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+/MACS2-2.2.7.1.tar.gz
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+%global _empty_manifest_terminate_build 0
+Name:		python-MACS2
+Version:	2.2.7.1
+Release:	1
+Summary:	Model Based Analysis for ChIP-Seq data
+License:	BSD License
+URL:		http://github.com/taoliu/MACS/
+Source0:	https://mirrors.nju.edu.cn/pypi/web/packages/e2/61/85d30ecdd34525113e28cb0c5a9f393f93578165f8d848be5925c0208dfb/MACS2-2.2.7.1.tar.gz
+BuildArch:	noarch
+
+
+%description
+`callpeak` | Main MACS2 Function to call peaks from alignment results.
+`bdgpeakcall` | Call peaks from bedGraph output.
+`bdgbroadcall` | Call broad peaks from bedGraph output.
+`bdgcmp` | Comparing two signal tracks in bedGraph format.
+`bdgopt` | Operate the score column of bedGraph file.
+`cmbreps` | Combine BEDGraphs of scores from replicates.
+`bdgdiff` | Differential peak detection based on paired four bedGraph files.
+`filterdup` | Remove duplicate reads, then save in BED/BEDPE format.
+`predictd` | Predict d or fragment size from alignment results.
+`pileup` | Pileup aligned reads (single-end) or fragments (paired-end)
+`randsample` | Randomly choose a number/percentage of total reads.
+`refinepeak` | Take raw reads alignment, refine peak summits.
+We only cover `callpeak` subcommand in this document. Please use
+`macs2 COMMAND -h` to see the detail description for each option of
+each subcommand.
+### Call peaks
+This is the main function in MACS2. It can be invoked by `macs2
+callpeak` . If you type this command with `-h`, you will see a full
+description of command-line options. Here we only list the essentials.
+#### Essential Options
+##### `-t`/`--treatment FILENAME`
+This is the only REQUIRED parameter for MACS. The file can be in any
+supported format -- see detail in the `--format` option. If you have
+more than one alignment file, you can specify them as `-t A B C`. MACS
+will pool up all these files together.
+##### `-c`/`--control`
+The control, genomic input or mock IP data file. Please follow the
+same direction as for `-t`/`--treatment`.
+##### `-n`/`--name`
+The name string of the experiment. MACS will use this string NAME to
+create output files like `NAME_peaks.xls`, `NAME_negative_peaks.xls`,
+`NAME_peaks.bed` , `NAME_summits.bed`, `NAME_model.r` and so on. So
+please avoid any confliction between these filenames and your existing
+files.
+##### `--outdir`
+MACS2 will save all output files into the specified folder for this
+option. A new folder will be created if necessary.
+##### `-f`/`--format FORMAT`
+Format of tag file can be `ELAND`, `BED`, `ELANDMULTI`, `ELANDEXPORT`,
+`SAM`, `BAM`, `BOWTIE`, `BAMPE`, or `BEDPE`. Default is `AUTO` which
+will allow MACS to decide the format automatically. `AUTO` is also
+useful when you combine different formats of files. Note that MACS
+can't detect `BAMPE` or `BEDPE` format with `AUTO`, and you have to
+implicitly specify the format for `BAMPE` and `BEDPE`.
+Nowadays, the most common formats are `BED` or `BAM` (including
+`BEDPE` and `BAMPE`). Our recommendation is to convert your data to
+`BED` or `BAM` first.
+Also, MACS2 can detect and read gzipped file. For example, `.bed.gz`
+file can be directly used without being uncompressed with `--format
+BED`.
+Here are detailed explanation of the recommanded formats:
+###### `BED`
+The BED format can be found at [UCSC genome browser
+website](http://genome.ucsc.edu/FAQ/FAQformat#format1).
+The essential columns in BED format input are the 1st column
+`chromosome name`, the 2nd `start position`, the 3rd `end position`,
+and the 6th, `strand`.
+Note that, for `BED` format, the 6th column of strand information is
+required by MACS. And please pay attention that the coordinates in BED
+format are zero-based and half-open. See more detail at
+[UCSC site](http://genome.ucsc.edu/FAQ/FAQtracks#tracks1).
+###### `BAM`/`SAM`
+If the format is `BAM`/`SAM`, please check the definition in
+(http://samtools.sourceforge.net/samtools.shtml).  If the `BAM` file is
+generated for paired-end data, MACS will only keep the left mate(5'
+end) tag. However, when format `BAMPE` is specified, MACS will use the
+real fragments inferred from alignment results for reads pileup.
+###### `BEDPE` or `BAMPE`
+A special mode will be triggered while the format is specified as
+`BAMPE` or `BEDPE`. In this way, MACS2 will process the `BAM` or `BED`
+files as paired-end data. Instead of building a bimodal distribution
+of plus and minus strand reads to predict fragment size, MACS2 will
+use actual insert sizes of pairs of reads to build fragment pileup.
+The `BAMPE` format is just a `BAM` format containing paired-end alignment
+information, such as those from `BWA` or `BOWTIE`.
