.826399	23.216457	*
+chr22	49401921	49553435	0.000000	0.000039	0.000000	0.000000
+chr22	49553435	49553624	1.000000	0.000039	28.826399	23.216457	*
+chr22	49553624	49746583	0.000000	0.000039	0.000000	0.000000
+chr22	49746583	49746773	1.000000	0.000039	28.826399	23.216457	*
+chr22	49746773	49988586	0.000000	0.000039	0.000000	0.000000
+chr22	49988586	49988885	0.000000	0.793817	0.000000	0.000000
+chr22	49988885	50049313	0.000000	0.000039	0.000000	0.000000
+chr22	50049313	50049602	0.000000	0.793817	0.000000	0.000000
+chr22	50049602	50059030	0.000000	0.000039	0.000000	0.000000
+chr22	50059030	50059315	0.000000	0.793817	0.000000	0.000000
+chr22	50059315	50125688	0.000000	0.000039	0.000000	0.000000
+chr22	50125688	50125865	0.000000	0.793817	0.000000	0.000000
+chr22	50125865	50214174	0.000000	0.000039	0.000000	0.000000
+chr22	50214174	50214574	0.000000	0.793817	0.000000	0.000000
+chr22	50214574	50233496	0.000000	0.000039	0.000000	0.000000
+chr22	50233496	50233928	0.000000	0.793817	0.000000	0.000000
+chr22	50233928	50234415	0.000000	0.000039	0.000000	0.000000
+chr22	50234415	50234797	0.000000	0.793817	0.000000	0.000000
+chr22	50234797	50338193	0.000000	0.000039	0.000000	0.000000
+chr22	50338193	50338471	0.000000	0.793817	0.000000	0.000000
+chr22	50338471	50354362	0.000000	0.000039	0.000000	0.000000
+chr22	50354362	50354742	0.000000	0.793817	0.000000	0.000000
+chr22	50354742	50418074	0.000000	0.000039	0.000000	0.000000
+chr22	50418074	50418305	1.000000	0.000039	28.826399	23.216457	*
+chr22	50418305	50451024	0.000000	0.000039	0.000000	0.000000
+chr22	50451024	50451324	0.000000	0.793817	0.000000	0.000000
+chr22	50451324	50468615	0.000000	0.000039	0.000000	0.000000
+chr22	50468615	50468733	1.000000	0.000039	28.826399	23.216457	*
+chr22	50468733	50468871	2.000000	0.000039	32.549095	25.871252	*
+chr22	50468871	50468928	1.000000	0.000039	28.826399	23.216457	*
+chr22	50468928	50472607	0.000000	0.000039	0.000000	0.000000
+chr22	50472607	50472929	0.000000	0.793817	0.000000	0.000000
+chr22	50472929	50512931	0.000000	0.000039	0.000000	0.000000
+chr22	50512931	50513121	1.000000	0.000039	28.826399	23.216457	*
+chr22	50513121	50574751	0.000000	0.000039	0.000000	0.000000
+chr22	50574751	50575063	0.000000	0.793817	0.000000	0.000000
+chr22	50575063	50628501	0.000000	0.000039	0.000000	0.000000
+chr22	50628501	50628741	1.000000	0.000039	28.826399	23.216457	*
+chr22	50628741	50630995	0.000000	0.000039	0.000000	0.000000
+chr22	50630995	50631224	1.000000	0.000039	28.826399	23.216457	*
+chr22	50631224	50645170	0.000000	0.000039	0.000000	0.000000
+chr22	50645170	50645459	1.000000	0.000039	28.826399	23.216457	*
+chr22	50645459	50658290	0.000000	0.000039	0.000000	0.000000
+chr22	50658290	50658656	0.000000	0.793817	0.000000	0.000000
+chr22	50658656	50716298	0.000000	0.000039	0.000000	0.000000
+chr22	50716298	50716549	1.000000	0.000039	28.826399	23.216457	*
+chr22	50716549	50728249	0.000000	0.000039	0.000000	0.000000
+chr22	50728249	50728594	0.000000	0.793817	0.000000	0.000000
+chr22	50728594	50757826	0.000000	0.000039	0.000000	0.000000
+chr22	50757826	50758150	0.000000	0.793817	0.000000	0.000000
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+chr22	50769460	50769676	1.000000	0.000039	28.826399	23.216457	*
+chr22	50769676	50802506	0.000000	0.000039	0.000000	0.000000
+chr22	50802506	50802827	0.000000	0.793817	0.000000	0.000000
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+chr22	50911511	50911831	1.000000	0.000039	28.826399	23.216457	*
+chr22	50911831	50936751	0.000000	0.000039	0.000000	0.000000
+chr22	50936751	50936936	1.000000	0.000039	28.826399	23.216457	*
+chr22	50936936	50965071	0.000000	0.000039	0.000000	0.000000
+chr22	50965071	50965340	1.000000	0.000039	28.826399	23.216457	*
+chr22	50965340	50972925	0.000000	0.000039	0.000000	0.000000
+chr22	50972925	50973062	1.000000	0.000039	28.826399	23.216457	*
+chr22	50973062	50982866	0.000000	0.000039	0.000000	0.000000
+chr22	50982866	50983075	1.000000	0.000039	28.826399	23.216457	*
+chr22	50983075	51058888	0.000000	0.000039	0.000000	0.000000
+chr22	51058888	51059217	1.000000	0.000039	28.826399	23.216457	*
+chr22	51059217	51066506	0.000000	0.000039	0.000000	0.000000
+chr22	51066506	51066791	1.000000	0.000039	28.826399	23.216457	*
+chr22	51066791	51102143	0.000000	0.000039	0.000000	0.000000
+chr22	51102143	51102471	0.000000	0.793817	0.000000	0.000000
+chr22	51102471	51103700	0.000000	0.000039	0.000000	0.000000
+chr22	51103700	51104012	0.000000	0.793817	0.000000	0.000000
+chr22	51104012	51130088	0.000000	0.000039	0.000000	0.000000
+chr22	51130088	51130096	1.000000	0.000039	28.826399	23.216457	*
+chr22	51130096	51130313	2.000000	0.000039	32.549095	25.871252	*
+chr22	51130313	51130412	1.000000	0.000039	28.826399	23.216457	*
+chr22	51130412	51208525	0.000000	0.000039	0.000000	0.000000
+chr22	51208525	51208735	0.000000	0.793817	0.000000	0.000000
+chr22	51208735	51213606	0.000000	0.000039	0.000000	0.000000
+chr22	51213606	51213856	1.000000	0.000039	28.826399	23.216457	*
+chr22	51213856	51304566	0.000000	0.000039	0.000000	0.000000
+chrX	0	155270560	0.000000	0.000039	0.000000	0.000000
+chrY	0	59373566	0.000000	0.000039	0.000000	0.000000
diff -r 000000000000 -r a41d96fc0b20 test-data/CTCF2.bedgraph
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/CTCF2.bedgraph	Mon Jul 15 09:43:27 2019 -0400