+The `BEDPE` format is a simplified and more flexible `BED` format,
+which only contains the first three columns defining the chromosome
+name, left and right position of the fragment from Paired-end
+sequencing. Please note, this is NOT the same format used by
+`BEDTOOLS`, and the `BEDTOOLS` version of `BEDPE` is actually not in a
+standard `BED` format. You can use MACS2 subcommand `randsample` to
+convert a `BAM` file containing paired-end information to a `BEDPE`
+format file:
+```
+macs2 randsample -i the_BAMPE_file.bam -f BAMPE -p 100 -o the_BEDPE_file.bed
+```
+##### `-g`/`--gsize`
+PLEASE assign this parameter to fit your needs!
+It's the mappable genome size or effective genome size which is
+defined as the genome size which can be sequenced. Because of the
+repetitive features on the chromosomes, the actual mappable genome
+size will be smaller than the original size, about 90% or 70% of the
+genome size. The default *hs* -- 2.7e9 is recommended for human
+genome. Here are all precompiled parameters for effective genome size:
+ * hs: 2.7e9
+ * mm: 1.87e9
+ * ce: 9e7
+ * dm: 1.2e8
+Users may want to use k-mer tools to simulate mapping of Xbps long
+reads to target genome, and to find the ideal effective genome
+size. However, usually by taking away the simple repeats and Ns from
+the total genome, one can get an approximate number of effective
+genome size. A slight difference in the number won't cause a big
+difference of peak calls, because this number is used to estimate a
+genome-wide noise level which is usually the least significant one
+compared with the *local biases* modeled by MACS.
+##### `-s`/`--tsize`
+The size of sequencing tags. If you don't specify it, MACS will try to
+use the first 10 sequences from your input treatment file to determine
+the tag size. Specifying it will override the automatically determined
+tag size.
+##### `-q`/`--qvalue`
+The q-value (minimum FDR) cutoff to call significant regions. Default
+is 0.05. For broad marks, you can try 0.05 as the cutoff. Q-values are
+calculated from p-values using the Benjamini-Hochberg procedure.
+##### `-p`/`--pvalue`
+The p-value cutoff. If `-p` is specified, MACS2 will use p-value instead
+of q-value.
+##### `--min-length`, `--max-gap`
+These two options can be used to fine-tune the peak calling behavior
+by specifying the minimum length of a called peak and the maximum
+allowed a gap between two nearby regions to be merged. In other words,
+a called peak has to be longer than `min-length`, and if the distance
+between two nearby peaks is smaller than `max-gap` then they will be
+merged as one. If they are not set, MACS2 will set the DEFAULT value
+for `min-length` as the predicted fragment size `d`, and the DEFAULT
+value for `max-gap` as the detected read length. Note, if you set a
+`min-length` value smaller than the fragment size, it may have NO
+effect on the result. For broad peak calling with `--broad` option
+set, the DEFAULT `max-gap` for merging nearby stronger peaks will be
+the same as narrow peak calling, and 4 times of the `max-gap` will be
+used to merge nearby weaker (broad) peaks. You can also use
+`--cutoff-analysis` option with the default setting, and check the
+column `avelpeak` under different cutoff values to decide a reasonable
+`min-length` value.
+##### `--nolambda`
+With this flag on, MACS will use the background lambda as local
+lambda. This means MACS will not consider the local bias at peak
+candidate regions.
+##### `--slocal`, `--llocal`
+These two parameters control which two levels of regions will be
+checked around the peak regions to calculate the maximum lambda as
+local lambda. By default, MACS considers 1000bp for small local
+region(`--slocal`), and 10000bps for large local region(`--llocal`)
+which captures the bias from a long-range effect like an open
+chromatin domain. You can tweak these according to your
+project. Remember that if the region is set too small, a sharp spike
+in the input data may kill a significant peak.
+##### `--nomodel`
+While on, MACS will bypass building the shifting model.
+##### `--extsize`
+While `--nomodel` is set, MACS uses this parameter to extend reads in
+5'->3' direction to fix-sized fragments. For example, if the size of
+the binding region for your transcription factor is 200 bp, and you
+want to bypass the model building by MACS, this parameter can be set
+as 200. This option is only valid when `--nomodel` is set or when MACS
+fails to build model and `--fix-bimodal` is on.
+##### `--shift`
+Note, this is NOT the legacy `--shiftsize` option which is replaced by
+`--extsize`! You can set an arbitrary shift in bp here. Please Use
+discretion while setting it other than the default value (0). When
+`--nomodel` is set, MACS will use this value to move cutting ends (5')
+then apply `--extsize` from 5' to 3' direction to extend them to
+fragments. When this value is negative, ends will be moved toward
+3'->5' direction, otherwise 5'->3' direction. Recommended to keep it
+as default 0 for ChIP-Seq datasets, or -1 * half of *EXTSIZE* together
+with `--extsize` option for detecting enriched cutting loci such as
+certain DNAseI-Seq datasets. Note, you can't set values other than 0
+if the format is BAMPE or BEDPE for paired-end data. The default is 0.
+Here are some examples for combining `--shift` and `--extsize`:
+1. To find enriched cutting sites such as some DNAse-Seq datasets. In
+this case, all 5' ends of sequenced reads should be extended in both
+directions to smooth the pileup signals. If the wanted smoothing
+window is 200bps, then use `--nomodel --shift -100 --extsize 200`.
+2. For certain nucleosome-seq data, we need to pile up the centers of
+nucleosomes using a half-nucleosome size for wavelet analysis
+(e.g. NPS algorithm). Since the DNA wrapped on nucleosome is about
+147bps, this option can be used: `--nomodel --shift 37 --extsize 73`.
+##### `--keep-dup`
+It controls the MACS behavior towards duplicate tags at the exact same
+location -- the same coordination and the same strand. The default
+`auto` option makes MACS calculate the maximum tags at the exact same
+location based on binomial distribution using 1e-5 as p-value cutoff;
+and the `all` option keeps every tag.  If an integer is given, at most
+this number of tags will be kept at the same location. The default is
+to keep one tag at the same location. Default: 1
+##### `--broad`
+When this flag is on, MACS will try to composite broad regions in
+BED12 ( a gene-model-like format ) by putting nearby highly enriched
+regions into a broad region with loose cutoff. The broad region is
+controlled by another cutoff through `--broad-cutoff`. Please note
+that, the `max-gap` value for merging nearby weaker/broad peaks is 4
+times of `max-gap` for merging nearby stronger peaks. The later one
+can be controlled by `--max-gap` option, and by default it is the
+average fragment/insertion length in the PE data. DEFAULT: False
+##### `--broad-cutoff`
+Cutoff for the broad region. This option is not available unless
+`--broad` is set. If `-p` is set, this is a p-value cutoff, otherwise,
+it's a q-value cutoff.  DEFAULT: 0.1
+##### `--scale-to <large|small>`
+When set to `large`, linearly scale the smaller dataset to the same
+depth as the larger dataset. By default or being set as `small`, the
+larger dataset will be scaled towards the smaller dataset. Beware, to
+scale up small data would cause more false positives.
+##### `-B`/`--bdg`
+If this flag is on, MACS will store the fragment pileup, control
+lambda in bedGraph files. The bedGraph files will be stored in the
+current directory named `NAME_treat_pileup.bdg` for treatment data,
+`NAME_control_lambda.bdg` for local lambda values from control.
+##### `--call-summits`
+MACS will now reanalyze the shape of signal profile (p or q-score
+depending on the cutoff setting) to deconvolve subpeaks within each
+peak called from the general procedure. It's highly recommended to
+detect adjacent binding events. While used, the output subpeaks of a
+big peak region will have the same peak boundaries, and different
+scores and peak summit positions.
+##### `--buffer-size`
+MACS uses a buffer size for incrementally increasing internal array
+size to store reads alignment information for each chromosome or
+contig. To increase the buffer size, MACS can run faster but will
+waste more memory if certain chromosome/contig only has very few
+reads. In most cases, the default value 100000 works fine. However, if
+there are a large number of chromosomes/contigs in your alignment and
+reads per chromosome/contigs are few, it's recommended to specify a
+smaller buffer size in order to decrease memory usage (but it will
+take longer time to read alignment files). Minimum memory requested
+for reading an alignment file is about # of CHROMOSOME * BUFFER_SIZE *
+8 Bytes. DEFAULT: 100000
+#### Output files
+1. `NAME_peaks.xls` is a tabular file which contains information about
+   called peaks. You can open it in excel and sort/filter using excel
+   functions. Information include:
+    - chromosome name
+    - start position of peak
+    - end position of peak
+    - length of peak region
+    - absolute peak summit position
+    - pileup height at peak summit
+    - -log10(pvalue) for the peak summit (e.g. pvalue =1e-10, then
+      this value should be 10)
+    - fold enrichment for this peak summit against random Poisson
+      distribution with local lambda,
+    - -log10(qvalue) at peak summit
+   Coordinates in XLS is 1-based which is different from BED
+   format. When `--broad` is enabled for broad peak calling, the
+   pileup, p-value, q-value, and fold change in the XLS file will be
+   the mean value across the entire peak region, since peak summit
+   won't be called in broad peak calling mode.
+2. `NAME_peaks.narrowPeak` is BED6+4 format file which contains the
+   peak locations together with peak summit, p-value, and q-value. You
+   can load it to the UCSC genome browser. Definition of some specific
+   columns are:
+   - 5th: integer score for display. It's calculated as
+     `int(-10*log10pvalue)` or `int(-10*log10qvalue)` depending on
+     whether `-p` (pvalue) or `-q` (qvalue) is used as score
+     cutoff. Please note that currently this value might be out of the
+     [0-1000] range defined in [UCSC ENCODE narrowPeak
+     format](https://genome.ucsc.edu/FAQ/FAQformat.html#format12). You
+     can let the value saturated at 1000 (i.e. p/q-value = 10^-100) by
+     using the following 1-liner awk: `awk -v OFS="\t"
+     '{$5=$5>1000?1000:$5} {print}' NAME_peaks.narrowPeak`
+   - 7th: fold-change at peak summit
+   - 8th: -log10pvalue at peak summit
+   - 9th: -log10qvalue at peak summit
+   - 10th: relative summit position to peak start
+   The file can be loaded directly to the UCSC genome browser. Remove
+   the beginning track line if you want to analyze it by other tools.