@@ -0,0 +1,1936 @@
+# experimental file: CTCF1.bam; control file: CTCF2.bam
+chr	start	end	experimental	control	-log(p)
+chr1	0	249250621	0.000000	0.000039	0.000000
+chr2	0	243199373	0.000000	0.000039	0.000000
+chr3	0	198022430	0.000000	0.000039	0.000000
+chr4	0	191154276	0.000000	0.000039	0.000000
+chr5	0	180915260	0.000000	0.000039	0.000000
+chr6	0	171115067	0.000000	0.000039	0.000000
+chr7	0	159138663	0.000000	0.000039	0.000000
+chr8	0	146364022	0.000000	0.000039	0.000000
+chr9	0	141213431	0.000000	0.000039	0.000000
+chr10	0	135534747	0.000000	0.000039	0.000000
+chr11	0	135006516	0.000000	0.000039	0.000000
+chr12	0	133851895	0.000000	0.000039	0.000000
+chr13	0	115169878	0.000000	0.000039	0.000000
+chr14	0	107349540	0.000000	0.000039	0.000000
+chr15	0	102531392	0.000000	0.000039	0.000000
+chr16	0	90354753	0.000000	0.000039	0.000000
+chr17	0	81195210	0.000000	0.000039	0.000000
+chr18	0	78077248	0.000000	0.000039	0.000000
+chr19	0	59128983	0.000000	0.000039	0.000000
+chr20	0	63025520	0.000000	0.000039	0.000000
+chr21	0	48129895	0.000000	0.000039	0.000000
+chr22	0	16874913	0.000000	0.000039	0.000000
+chr22	16874913	16875110	1.000000	0.000039	28.826399
+chr22	16875110	17213301	0.000000	0.000039	0.000000
+chr22	17213301	17213528	0.000000	0.793817	0.000000
+chr22	17213528	17305939	0.000000	0.000039	0.000000
+chr22	17305939	17306331	0.000000	0.793817	0.000000
+chr22	17306331	17331220	0.000000	0.000039	0.000000
+chr22	17331220	17331528	0.000000	0.793817	0.000000
+chr22	17331528	17333158	0.000000	0.000039	0.000000
+chr22	17333158	17333474	0.000000	0.793817	0.000000
+chr22	17333474	17374212	0.000000	0.000039	0.000000
+chr22	17374212	17374535	0.000000	0.793817	0.000000
+chr22	17374535	17377196	0.000000	0.000039	0.000000
+chr22	17377196	17377428	1.000000	0.000039	28.826399
+chr22	17377428	17529435	0.000000	0.000039	0.000000
+chr22	17529435	17529809	0.000000	0.793817	0.000000
+chr22	17529809	17555930	0.000000	0.000039	0.000000
+chr22	17555930	17556245	1.000000	0.000039	28.826399
+chr22	17556245	17574927	0.000000	0.000039	0.000000
+chr22	17574927	17575208	0.000000	0.793817	0.000000
+chr22	17575208	17652822	0.000000	0.000039	0.000000
+chr22	17652822	17652841	1.000000	0.000039	28.826399
+chr22	17652841	17653093	2.000000	0.000039	32.549095
+chr22	17653093	17653159	1.000000	0.000039	28.826399
+chr22	17653159	17686483	0.000000	0.000039	0.000000
+chr22	17686483	17686744	1.000000	0.000039	28.826399
+chr22	17686744	17697561	0.000000	0.000039	0.000000
+chr22	17697561	17697877	0.000000	0.793817	0.000000
+chr22	17697877	17718259	0.000000	0.000039	0.000000
+chr22	17718259	17718522	1.000000	0.000039	28.826399
+chr22	17718522	17836468	0.000000	0.000039	0.000000
+chr22	17836468	17836780	1.000000	0.000039	28.826399
+chr22	17836780	17847348	0.000000	0.000039	0.000000
+chr22	17847348	17847549	1.000000	0.000039	28.826399
+chr22	17847549	17979862	0.000000	0.000039	0.000000
+chr22	17979862	17980115	1.000000	0.000039	28.826399
+chr22	17980115	17999764	0.000000	0.000039	0.000000
+chr22	17999764	17999976	1.000000	0.000039	28.826399
+chr22	17999976	18137643	0.000000	0.000039	0.000000
+chr22	18137643	18137939	0.000000	0.793817	0.000000
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+chr22	18178995	18179198	1.000000	0.000039	28.826399
+chr22	18179198	18201532	0.000000	0.000039	0.000000
+chr22	18201532	18201830	0.000000	0.793817	0.000000
+chr22	18201830	18225329	0.000000	0.000039	0.000000
+chr22	18225329	18225542	1.000000	0.000039	28.826399
+chr22	18225542	18259249	0.000000	0.000039	0.000000
+chr22	18259249	18259606	0.000000	0.793817	0.000000
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+chr22	18263815	18264099	0.000000	0.793817	0.000000
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+chr22	18267916	18268161	1.000000	0.000039	28.826399
+chr22	18268161	18281979	0.000000	0.000039	0.000000
+chr22	18281979	18282182	1.000000	0.000039	28.826399
+chr22	18282182	18379432	0.000000	0.000039	0.000000
+chr22	18379432	18379662	1.000000	0.000039	28.826399
+chr22	18379662	18394708	0.000000	0.000039	0.000000
+chr22	18394708	18395062	0.000000	0.793817	0.000000
+chr22	18395062	18479380	0.000000	0.000039	0.000000
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+chr22	18548727	18548914	1.000000	0.000039	28.826399
+chr22	18548914	18558818	0.000000	0.000039	0.000000
+chr22	18558818	18558964	1.000000	0.000039	28.826399
+chr22	18558964	18559099	2.000000	0.000039	32.549095
+chr22	18559099	18559167	1.000000	0.000039	28.826399
+chr22	18559167	18559279	0.000000	0.000039	0.000000
+chr22	18559279	18559477	1.000000	0.000039	28.826399
+chr22	18559477	18566281	0.000000	0.000039	0.000000
+chr22	18566281	18566568	0.000000	0.793817	0.000000
+chr22	18566568	18588889	0.000000	0.000039	0.000000
+chr22	18588889	18589127	1.000000	0.000039	28.826399
+chr22	18589127	18632607	0.000000	0.000039	0.000000
+chr22	18632607	18632823	1.000000	0.000039	28.826399
+chr22	18632823	18633120	0.000000	0.000039	0.000000
+chr22	18633120	18633461	0.000000	0.793817	0.000000
+chr22	18633461	18847100	0.000000	0.000039	0.000000
+chr22	18847100	18847283	0.000000	0.793817	0.000000
+chr22	18847283	18941875	0.000000	0.000039	0.000000
+chr22	18941875	18942127	1.000000	0.000039	28.826399
+chr22	18942127	18979364	0.000000	0.000039	0.000000
+chr22	18979364	18979617	1.000000	0.000039	28.826399