+3. `NAME_summits.bed` is in BED format, which contains the peak
+   summits locations for every peak. The 5th column in this file is
+   the same as what is in the `narrowPeak` file. If you want to find
+   the motifs at the binding sites, this file is recommended. The file
+   can be loaded directly to the UCSC genome browser. Remove the
+   beginning track line if you want to analyze it by other tools.
+4. `NAME_peaks.broadPeak` is in BED6+3 format which is similar to
+   `narrowPeak` file, except for missing the 10th column for
+   annotating peak summits. This file and the `gappedPeak` file will
+   only be available when `--broad` is enabled. Since in the broad
+   peak calling mode, the peak summit won't be called, the values in
+   the 5th, and 7-9th columns are the mean value across all positions
+   in the peak region. Refer to `narrowPeak` if you want to fix the
+   value issue in the 5th column.
+5. `NAME_peaks.gappedPeak` is in BED12+3 format which contains both
+   the broad region and narrow peaks. The 5th column is the score for
+   showing grey levels on the UCSC browser as in `narrowPeak`. The 7th
+   is the start of the first narrow peak in the region, and the 8th
+   column is the end. The 9th column should be RGB color key, however,
+   we keep 0 here to use the default color, so change it if you
+   want. The 10th column tells how many blocks including the starting
+   1bp and ending 1bp of broad regions. The 11th column shows the
+   length of each block and 12th for the start of each block. 13th:
+   fold-change, 14th: *-log10pvalue*, 15th: *-log10qvalue*. The file can
+   be loaded directly to the UCSC genome browser. Refer to
+   `narrowPeak` if you want to fix the value issue in the 5th column.
+6. `NAME_model.r` is an R script which you can use to produce a PDF
+   image of the model based on your data. Load it to R by:
+   `$ Rscript NAME_model.r`
+   Then a pdf file `NAME_model.pdf` will be generated in your current
+   directory. Note, R is required to draw this figure.
+7. The `NAME_treat_pileup.bdg` and `NAME_control_lambda.bdg` files are
+   in bedGraph format which can be imported to the UCSC genome browser
+   or be converted into even smaller bigWig files. The
+   `NAME_treat_pielup.bdg` contains the pileup signals (normalized
+   according to `--scale-to` option) from ChIP/treatment sample. The
+   `NAME_control_lambda.bdg` contains local biases estimated for each
+   genomic location from the control sample, or from treatment sample
+   when the control sample is absent. The subcommand `bdgcmp` can be
+   used to compare these two files and make a bedGraph file of scores
+   such as p-value, q-value, log-likelihood, and log fold changes.
+## Other useful links
+ * [Cistrome](http://cistrome.org/ap/)
+ * [bedTools](http://code.google.com/p/bedtools/)
+ * [UCSC toolkits](http://hgdownload.cse.ucsc.edu/admin/exe/)
+## Tips of fine-tuning peak calling
+There are several subcommands within MACSv2 package to fine-tune or
+customize your analysis:
+1. `bdgcmp` can be used on `*_treat_pileup.bdg` and
+   `*_control_lambda.bdg` or bedGraph files from other resources to
+   calculate the score track.
+2. `bdgpeakcall` can be used on `*_treat_pvalue.bdg` or the file
+   generated from bdgcmp or bedGraph file from other resources to call
+   peaks with given cutoff, maximum-gap between nearby mergeable peaks
+   and a minimum length of peak. bdgbroadcall works similarly to
+   bdgpeakcall, however, it will output `_broad_peaks.bed` in BED12
+   format.
+3. Differential calling tool -- `bdgdiff`, can be used on 4 bedGraph
+   files which are scores between treatment 1 and control 1, treatment
+   2 and control 2, treatment 1 and treatment 2, treatment 2 and
+   treatment 1. It will output consistent and unique sites according
+   to parameter settings for minimum length, the maximum gap and
+   cutoff.
+4. You can combine subcommands to do a step-by-step peak calling. Read
+   detail at [MACS2
+   wikipage](https://github.com/taoliu/MACS/wiki/Advanced%3A-Call-peaks-using-MACS2-subcommands)
+
+%package -n python3-MACS2
+Summary:	Model Based Analysis for ChIP-Seq data
+Provides:	python-MACS2
+BuildRequires:	python3-devel
+BuildRequires:	python3-setuptools
+BuildRequires:	python3-pip
+%description -n python3-MACS2
+`callpeak` | Main MACS2 Function to call peaks from alignment results.
+`bdgpeakcall` | Call peaks from bedGraph output.
+`bdgbroadcall` | Call broad peaks from bedGraph output.
+`bdgcmp` | Comparing two signal tracks in bedGraph format.
+`bdgopt` | Operate the score column of bedGraph file.
+`cmbreps` | Combine BEDGraphs of scores from replicates.
+`bdgdiff` | Differential peak detection based on paired four bedGraph files.
+`filterdup` | Remove duplicate reads, then save in BED/BEDPE format.
+`predictd` | Predict d or fragment size from alignment results.
+`pileup` | Pileup aligned reads (single-end) or fragments (paired-end)
+`randsample` | Randomly choose a number/percentage of total reads.
+`refinepeak` | Take raw reads alignment, refine peak summits.
+We only cover `callpeak` subcommand in this document. Please use
+`macs2 COMMAND -h` to see the detail description for each option of
+each subcommand.
+### Call peaks
+This is the main function in MACS2. It can be invoked by `macs2
+callpeak` . If you type this command with `-h`, you will see a full
+description of command-line options. Here we only list the essentials.
+#### Essential Options
+##### `-t`/`--treatment FILENAME`
+This is the only REQUIRED parameter for MACS. The file can be in any
+supported format -- see detail in the `--format` option. If you have
+more than one alignment file, you can specify them as `-t A B C`. MACS
+will pool up all these files together.
+##### `-c`/`--control`
+The control, genomic input or mock IP data file. Please follow the
+same direction as for `-t`/`--treatment`.
+##### `-n`/`--name`
+The name string of the experiment. MACS will use this string NAME to
+create output files like `NAME_peaks.xls`, `NAME_negative_peaks.xls`,
+`NAME_peaks.bed` , `NAME_summits.bed`, `NAME_model.r` and so on. So
+please avoid any confliction between these filenames and your existing
+files.
+##### `--outdir`
+MACS2 will save all output files into the specified folder for this
+option. A new folder will be created if necessary.
+##### `-f`/`--format FORMAT`
+Format of tag file can be `ELAND`, `BED`, `ELANDMULTI`, `ELANDEXPORT`,
+`SAM`, `BAM`, `BOWTIE`, `BAMPE`, or `BEDPE`. Default is `AUTO` which
+will allow MACS to decide the format automatically. `AUTO` is also
+useful when you combine different formats of files. Note that MACS
+can't detect `BAMPE` or `BEDPE` format with `AUTO`, and you have to
+implicitly specify the format for `BAMPE` and `BEDPE`.
+Nowadays, the most common formats are `BED` or `BAM` (including
+`BEDPE` and `BAMPE`). Our recommendation is to convert your data to
+`BED` or `BAM` first.
+Also, MACS2 can detect and read gzipped file. For example, `.bed.gz`
+file can be directly used without being uncompressed with `--format
+BED`.
+Here are detailed explanation of the recommanded formats:
+###### `BED`
+The BED format can be found at [UCSC genome browser
+website](http://genome.ucsc.edu/FAQ/FAQformat#format1).
+The essential columns in BED format input are the 1st column
+`chromosome name`, the 2nd `start position`, the 3rd `end position`,
+and the 6th, `strand`.
+Note that, for `BED` format, the 6th column of strand information is
+required by MACS. And please pay attention that the coordinates in BED
+format are zero-based and half-open. See more detail at
+[UCSC site](http://genome.ucsc.edu/FAQ/FAQtracks#tracks1).
+###### `BAM`/`SAM`
+If the format is `BAM`/`SAM`, please check the definition in
+(http://samtools.sourceforge.net/samtools.shtml).  If the `BAM` file is
+generated for paired-end data, MACS will only keep the left mate(5'
+end) tag. However, when format `BAMPE` is specified, MACS will use the
+real fragments inferred from alignment results for reads pileup.
+###### `BEDPE` or `BAMPE`
+A special mode will be triggered while the format is specified as
+`BAMPE` or `BEDPE`. In this way, MACS2 will process the `BAM` or `BED`
+files as paired-end data. Instead of building a bimodal distribution
+of plus and minus strand reads to predict fragment size, MACS2 will
+use actual insert sizes of pairs of reads to build fragment pileup.
+The `BAMPE` format is just a `BAM` format containing paired-end alignment
+information, such as those from `BWA` or `BOWTIE`.
+The `BEDPE` format is a simplified and more flexible `BED` format,
+which only contains the first three columns defining the chromosome
+name, left and right position of the fragment from Paired-end
+sequencing. Please note, this is NOT the same format used by
+`BEDTOOLS`, and the `BEDTOOLS` version of `BEDPE` is actually not in a
+standard `BED` format. You can use MACS2 subcommand `randsample` to
+convert a `BAM` file containing paired-end information to a `BEDPE`
+format file:
+```
+macs2 randsample -i the_BAMPE_file.bam -f BAMPE -p 100 -o the_BEDPE_file.bed
+```
+##### `-g`/`--gsize`
+PLEASE assign this parameter to fit your needs!
+It's the mappable genome size or effective genome size which is
+defined as the genome size which can be sequenced. Because of the
+repetitive features on the chromosomes, the actual mappable genome
+size will be smaller than the original size, about 90% or 70% of the
+genome size. The default *hs* -- 2.7e9 is recommended for human
+genome. Here are all precompiled parameters for effective genome size:
+ * hs: 2.7e9
+ * mm: 1.87e9
+ * ce: 9e7
+ * dm: 1.2e8
+Users may want to use k-mer tools to simulate mapping of Xbps long
+reads to target genome, and to find the ideal effective genome
+size. However, usually by taking away the simple repeats and Ns from
+the total genome, one can get an approximate number of effective
+genome size. A slight difference in the number won't cause a big
+difference of peak calls, because this number is used to estimate a
+genome-wide noise level which is usually the least significant one
+compared with the *local biases* modeled by MACS.