+chr22	18979617	19072523	0.000000	0.000039	0.000000
+chr22	19072523	19072736	1.000000	0.000039	28.826399
+chr22	19072736	19073753	0.000000	0.000039	0.000000
+chr22	19073753	19074058	1.000000	0.000039	28.826399
+chr22	19074058	19107255	0.000000	0.000039	0.000000
+chr22	19107255	19107575	0.000000	0.793817	0.000000
+chr22	19107575	19157356	0.000000	0.000039	0.000000
+chr22	19157356	19157690	0.000000	0.793817	0.000000
+chr22	19157690	19166731	0.000000	0.000039	0.000000
+chr22	19166731	19167005	1.000000	0.000039	28.826399
+chr22	19167005	19186862	0.000000	0.000039	0.000000
+chr22	19186862	19187126	0.000000	0.793817	0.000000
+chr22	19187126	19238441	0.000000	0.000039	0.000000
+chr22	19238441	19238808	0.000000	0.793817	0.000000
+chr22	19238808	19307238	0.000000	0.000039	0.000000
+chr22	19307238	19307559	0.000000	0.793817	0.000000
+chr22	19307559	19360117	0.000000	0.000039	0.000000
+chr22	19360117	19360433	0.000000	0.793817	0.000000
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diff -r 000000000000 -r a41d96fc0b20 test-data/CTCF_PE_CTRL_chr22.bam
Binary file test-data/CTCF_PE_CTRL_chr22.bam has changed
diff -r 000000000000 -r a41d96fc0b20 test-data/CTCF_PE_ChIP_chr22.bam
Binary file test-data/CTCF_PE_ChIP_chr22.bam has changed
diff -r 000000000000 -r a41d96fc0b20 test-data/atac_out.encodepeak
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/atac_out.encodepeak	Mon Jul 15 09:43:27 2019 -0400
@@ -0,0 +1,1720 @@
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+chr22	50562570	50562711	peak_1700	1000	.	2545.010010	25.087999	19.350746	70
+chr22	50562977	50563259	peak_1701	1000	.	3609.943359	25.087999	19.350746	50
+chr22	50570532	50570675	peak_1702	1000	.	2581.109619	25.087999	19.350746	71
+chr22	50582639	50583150	peak_1703	1000	.	8841.138672	30.700907	22.760651	407
+chr22	50596834	50596934	peak_1704	1000	.	1804.971680	25.087999	19.350746	50
+chr22	50597090	50597190	peak_1705	1000	.	1804.971680	25.087999	19.350746	50
+chr22	50609140	50609240	peak_1706	1000	.	1804.971680	25.087999	19.350746	50
+chr22	50609362	50609462	peak_1707	1000	.	1804.971680	25.087999	19.350746	50
+chr22	50610464	50610564	peak_1708	1000	.	1804.971680	25.087999	19.350746	50
+chr22	50610671	50610771	peak_1709	1000	.	1804.971680	25.087999	19.350746	50
+chr22	50621779	50622067	peak_1710	1000	.	3609.943359	25.087999	19.350746	50
+chr22	50622844	50623203	peak_1711	1000	.	5414.915039	25.087999	19.350746	50
+chr22	50623435	50623535	peak_1712	1000	.	1804.971680	25.087999	19.350746	50
+chr22	50628191	50628334	peak_1713	1000	.	2581.109619	25.087999	19.350746	71
+chr22	50675198	50675298	peak_1714	1000	.	1804.971680	25.087999	19.350746	50
+chr22	50675430	50675530	peak_1715	1000	.	1804.971680	25.087999	19.350746	50
+chr22	50708813	50709078	peak_1716	1000	.	3609.943359	25.087999	19.350746	50
+chr22	50722110	50722384	peak_1717	1000	.	3609.943359	25.087999	19.350746	50
+chr22	50724764	50725016	peak_1718	1000	.	3609.943359	25.087999	19.350746	50
+chr22	50754667	50754811	peak_1719	1000	.	2599.159180	25.087999	19.350746	72
diff -r 000000000000 -r a41d96fc0b20 test-data/atac_out2.bedgraph
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/atac_out2.bedgraph	Mon Jul 15 09:43:27 2019 -0400
@@ -0,0 +1,4769 @@
+chr	start	end	experimental	control	-log(p)	-log(q)	signif
+chr1	0	248956422	0.000000	0.000082	0.000000	0.000000
+chr10	0	133797422	0.000000	0.000082	0.000000	0.000000
+chr11	0	135086622	0.000000	0.000082	0.000000	0.000000
+chr11_KI270721v1_random	0	100316	0.000000	0.000082	0.000000	0.000000
+chr12	0	133275309	0.000000	0.000082	0.000000	0.000000
+chr13	0	114364328	0.000000	0.000082	0.000000	0.000000
+chr14	0	107043718	0.000000	0.000082	0.000000	0.000000
+chr14_GL000009v2_random	0	201709	0.000000	0.000082	0.000000	0.000000
+chr14_GL000225v1_random	0	211173	0.000000	0.000082	0.000000	0.000000
+chr14_KI270722v1_random	0	194050	0.000000	0.000082	0.000000	0.000000
+chr14_GL000194v1_random	0	191469	0.000000	0.000082	0.000000	0.000000
+chr14_KI270723v1_random	0	38115	0.000000	0.000082	0.000000	0.000000
+chr14_KI270724v1_random	0	39555	0.000000	0.000082	0.000000	0.000000
+chr14_KI270725v1_random	0	172810	0.000000	0.000082	0.000000	0.000000
+chr14_KI270726v1_random	0	43739	0.000000	0.000082	0.000000	0.000000
+chr15	0	101991189	0.000000	0.000082	0.000000	0.000000
+chr15_KI270727v1_random	0	448248	0.000000	0.000082	0.000000	0.000000
+chr16	0	90338345	0.000000	0.000082	0.000000	0.000000
+chr16_KI270728v1_random	0	1872759	0.000000	0.000082	0.000000	0.000000
+chr17	0	83257441	0.000000	0.000082	0.000000	0.000000
+chr17_GL000205v2_random	0	185591	0.000000	0.000082	0.000000	0.000000
+chr17_KI270729v1_random	0	280839	0.000000	0.000082	0.000000	0.000000
+chr17_KI270730v1_random	0	112551	0.000000	0.000082	0.000000	0.000000
+chr18	0	80373285	0.000000	0.000082	0.000000	0.000000
+chr19	0	58617616	0.000000	0.000082	0.000000	0.000000
+chr1_KI270706v1_random	0	175055	0.000000	0.000082	0.000000	0.000000
+chr1_KI270707v1_random	0	32032	0.000000	0.000082	0.000000	0.000000
+chr1_KI270708v1_random	0	127682	0.000000	0.000082	0.000000	0.000000
+chr1_KI270709v1_random	0	66860	0.000000	0.000082	0.000000	0.000000
+chr1_KI270710v1_random	0	40176	0.000000	0.000082	0.000000	0.000000
+chr1_KI270711v1_random	0	42210	0.000000	0.000082	0.000000	0.000000
+chr1_KI270712v1_random	0	176043	0.000000	0.000082	0.000000	0.000000
+chr1_KI270713v1_random	0	40745	0.000000	0.000082	0.000000	0.000000
+chr1_KI270714v1_random	0	41717	0.000000	0.000082	0.000000	0.000000
+chr2	0	242193529	0.000000	0.000082	0.000000	0.000000
+chr20	0	64444167	0.000000	0.000082	0.000000	0.000000
+chr21	0	46709983	0.000000	0.000082	0.000000	0.000000
+chr22	0	10741211	0.000000	0.000082	0.000000	0.000000
+chr22	10741211	10741383	1.000000	0.000082	25.087999	19.350746	*
+chr22	10741383	10783762	0.000000	0.000082	0.000000	0.000000
+chr22	10783762	10783951	1.000000	0.000082	25.087999	19.350746	*
+chr22	10783951	10941132	0.000000	0.000082	0.000000	0.000000
+chr22	10941132	10941232	1.000000	0.000082	25.087999	19.350746	*
+chr22	10941232	10941258	0.000000	0.000082	0.000000	0.000000
+chr22	10941258	10941358	1.000000	0.000082	25.087999	19.350746	*
+chr22	10941358	11288260	0.000000	0.000082	0.000000	0.000000
+chr22	11288260	11288400	1.000000	0.000082	25.087999	19.350746	*
+chr22	11288400	11294541	0.000000	0.000082	0.000000	0.000000
+chr22	11294541	11294641	1.000000	0.000082	25.087999	19.350746	*
+chr22	11294641	11294678	0.000000	0.000082	0.000000	0.000000
+chr22	11294678	11294778	1.000000	0.000082	25.087999	19.350746	*
+chr22	11294778	11308120	0.000000	0.000082	0.000000	0.000000
+chr22	11308120	11308220	1.000000	0.000082	25.087999	19.350746	*
+chr22	11308220	11308290	0.000000	0.000082	0.000000	0.000000
+chr22	11308290	11308390	1.000000	0.000082	25.087999	19.350746	*
+chr22	11308390	11353133	0.000000	0.000082	0.000000	0.000000
+chr22	11353133	11353270	1.000000	0.000082	25.087999	19.350746	*
+chr22	11353270	11552745	0.000000	0.000082	0.000000	0.000000
+chr22	11552745	11552929	1.000000	0.000082	25.087999	19.350746	*
+chr22	11552929	11968830	0.000000	0.000082	0.000000	0.000000
+chr22	11968830	11968965	1.000000	0.000082	25.087999	19.350746	*
+chr22	11968965	12368335	0.000000	0.000082	0.000000	0.000000
+chr22	12368335	12368524	1.000000	0.000082	25.087999	19.350746	*
+chr22	12368524	12602352	0.000000	0.000082	0.000000	0.000000
+chr22	12602352	12602487	1.000000	0.000082	25.087999	19.350746	*
+chr22	12602487	12604334	0.000000	0.000082	0.000000	0.000000
+chr22	12604334	12604434	1.000000	0.000082	25.087999	19.350746	*
+chr22	12604434	12604536	0.000000	0.000082	0.000000	0.000000
+chr22	12604536	12604636	1.000000	0.000082	25.087999	19.350746	*
+chr22	12604636	12636264	0.000000	0.000082	0.000000	0.000000
+chr22	12636264	12636400	1.000000	0.000082	25.087999	19.350746	*
+chr22	12636400	12721963	0.000000	0.000082	0.000000	0.000000
+chr22	12721963	12722063	1.000000	0.000082	25.087999	19.350746	*
+chr22	12722063	12722141	0.000000	0.000082	0.000000	0.000000
+chr22	12722141	12722241	1.000000	0.000082	25.087999	19.350746	*
+chr22	12722241	16099521	0.000000	0.000082	0.000000	0.000000
+chr22	16099521	16099665	1.000000	0.000082	25.087999	19.350746	*
+chr22	16099665	16415232	0.000000	0.000082	0.000000	0.000000
+chr22	16415232	16415332	1.000000	0.000082	25.087999	19.350746	*
+chr22	16415332	16415515	0.000000	0.000082	0.000000	0.000000
+chr22	16415515	16415615	1.000000	0.000082	25.087999	19.350746	*
+chr22	16415615	16582465	0.000000	0.000082	0.000000	0.000000
+chr22	16582465	16582565	1.000000	0.000082	25.087999	19.350746	*
+chr22	16582565	16582584	0.000000	0.000082	0.000000	0.000000
+chr22	16582584	16582684	1.000000	0.000082	25.087999	19.350746	*
+chr22	16582684	16597062	0.000000	0.000082	0.000000	0.000000
+chr22	16597062	16597205	1.000000	0.000082	25.087999	19.350746	*
+chr22	16597205	16609678	0.000000	0.000082	0.000000	0.000000
+chr22	16609678	16609874	1.000000	0.000082	25.087999	19.350746	*
+chr22	16609874	16670291	0.000000	0.000082	0.000000	0.000000
+chr22	16670291	16670391	1.000000	0.000082	25.087999	19.350746	*
+chr22	16670391	16670516	0.000000	0.000082	0.000000	0.000000
+chr22	16670516	16670616	1.000000	0.000082	25.087999	19.350746	*
+chr22	16670616	16806452	0.000000	0.000082	0.000000	0.000000
+chr22	16806452	16806552	1.000000	0.000082	25.087999	19.350746	*
+chr22	16806552	16806583	0.000000	0.000082	0.000000	0.000000
+chr22	16806583	16806683	1.000000	0.000082	25.087999	19.350746	*
+chr22	16806683	16922061	0.000000	0.000082	0.000000	0.000000
+chr22	16922061	16922193	1.000000	0.000082	25.087999	19.350746	*
+chr22	16922193	17075614	0.000000	0.000082	0.000000	0.000000
+chr22	17075614	17075761	1.000000	0.000082	25.087999	19.350746	*
+chr22	17075761	17085376	0.000000	0.000082	0.000000	0.000000
+chr22	17085376	17085459	1.000000	0.000082	25.087999	19.350746	*
+chr22	17085459	17085528	2.000000	0.000082	28.561464	21.684465	*
+chr22	17085528	17085559	1.000000	0.000082	25.087999	19.350746	*
+chr22	17085559	17085622	0.000000	0.000082	0.000000	0.000000
+chr22	17085622	17085722	1.000000	0.000082	25.087999	19.350746	*
+chr22	17085722	17107363	0.000000	0.000082	0.000000	0.000000
+chr22	17107363	17107463	1.000000	0.000082	25.087999	19.350746	*
+chr22	17107463	17107537	0.000000	0.000082	0.000000	0.000000
+chr22	17107537	17107637	1.000000	0.000082	25.087999	19.350746	*
+chr22	17107637	17121710	0.000000	0.000082	0.000000	0.000000
+chr22	17121710	17121897	1.000000	0.000082	25.087999	19.350746	*
+chr22	17121897	17158863	0.000000	0.000082	0.000000	0.000000
+chr22	17158863	17158963	1.000000	0.000082	25.087999	19.350746	*
+chr22	17158963	17159194	0.000000	0.000082	0.000000	0.000000