+##### `-s`/`--tsize`
+The size of sequencing tags. If you don't specify it, MACS will try to
+use the first 10 sequences from your input treatment file to determine
+the tag size. Specifying it will override the automatically determined
+tag size.
+##### `-q`/`--qvalue`
+The q-value (minimum FDR) cutoff to call significant regions. Default
+is 0.05. For broad marks, you can try 0.05 as the cutoff. Q-values are
+calculated from p-values using the Benjamini-Hochberg procedure.
+##### `-p`/`--pvalue`
+The p-value cutoff. If `-p` is specified, MACS2 will use p-value instead
+of q-value.
+##### `--min-length`, `--max-gap`
+These two options can be used to fine-tune the peak calling behavior
+by specifying the minimum length of a called peak and the maximum
+allowed a gap between two nearby regions to be merged. In other words,
+a called peak has to be longer than `min-length`, and if the distance
+between two nearby peaks is smaller than `max-gap` then they will be
+merged as one. If they are not set, MACS2 will set the DEFAULT value
+for `min-length` as the predicted fragment size `d`, and the DEFAULT
+value for `max-gap` as the detected read length. Note, if you set a
+`min-length` value smaller than the fragment size, it may have NO
+effect on the result. For broad peak calling with `--broad` option
+set, the DEFAULT `max-gap` for merging nearby stronger peaks will be
+the same as narrow peak calling, and 4 times of the `max-gap` will be
+used to merge nearby weaker (broad) peaks. You can also use
+`--cutoff-analysis` option with the default setting, and check the
+column `avelpeak` under different cutoff values to decide a reasonable
+`min-length` value.
+##### `--nolambda`
+With this flag on, MACS will use the background lambda as local
+lambda. This means MACS will not consider the local bias at peak
+candidate regions.
+##### `--slocal`, `--llocal`
+These two parameters control which two levels of regions will be
+checked around the peak regions to calculate the maximum lambda as
+local lambda. By default, MACS considers 1000bp for small local
+region(`--slocal`), and 10000bps for large local region(`--llocal`)
+which captures the bias from a long-range effect like an open
+chromatin domain. You can tweak these according to your
+project. Remember that if the region is set too small, a sharp spike
+in the input data may kill a significant peak.
+##### `--nomodel`
+While on, MACS will bypass building the shifting model.
+##### `--extsize`
+While `--nomodel` is set, MACS uses this parameter to extend reads in
+5'->3' direction to fix-sized fragments. For example, if the size of
+the binding region for your transcription factor is 200 bp, and you
+want to bypass the model building by MACS, this parameter can be set
+as 200. This option is only valid when `--nomodel` is set or when MACS
+fails to build model and `--fix-bimodal` is on.
+##### `--shift`
+Note, this is NOT the legacy `--shiftsize` option which is replaced by
+`--extsize`! You can set an arbitrary shift in bp here. Please Use
+discretion while setting it other than the default value (0). When
+`--nomodel` is set, MACS will use this value to move cutting ends (5')
+then apply `--extsize` from 5' to 3' direction to extend them to
+fragments. When this value is negative, ends will be moved toward
+3'->5' direction, otherwise 5'->3' direction. Recommended to keep it
+as default 0 for ChIP-Seq datasets, or -1 * half of *EXTSIZE* together
+with `--extsize` option for detecting enriched cutting loci such as
+certain DNAseI-Seq datasets. Note, you can't set values other than 0
+if the format is BAMPE or BEDPE for paired-end data. The default is 0.
+Here are some examples for combining `--shift` and `--extsize`:
+1. To find enriched cutting sites such as some DNAse-Seq datasets. In
+this case, all 5' ends of sequenced reads should be extended in both
+directions to smooth the pileup signals. If the wanted smoothing
+window is 200bps, then use `--nomodel --shift -100 --extsize 200`.
+2. For certain nucleosome-seq data, we need to pile up the centers of
+nucleosomes using a half-nucleosome size for wavelet analysis
+(e.g. NPS algorithm). Since the DNA wrapped on nucleosome is about
+147bps, this option can be used: `--nomodel --shift 37 --extsize 73`.
+##### `--keep-dup`
+It controls the MACS behavior towards duplicate tags at the exact same
+location -- the same coordination and the same strand. The default
+`auto` option makes MACS calculate the maximum tags at the exact same
+location based on binomial distribution using 1e-5 as p-value cutoff;
+and the `all` option keeps every tag.  If an integer is given, at most
+this number of tags will be kept at the same location. The default is
+to keep one tag at the same location. Default: 1
+##### `--broad`
+When this flag is on, MACS will try to composite broad regions in
+BED12 ( a gene-model-like format ) by putting nearby highly enriched
+regions into a broad region with loose cutoff. The broad region is
+controlled by another cutoff through `--broad-cutoff`. Please note
+that, the `max-gap` value for merging nearby weaker/broad peaks is 4
+times of `max-gap` for merging nearby stronger peaks. The later one
+can be controlled by `--max-gap` option, and by default it is the
+average fragment/insertion length in the PE data. DEFAULT: False
+##### `--broad-cutoff`
+Cutoff for the broad region. This option is not available unless
+`--broad` is set. If `-p` is set, this is a p-value cutoff, otherwise,
+it's a q-value cutoff.  DEFAULT: 0.1
+##### `--scale-to <large|small>`
+When set to `large`, linearly scale the smaller dataset to the same
+depth as the larger dataset. By default or being set as `small`, the
+larger dataset will be scaled towards the smaller dataset. Beware, to
+scale up small data would cause more false positives.