+chr22	17159194	17159294	1.000000	0.000082	25.087999	19.350746	*
+chr22	17159294	17166346	0.000000	0.000082	0.000000	0.000000
+chr22	17166346	17166446	1.000000	0.000082	25.087999	19.350746	*
+chr22	17166446	17166596	0.000000	0.000082	0.000000	0.000000
+chr22	17166596	17166696	1.000000	0.000082	25.087999	19.350746	*
+chr22	17166696	17243742	0.000000	0.000082	0.000000	0.000000
+chr22	17243742	17243842	1.000000	0.000082	25.087999	19.350746	*
+chr22	17243842	17243931	0.000000	0.000082	0.000000	0.000000
+chr22	17243931	17244031	1.000000	0.000082	25.087999	19.350746	*
+chr22	17244031	17260757	0.000000	0.000082	0.000000	0.000000
+chr22	17260757	17260857	1.000000	0.000082	25.087999	19.350746	*
+chr22	17260857	17260899	0.000000	0.000082	0.000000	0.000000
+chr22	17260899	17260999	1.000000	0.000082	25.087999	19.350746	*
+chr22	17260999	17368675	0.000000	0.000082	0.000000	0.000000
+chr22	17368675	17368775	1.000000	0.000082	25.087999	19.350746	*
+chr22	17368775	17368902	0.000000	0.000082	0.000000	0.000000
+chr22	17368902	17369002	1.000000	0.000082	25.087999	19.350746	*
+chr22	17369002	17375500	0.000000	0.000082	0.000000	0.000000
+chr22	17375500	17375635	1.000000	0.000082	25.087999	19.350746	*
+chr22	17375635	17397311	0.000000	0.000082	0.000000	0.000000
+chr22	17397311	17397475	1.000000	0.000082	25.087999	19.350746	*
+chr22	17397475	17433017	0.000000	0.000082	0.000000	0.000000
+chr22	17433017	17433117	1.000000	0.000082	25.087999	19.350746	*
+chr22	17433117	17433133	0.000000	0.000082	0.000000	0.000000
+chr22	17433133	17433233	1.000000	0.000082	25.087999	19.350746	*
+chr22	17433233	17474600	0.000000	0.000082	0.000000	0.000000
+chr22	17474600	17474734	1.000000	0.000082	25.087999	19.350746	*
+chr22	17474734	17541883	0.000000	0.000082	0.000000	0.000000
+chr22	17541883	17542069	1.000000	0.000082	25.087999	19.350746	*
+chr22	17542069	17549638	0.000000	0.000082	0.000000	0.000000
+chr22	17549638	17549819	1.000000	0.000082	25.087999	19.350746	*
+chr22	17549819	17552085	0.000000	0.000082	0.000000	0.000000
+chr22	17552085	17552185	1.000000	0.000082	25.087999	19.350746	*
+chr22	17552185	17552287	0.000000	0.000082	0.000000	0.000000
+chr22	17552287	17552387	1.000000	0.000082	25.087999	19.350746	*
+chr22	17552387	17570180	0.000000	0.000082	0.000000	0.000000
+chr22	17570180	17570280	1.000000	0.000082	25.087999	19.350746	*
+chr22	17570280	17570309	0.000000	0.000082	0.000000	0.000000
+chr22	17570309	17570409	1.000000	0.000082	25.087999	19.350746	*
+chr22	17570409	17576283	0.000000	0.000082	0.000000	0.000000
+chr22	17576283	17576287	1.000000	0.000082	25.087999	19.350746	*
+chr22	17576287	17576383	2.000000	0.000082	28.561464	21.684465	*
+chr22	17576383	17576387	1.000000	0.000082	25.087999	19.350746	*
+chr22	17576387	17576409	0.000000	0.000082	0.000000	0.000000
+chr22	17576409	17576427	1.000000	0.000082	25.087999	19.350746	*
+chr22	17576427	17576509	2.000000	0.000082	28.561464	21.684465	*
+chr22	17576509	17576527	1.000000	0.000082	25.087999	19.350746	*
+chr22	17576527	17595913	0.000000	0.000082	0.000000	0.000000
+chr22	17595913	17596013	1.000000	0.000082	25.087999	19.350746	*
+chr22	17596013	17596134	0.000000	0.000082	0.000000	0.000000
+chr22	17596134	17596234	1.000000	0.000082	25.087999	19.350746	*
+chr22	17596234	17628693	0.000000	0.000082	0.000000	0.000000
+chr22	17628693	17628793	1.000000	0.000082	25.087999	19.350746	*
+chr22	17628793	17629351	0.000000	0.000082	0.000000	0.000000
+chr22	17629351	17629451	1.000000	0.000082	25.087999	19.350746	*
+chr22	17629451	17649951	0.000000	0.000082	0.000000	0.000000
+chr22	17649951	17650051	1.000000	0.000082	25.087999	19.350746	*
+chr22	17650051	17650057	0.000000	0.000082	0.000000	0.000000
+chr22	17650057	17650157	1.000000	0.000082	25.087999	19.350746	*
+chr22	17650157	17672156	0.000000	0.000082	0.000000	0.000000
+chr22	17672156	17672298	1.000000	0.000082	25.087999	19.350746	*
+chr22	17672298	17706566	0.000000	0.000082	0.000000	0.000000
+chr22	17706566	17706666	1.000000	0.000082	25.087999	19.350746	*
+chr22	17706666	17706735	0.000000	0.000082	0.000000	0.000000
+chr22	17706735	17706835	1.000000	0.000082	25.087999	19.350746	*
+chr22	17706835	17712516	0.000000	0.000082	0.000000	0.000000
+chr22	17712516	17712673	1.000000	0.000082	25.087999	19.350746	*
+chr22	17712673	17743921	0.000000	0.000082	0.000000	0.000000
+chr22	17743921	17744021	1.000000	0.000082	25.087999	19.350746	*
+chr22	17744021	17744126	0.000000	0.000082	0.000000	0.000000
+chr22	17744126	17744226	1.000000	0.000082	25.087999	19.350746	*
+chr22	17744226	17785404	0.000000	0.000082	0.000000	0.000000
+chr22	17785404	17785504	1.000000	0.000082	25.087999	19.350746	*
+chr22	17785504	17785605	0.000000	0.000082	0.000000	0.000000
+chr22	17785605	17785705	1.000000	0.000082	25.087999	19.350746	*
+chr22	17785705	17804026	0.000000	0.000082	0.000000	0.000000
+chr22	17804026	17804126	1.000000	0.000082	25.087999	19.350746	*
+chr22	17804126	17804459	0.000000	0.000082	0.000000	0.000000
+chr22	17804459	17804559	1.000000	0.000082	25.087999	19.350746	*
+chr22	17804559	17813432	0.000000	0.000082	0.000000	0.000000
+chr22	17813432	17813569	1.000000	0.000082	25.087999	19.350746	*
+chr22	17813569	17823554	0.000000	0.000082	0.000000	0.000000
+chr22	17823554	17823654	1.000000	0.000082	25.087999	19.350746	*
+chr22	17823654	17823869	0.000000	0.000082	0.000000	0.000000
+chr22	17823869	17823969	1.000000	0.000082	25.087999	19.350746	*
+chr22	17823969	17829403	0.000000	0.000082	0.000000	0.000000
+chr22	17829403	17829503	1.000000	0.000082	25.087999	19.350746	*
+chr22	17829503	17829703	0.000000	0.000082	0.000000	0.000000
+chr22	17829703	17829803	1.000000	0.000082	25.087999	19.350746	*
+chr22	17829803	17847718	0.000000	0.000082	0.000000	0.000000
+chr22	17847718	17847860	1.000000	0.000082	25.087999	19.350746	*
+chr22	17847860	17858261	0.000000	0.000082	0.000000	0.000000
+chr22	17858261	17858361	1.000000	0.000082	25.087999	19.350746	*
+chr22	17858361	17858378	0.000000	0.000082	0.000000	0.000000
+chr22	17858378	17858478	1.000000	0.000082	25.087999	19.350746	*
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+chr19_KI270885v1_alt	0	171027	0.000000	0.000082	0.000000	0.000000
+chr19_KI270886v1_alt	0	204239	0.000000	0.000082	0.000000	0.000000
+chr19_KI270887v1_alt	0	209512	0.000000	0.000082	0.000000	0.000000
+chr19_KI270888v1_alt	0	155532	0.000000	0.000082	0.000000	0.000000
+chr19_KI270889v1_alt	0	170698	0.000000	0.000082	0.000000	0.000000
+chr19_KI270890v1_alt	0	184499	0.000000	0.000082	0.000000	0.000000
+chr19_KI270891v1_alt	0	170680	0.000000	0.000082	0.000000	0.000000
+chr1_KI270892v1_alt	0	162212	0.000000	0.000082	0.000000	0.000000
+chr2_KI270894v1_alt	0	214158	0.000000	0.000082	0.000000	0.000000
+chr2_KI270893v1_alt	0	161218	0.000000	0.000082	0.000000	0.000000
+chr3_KI270895v1_alt	0	162896	0.000000	0.000082	0.000000	0.000000
+chr4_KI270896v1_alt	0	378547	0.000000	0.000082	0.000000	0.000000
+chr5_KI270897v1_alt	0	1144418	0.000000	0.000082	0.000000	0.000000
+chr5_KI270898v1_alt	0	130957	0.000000	0.000082	0.000000	0.000000
+chr6_GL000251v2_alt	0	4795265	0.000000	0.000082	0.000000	0.000000
+chr7_KI270899v1_alt	0	190869	0.000000	0.000082	0.000000	0.000000
+chr8_KI270901v1_alt	0	136959	0.000000	0.000082	0.000000	0.000000
+chr8_KI270900v1_alt	0	318687	0.000000	0.000082	0.000000	0.000000
+chr11_KI270902v1_alt	0	106711	0.000000	0.000082	0.000000	0.000000
+chr11_KI270903v1_alt	0	214625	0.000000	0.000082	0.000000	0.000000
+chr12_KI270904v1_alt	0	572349	0.000000	0.000082	0.000000	0.000000
+chr15_KI270906v1_alt	0	196384	0.000000	0.000082	0.000000	0.000000
+chr15_KI270905v1_alt	0	5161414	0.000000	0.000082	0.000000	0.000000
+chr17_KI270907v1_alt	0	137721	0.000000	0.000082	0.000000	0.000000
+chr17_KI270910v1_alt	0	157099	0.000000	0.000082	0.000000	0.000000
+chr17_KI270909v1_alt	0	325800	0.000000	0.000082	0.000000	0.000000
+chr17_JH159148v1_alt	0	88070	0.000000	0.000082	0.000000	0.000000
+chr17_KI270908v1_alt	0	1423190	0.000000	0.000082	0.000000	0.000000
+chr18_KI270912v1_alt	0	174061	0.000000	0.000082	0.000000	0.000000
+chr18_KI270911v1_alt	0	157710	0.000000	0.000082	0.000000	0.000000
+chr19_GL949747v2_alt	0	729520	0.000000	0.000082	0.000000	0.000000
+chr22_KB663609v1_alt	0	74013	0.000000	0.000082	0.000000	0.000000
+chrX_KI270913v1_alt	0	274009	0.000000	0.000082	0.000000	0.000000
+chr19_KI270914v1_alt	0	205194	0.000000	0.000082	0.000000	0.000000
+chr19_KI270915v1_alt	0	170665	0.000000	0.000082	0.000000	0.000000
+chr19_KI270916v1_alt	0	184516	0.000000	0.000082	0.000000	0.000000
+chr19_KI270917v1_alt	0	190932	0.000000	0.000082	0.000000	0.000000
+chr19_KI270918v1_alt	0	123111	0.000000	0.000082	0.000000	0.000000
+chr19_KI270919v1_alt	0	170701	0.000000	0.000082	0.000000	0.000000
+chr19_KI270920v1_alt	0	198005	0.000000	0.000082	0.000000	0.000000
+chr19_KI270921v1_alt	0	282224	0.000000	0.000082	0.000000	0.000000
+chr19_KI270922v1_alt	0	187935	0.000000	0.000082	0.000000	0.000000
+chr19_KI270923v1_alt	0	189352	0.000000	0.000082	0.000000	0.000000
+chr3_KI270924v1_alt	0	166540	0.000000	0.000082	0.000000	0.000000
+chr4_KI270925v1_alt	0	555799	0.000000	0.000082	0.000000	0.000000
+chr6_GL000252v2_alt	0	4604811	0.000000	0.000082	0.000000	0.000000
+chr8_KI270926v1_alt	0	229282	0.000000	0.000082	0.000000	0.000000
+chr11_KI270927v1_alt	0	218612	0.000000	0.000082	0.000000	0.000000
+chr19_GL949748v2_alt	0	1064304	0.000000	0.000082	0.000000	0.000000
+chr22_KI270928v1_alt	0	176103	0.000000	0.000082	0.000000	0.000000
+chr19_KI270929v1_alt	0	186203	0.000000	0.000082	0.000000	0.000000
+chr19_KI270930v1_alt	0	200773	0.000000	0.000082	0.000000	0.000000
+chr19_KI270931v1_alt	0	170148	0.000000	0.000082	0.000000	0.000000
+chr19_KI270932v1_alt	0	215732	0.000000	0.000082	0.000000	0.000000
+chr19_KI270933v1_alt	0	170537	0.000000	0.000082	0.000000	0.000000
+chr19_GL000209v2_alt	0	177381	0.000000	0.000082	0.000000	0.000000
+chr3_KI270934v1_alt	0	163458	0.000000	0.000082	0.000000	0.000000
+chr6_GL000253v2_alt	0	4677643	0.000000	0.000082	0.000000	0.000000
+chr19_GL949749v2_alt	0	1091841	0.000000	0.000082	0.000000	0.000000
+chr3_KI270935v1_alt	0	197351	0.000000	0.000082	0.000000	0.000000
+chr6_GL000254v2_alt	0	4827813	0.000000	0.000082	0.000000	0.000000
+chr19_GL949750v2_alt	0	1066390	0.000000	0.000082	0.000000	0.000000
+chr3_KI270936v1_alt	0	164170	0.000000	0.000082	0.000000	0.000000
+chr6_GL000255v2_alt	0	4606388	0.000000	0.000082	0.000000	0.000000
+chr19_GL949751v2_alt	0	1002683	0.000000	0.000082	0.000000	0.000000
+chr3_KI270937v1_alt	0	165607	0.000000	0.000082	0.000000	0.000000
+chr6_GL000256v2_alt	0	4929269	0.000000	0.000082	0.000000	0.000000
+chr19_GL949752v1_alt	0	987100	0.000000	0.000082	0.000000	0.000000