+##### `-B`/`--bdg`
+If this flag is on, MACS will store the fragment pileup, control
+lambda in bedGraph files. The bedGraph files will be stored in the
+current directory named `NAME_treat_pileup.bdg` for treatment data,
+`NAME_control_lambda.bdg` for local lambda values from control.
+##### `--call-summits`
+MACS will now reanalyze the shape of signal profile (p or q-score
+depending on the cutoff setting) to deconvolve subpeaks within each
+peak called from the general procedure. It's highly recommended to
+detect adjacent binding events. While used, the output subpeaks of a
+big peak region will have the same peak boundaries, and different
+scores and peak summit positions.
+##### `--buffer-size`
+MACS uses a buffer size for incrementally increasing internal array
+size to store reads alignment information for each chromosome or
+contig. To increase the buffer size, MACS can run faster but will
+waste more memory if certain chromosome/contig only has very few
+reads. In most cases, the default value 100000 works fine. However, if
+there are a large number of chromosomes/contigs in your alignment and
+reads per chromosome/contigs are few, it's recommended to specify a
+smaller buffer size in order to decrease memory usage (but it will
+take longer time to read alignment files). Minimum memory requested
+for reading an alignment file is about # of CHROMOSOME * BUFFER_SIZE *
+8 Bytes. DEFAULT: 100000
+#### Output files
+1. `NAME_peaks.xls` is a tabular file which contains information about
+   called peaks. You can open it in excel and sort/filter using excel
+   functions. Information include:
+    - chromosome name
+    - start position of peak
+    - end position of peak
+    - length of peak region
+    - absolute peak summit position
+    - pileup height at peak summit
+    - -log10(pvalue) for the peak summit (e.g. pvalue =1e-10, then
+      this value should be 10)
+    - fold enrichment for this peak summit against random Poisson
+      distribution with local lambda,
+    - -log10(qvalue) at peak summit
+   Coordinates in XLS is 1-based which is different from BED
+   format. When `--broad` is enabled for broad peak calling, the
+   pileup, p-value, q-value, and fold change in the XLS file will be
+   the mean value across the entire peak region, since peak summit
+   won't be called in broad peak calling mode.
+2. `NAME_peaks.narrowPeak` is BED6+4 format file which contains the
+   peak locations together with peak summit, p-value, and q-value. You
+   can load it to the UCSC genome browser. Definition of some specific
+   columns are:
+   - 5th: integer score for display. It's calculated as
+     `int(-10*log10pvalue)` or `int(-10*log10qvalue)` depending on
+     whether `-p` (pvalue) or `-q` (qvalue) is used as score
+     cutoff. Please note that currently this value might be out of the
+     [0-1000] range defined in [UCSC ENCODE narrowPeak
+     format](https://genome.ucsc.edu/FAQ/FAQformat.html#format12). You
+     can let the value saturated at 1000 (i.e. p/q-value = 10^-100) by
+     using the following 1-liner awk: `awk -v OFS="\t"
+     '{$5=$5>1000?1000:$5} {print}' NAME_peaks.narrowPeak`
+   - 7th: fold-change at peak summit
+   - 8th: -log10pvalue at peak summit
+   - 9th: -log10qvalue at peak summit
+   - 10th: relative summit position to peak start
+   The file can be loaded directly to the UCSC genome browser. Remove
+   the beginning track line if you want to analyze it by other tools.
+3. `NAME_summits.bed` is in BED format, which contains the peak
+   summits locations for every peak. The 5th column in this file is
+   the same as what is in the `narrowPeak` file. If you want to find
+   the motifs at the binding sites, this file is recommended. The file
+   can be loaded directly to the UCSC genome browser. Remove the
+   beginning track line if you want to analyze it by other tools.
+4. `NAME_peaks.broadPeak` is in BED6+3 format which is similar to
+   `narrowPeak` file, except for missing the 10th column for
+   annotating peak summits. This file and the `gappedPeak` file will
+   only be available when `--broad` is enabled. Since in the broad
+   peak calling mode, the peak summit won't be called, the values in
+   the 5th, and 7-9th columns are the mean value across all positions
+   in the peak region. Refer to `narrowPeak` if you want to fix the
+   value issue in the 5th column.
+5. `NAME_peaks.gappedPeak` is in BED12+3 format which contains both
+   the broad region and narrow peaks. The 5th column is the score for
+   showing grey levels on the UCSC browser as in `narrowPeak`. The 7th
+   is the start of the first narrow peak in the region, and the 8th
+   column is the end. The 9th column should be RGB color key, however,
+   we keep 0 here to use the default color, so change it if you
+   want. The 10th column tells how many blocks including the starting
+   1bp and ending 1bp of broad regions. The 11th column shows the
+   length of each block and 12th for the start of each block. 13th:
+   fold-change, 14th: *-log10pvalue*, 15th: *-log10qvalue*. The file can
+   be loaded directly to the UCSC genome browser. Refer to
+   `narrowPeak` if you want to fix the value issue in the 5th column.