+chr6_KI270758v1_alt	0	76752	0.000000	0.000082	0.000000	0.000000
+chr19_GL949753v2_alt	0	796479	0.000000	0.000082	0.000000	0.000000
+chr19_KI270938v1_alt	0	1066800	0.000000	0.000082	0.000000	0.000000
+chrM	0	16569	0.000000	0.000082	0.000000	0.000000
+chrUn_KI270302v1	0	2274	0.000000	0.000082	0.000000	0.000000
+chrUn_KI270304v1	0	2165	0.000000	0.000082	0.000000	0.000000
+chrUn_KI270303v1	0	1942	0.000000	0.000082	0.000000	0.000000
+chrUn_KI270305v1	0	1472	0.000000	0.000082	0.000000	0.000000
+chrUn_KI270322v1	0	21476	0.000000	0.000082	0.000000	0.000000
+chrUn_KI270320v1	0	4416	0.000000	0.000082	0.000000	0.000000
+chrUn_KI270310v1	0	1201	0.000000	0.000082	0.000000	0.000000
+chrUn_KI270316v1	0	1444	0.000000	0.000082	0.000000	0.000000
+chrUn_KI270315v1	0	2276	0.000000	0.000082	0.000000	0.000000
+chrUn_KI270312v1	0	998	0.000000	0.000082	0.000000	0.000000
+chrUn_KI270311v1	0	12399	0.000000	0.000082	0.000000	0.000000
+chrUn_KI270317v1	0	37690	0.000000	0.000082	0.000000	0.000000
+chrUn_KI270412v1	0	1179	0.000000	0.000082	0.000000	0.000000
+chrUn_KI270411v1	0	2646	0.000000	0.000082	0.000000	0.000000
+chrUn_KI270414v1	0	2489	0.000000	0.000082	0.000000	0.000000
+chrUn_KI270419v1	0	1029	0.000000	0.000082	0.000000	0.000000
+chrUn_KI270418v1	0	2145	0.000000	0.000082	0.000000	0.000000
+chrUn_KI270420v1	0	2321	0.000000	0.000082	0.000000	0.000000
+chrUn_KI270424v1	0	2140	0.000000	0.000082	0.000000	0.000000
+chrUn_KI270417v1	0	2043	0.000000	0.000082	0.000000	0.000000
+chrUn_KI270422v1	0	1445	0.000000	0.000082	0.000000	0.000000
+chrUn_KI270423v1	0	981	0.000000	0.000082	0.000000	0.000000
+chrUn_KI270425v1	0	1884	0.000000	0.000082	0.000000	0.000000
+chrUn_KI270429v1	0	1361	0.000000	0.000082	0.000000	0.000000
+chrUn_KI270442v1	0	392061	0.000000	0.000082	0.000000	0.000000
+chrUn_KI270466v1	0	1233	0.000000	0.000082	0.000000	0.000000
+chrUn_KI270465v1	0	1774	0.000000	0.000082	0.000000	0.000000
+chrUn_KI270467v1	0	3920	0.000000	0.000082	0.000000	0.000000
+chrUn_KI270435v1	0	92983	0.000000	0.000082	0.000000	0.000000
+chrUn_KI270438v1	0	112505	0.000000	0.000082	0.000000	0.000000
+chrUn_KI270468v1	0	4055	0.000000	0.000082	0.000000	0.000000
+chrUn_KI270510v1	0	2415	0.000000	0.000082	0.000000	0.000000
+chrUn_KI270509v1	0	2318	0.000000	0.000082	0.000000	0.000000
+chrUn_KI270518v1	0	2186	0.000000	0.000082	0.000000	0.000000
+chrUn_KI270508v1	0	1951	0.000000	0.000082	0.000000	0.000000
+chrUn_KI270516v1	0	1300	0.000000	0.000082	0.000000	0.000000
+chrUn_KI270512v1	0	22689	0.000000	0.000082	0.000000	0.000000
+chrUn_KI270519v1	0	138126	0.000000	0.000082	0.000000	0.000000
+chrUn_KI270522v1	0	5674	0.000000	0.000082	0.000000	0.000000
+chrUn_KI270511v1	0	8127	0.000000	0.000082	0.000000	0.000000
+chrUn_KI270515v1	0	6361	0.000000	0.000082	0.000000	0.000000
+chrUn_KI270507v1	0	5353	0.000000	0.000082	0.000000	0.000000
+chrUn_KI270517v1	0	3253	0.000000	0.000082	0.000000	0.000000
+chrUn_KI270529v1	0	1899	0.000000	0.000082	0.000000	0.000000
+chrUn_KI270528v1	0	2983	0.000000	0.000082	0.000000	0.000000
+chrUn_KI270530v1	0	2168	0.000000	0.000082	0.000000	0.000000
+chrUn_KI270539v1	0	993	0.000000	0.000082	0.000000	0.000000
+chrUn_KI270538v1	0	91309	0.000000	0.000082	0.000000	0.000000
+chrUn_KI270544v1	0	1202	0.000000	0.000082	0.000000	0.000000
+chrUn_KI270548v1	0	1599	0.000000	0.000082	0.000000	0.000000
+chrUn_KI270583v1	0	1400	0.000000	0.000082	0.000000	0.000000
+chrUn_KI270587v1	0	2969	0.000000	0.000082	0.000000	0.000000
+chrUn_KI270580v1	0	1553	0.000000	0.000082	0.000000	0.000000
+chrUn_KI270581v1	0	7046	0.000000	0.000082	0.000000	0.000000
+chrUn_KI270579v1	0	31033	0.000000	0.000082	0.000000	0.000000
+chrUn_KI270589v1	0	44474	0.000000	0.000082	0.000000	0.000000
+chrUn_KI270590v1	0	4685	0.000000	0.000082	0.000000	0.000000
+chrUn_KI270584v1	0	4513	0.000000	0.000082	0.000000	0.000000
+chrUn_KI270582v1	0	6504	0.000000	0.000082	0.000000	0.000000
+chrUn_KI270588v1	0	6158	0.000000	0.000082	0.000000	0.000000
+chrUn_KI270593v1	0	3041	0.000000	0.000082	0.000000	0.000000
+chrUn_KI270591v1	0	5796	0.000000	0.000082	0.000000	0.000000
+chrUn_KI270330v1	0	1652	0.000000	0.000082	0.000000	0.000000
+chrUn_KI270329v1	0	1040	0.000000	0.000082	0.000000	0.000000
+chrUn_KI270334v1	0	1368	0.000000	0.000082	0.000000	0.000000
+chrUn_KI270333v1	0	2699	0.000000	0.000082	0.000000	0.000000
+chrUn_KI270335v1	0	1048	0.000000	0.000082	0.000000	0.000000
+chrUn_KI270338v1	0	1428	0.000000	0.000082	0.000000	0.000000
+chrUn_KI270340v1	0	1428	0.000000	0.000082	0.000000	0.000000
+chrUn_KI270336v1	0	1026	0.000000	0.000082	0.000000	0.000000
+chrUn_KI270337v1	0	1121	0.000000	0.000082	0.000000	0.000000
+chrUn_KI270363v1	0	1803	0.000000	0.000082	0.000000	0.000000
+chrUn_KI270364v1	0	2855	0.000000	0.000082	0.000000	0.000000
+chrUn_KI270362v1	0	3530	0.000000	0.000082	0.000000	0.000000
+chrUn_KI270366v1	0	8320	0.000000	0.000082	0.000000	0.000000
+chrUn_KI270378v1	0	1048	0.000000	0.000082	0.000000	0.000000
+chrUn_KI270379v1	0	1045	0.000000	0.000082	0.000000	0.000000
+chrUn_KI270389v1	0	1298	0.000000	0.000082	0.000000	0.000000
+chrUn_KI270390v1	0	2387	0.000000	0.000082	0.000000	0.000000
+chrUn_KI270387v1	0	1537	0.000000	0.000082	0.000000	0.000000
+chrUn_KI270395v1	0	1143	0.000000	0.000082	0.000000	0.000000
+chrUn_KI270396v1	0	1880	0.000000	0.000082	0.000000	0.000000
+chrUn_KI270388v1	0	1216	0.000000	0.000082	0.000000	0.000000
+chrUn_KI270394v1	0	970	0.000000	0.000082	0.000000	0.000000
+chrUn_KI270386v1	0	1788	0.000000	0.000082	0.000000	0.000000
+chrUn_KI270391v1	0	1484	0.000000	0.000082	0.000000	0.000000
+chrUn_KI270383v1	0	1750	0.000000	0.000082	0.000000	0.000000
+chrUn_KI270393v1	0	1308	0.000000	0.000082	0.000000	0.000000
+chrUn_KI270384v1	0	1658	0.000000	0.000082	0.000000	0.000000
+chrUn_KI270392v1	0	971	0.000000	0.000082	0.000000	0.000000
+chrUn_KI270381v1	0	1930	0.000000	0.000082	0.000000	0.000000
+chrUn_KI270385v1	0	990	0.000000	0.000082	0.000000	0.000000
+chrUn_KI270382v1	0	4215	0.000000	0.000082	0.000000	0.000000
+chrUn_KI270376v1	0	1136	0.000000	0.000082	0.000000	0.000000
+chrUn_KI270374v1	0	2656	0.000000	0.000082	0.000000	0.000000
+chrUn_KI270372v1	0	1650	0.000000	0.000082	0.000000	0.000000
+chrUn_KI270373v1	0	1451	0.000000	0.000082	0.000000	0.000000
+chrUn_KI270375v1	0	2378	0.000000	0.000082	0.000000	0.000000
+chrUn_KI270371v1	0	2805	0.000000	0.000082	0.000000	0.000000
+chrUn_KI270448v1	0	7992	0.000000	0.000082	0.000000	0.000000
+chrUn_KI270521v1	0	7642	0.000000	0.000082	0.000000	0.000000
+chrUn_GL000195v1	0	182896	0.000000	0.000082	0.000000	0.000000
+chrUn_GL000219v1	0	179198	0.000000	0.000082	0.000000	0.000000
+chrUn_GL000220v1	0	161802	0.000000	0.000082	0.000000	0.000000
+chrUn_GL000224v1	0	179693	0.000000	0.000082	0.000000	0.000000
+chrUn_KI270741v1	0	157432	0.000000	0.000082	0.000000	0.000000
+chrUn_GL000226v1	0	15008	0.000000	0.000082	0.000000	0.000000
+chrUn_GL000213v1	0	164239	0.000000	0.000082	0.000000	0.000000
+chrUn_KI270743v1	0	210658	0.000000	0.000082	0.000000	0.000000
+chrUn_KI270744v1	0	168472	0.000000	0.000082	0.000000	0.000000
+chrUn_KI270745v1	0	41891	0.000000	0.000082	0.000000	0.000000
+chrUn_KI270746v1	0	66486	0.000000	0.000082	0.000000	0.000000
+chrUn_KI270747v1	0	198735	0.000000	0.000082	0.000000	0.000000
+chrUn_KI270748v1	0	93321	0.000000	0.000082	0.000000	0.000000
+chrUn_KI270749v1	0	158759	0.000000	0.000082	0.000000	0.000000
+chrUn_KI270750v1	0	148850	0.000000	0.000082	0.000000	0.000000
+chrUn_KI270751v1	0	150742	0.000000	0.000082	0.000000	0.000000
+chrUn_KI270752v1	0	27745	0.000000	0.000082	0.000000	0.000000
+chrUn_KI270753v1	0	62944	0.000000	0.000082	0.000000	0.000000
+chrUn_KI270754v1	0	40191	0.000000	0.000082	0.000000	0.000000
+chrUn_KI270755v1	0	36723	0.000000	0.000082	0.000000	0.000000
+chrUn_KI270756v1	0	79590	0.000000	0.000082	0.000000	0.000000
+chrUn_KI270757v1	0	71251	0.000000	0.000082	0.000000	0.000000
+chrUn_GL000214v1	0	137718	0.000000	0.000082	0.000000	0.000000
+chrUn_KI270742v1	0	186739	0.000000	0.000082	0.000000	0.000000
+chrUn_GL000216v2	0	176608	0.000000	0.000082	0.000000	0.000000
+chrUn_GL000218v1	0	161147	0.000000	0.000082	0.000000	0.000000
+chrX	0	156040895	0.000000	0.000082	0.000000	0.000000
+chrY	0	57227415	0.000000	0.000082	0.000000	0.000000
+chrY_KI270740v1_random	0	37240	0.000000	0.000082	0.000000	0.000000
diff -r 000000000000 -r a41d96fc0b20 test-data/atac_out3.bedgraph
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/atac_out3.bedgraph	Mon Jul 15 09:43:27 2019 -0400
@@ -0,0 +1,4770 @@
+# experimental file: atac_test.bam; control file: NA
+chr	start	end	experimental	control	-log(p)
+chr1	0	248956422	0.000000	0.000082	0.000000
+chr10	0	133797422	0.000000	0.000082	0.000000
+chr11	0	135086622	0.000000	0.000082	0.000000
+chr11_KI270721v1_random	0	100316	0.000000	0.000082	0.000000
+chr12	0	133275309	0.000000	0.000082	0.000000
+chr13	0	114364328	0.000000	0.000082	0.000000
+chr14	0	107043718	0.000000	0.000082	0.000000
+chr14_GL000009v2_random	0	201709	0.000000	0.000082	0.000000
+chr14_GL000225v1_random	0	211173	0.000000	0.000082	0.000000
+chr14_KI270722v1_random	0	194050	0.000000	0.000082	0.000000
+chr14_GL000194v1_random	0	191469	0.000000	0.000082	0.000000
+chr14_KI270723v1_random	0	38115	0.000000	0.000082	0.000000
+chr14_KI270724v1_random	0	39555	0.000000	0.000082	0.000000
+chr14_KI270725v1_random	0	172810	0.000000	0.000082	0.000000
+chr14_KI270726v1_random	0	43739	0.000000	0.000082	0.000000
+chr15	0	101991189	0.000000	0.000082	0.000000
+chr15_KI270727v1_random	0	448248	0.000000	0.000082	0.000000
+chr16	0	90338345	0.000000	0.000082	0.000000
+chr16_KI270728v1_random	0	1872759	0.000000	0.000082	0.000000
+chr17	0	83257441	0.000000	0.000082	0.000000
+chr17_GL000205v2_random	0	185591	0.000000	0.000082	0.000000
+chr17_KI270729v1_random	0	280839	0.000000	0.000082	0.000000
+chr17_KI270730v1_random	0	112551	0.000000	0.000082	0.000000
+chr18	0	80373285	0.000000	0.000082	0.000000
+chr19	0	58617616	0.000000	0.000082	0.000000
+chr1_KI270706v1_random	0	175055	0.000000	0.000082	0.000000
+chr1_KI270707v1_random	0	32032	0.000000	0.000082	0.000000
+chr1_KI270708v1_random	0	127682	0.000000	0.000082	0.000000
+chr1_KI270709v1_random	0	66860	0.000000	0.000082	0.000000
+chr1_KI270710v1_random	0	40176	0.000000	0.000082	0.000000
+chr1_KI270711v1_random	0	42210	0.000000	0.000082	0.000000
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diff -r 000000000000 -r a41d96fc0b20 test-data/atac_out4.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/atac_out4.bed	Mon Jul 15 09:43:27 2019 -0400
@@ -0,0 +1,2160 @@
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diff -r 000000000000 -r a41d96fc0b20 test-data/atac_test.bam
Binary file test-data/atac_test.bam has changed