+6. `NAME_model.r` is an R script which you can use to produce a PDF
+   image of the model based on your data. Load it to R by:
+   `$ Rscript NAME_model.r`
+   Then a pdf file `NAME_model.pdf` will be generated in your current
+   directory. Note, R is required to draw this figure.
+7. The `NAME_treat_pileup.bdg` and `NAME_control_lambda.bdg` files are
+   in bedGraph format which can be imported to the UCSC genome browser
+   or be converted into even smaller bigWig files. The
+   `NAME_treat_pielup.bdg` contains the pileup signals (normalized
+   according to `--scale-to` option) from ChIP/treatment sample. The
+   `NAME_control_lambda.bdg` contains local biases estimated for each
+   genomic location from the control sample, or from treatment sample
+   when the control sample is absent. The subcommand `bdgcmp` can be
+   used to compare these two files and make a bedGraph file of scores
+   such as p-value, q-value, log-likelihood, and log fold changes.
+## Other useful links
+ * [Cistrome](http://cistrome.org/ap/)
+ * [bedTools](http://code.google.com/p/bedtools/)
+ * [UCSC toolkits](http://hgdownload.cse.ucsc.edu/admin/exe/)
+## Tips of fine-tuning peak calling
+There are several subcommands within MACSv2 package to fine-tune or
+customize your analysis:
+1. `bdgcmp` can be used on `*_treat_pileup.bdg` and
+   `*_control_lambda.bdg` or bedGraph files from other resources to
+   calculate the score track.
+2. `bdgpeakcall` can be used on `*_treat_pvalue.bdg` or the file
+   generated from bdgcmp or bedGraph file from other resources to call
+   peaks with given cutoff, maximum-gap between nearby mergeable peaks
+   and a minimum length of peak. bdgbroadcall works similarly to
+   bdgpeakcall, however, it will output `_broad_peaks.bed` in BED12
+   format.
+3. Differential calling tool -- `bdgdiff`, can be used on 4 bedGraph
+   files which are scores between treatment 1 and control 1, treatment
+   2 and control 2, treatment 1 and treatment 2, treatment 2 and
+   treatment 1. It will output consistent and unique sites according
+   to parameter settings for minimum length, the maximum gap and
+   cutoff.
+4. You can combine subcommands to do a step-by-step peak calling. Read
+   detail at [MACS2
+   wikipage](https://github.com/taoliu/MACS/wiki/Advanced%3A-Call-peaks-using-MACS2-subcommands)
+
+%package help
+Summary:	Development documents and examples for MACS2
+Provides:	python3-MACS2-doc
+%description help
+`callpeak` | Main MACS2 Function to call peaks from alignment results.
+`bdgpeakcall` | Call peaks from bedGraph output.
+`bdgbroadcall` | Call broad peaks from bedGraph output.
+`bdgcmp` | Comparing two signal tracks in bedGraph format.
+`bdgopt` | Operate the score column of bedGraph file.
+`cmbreps` | Combine BEDGraphs of scores from replicates.
+`bdgdiff` | Differential peak detection based on paired four bedGraph files.
+`filterdup` | Remove duplicate reads, then save in BED/BEDPE format.
+`predictd` | Predict d or fragment size from alignment results.
+`pileup` | Pileup aligned reads (single-end) or fragments (paired-end)
+`randsample` | Randomly choose a number/percentage of total reads.
+`refinepeak` | Take raw reads alignment, refine peak summits.
+We only cover `callpeak` subcommand in this document. Please use
+`macs2 COMMAND -h` to see the detail description for each option of
+each subcommand.
+### Call peaks
+This is the main function in MACS2. It can be invoked by `macs2
+callpeak` . If you type this command with `-h`, you will see a full
+description of command-line options. Here we only list the essentials.
+#### Essential Options
+##### `-t`/`--treatment FILENAME`
+This is the only REQUIRED parameter for MACS. The file can be in any
+supported format -- see detail in the `--format` option. If you have
+more than one alignment file, you can specify them as `-t A B C`. MACS
+will pool up all these files together.
+##### `-c`/`--control`
+The control, genomic input or mock IP data file. Please follow the
+same direction as for `-t`/`--treatment`.
+##### `-n`/`--name`
+The name string of the experiment. MACS will use this string NAME to
+create output files like `NAME_peaks.xls`, `NAME_negative_peaks.xls`,
+`NAME_peaks.bed` , `NAME_summits.bed`, `NAME_model.r` and so on. So
+please avoid any confliction between these filenames and your existing
+files.
+##### `--outdir`
+MACS2 will save all output files into the specified folder for this
+option. A new folder will be created if necessary.
+##### `-f`/`--format FORMAT`
+Format of tag file can be `ELAND`, `BED`, `ELANDMULTI`, `ELANDEXPORT`,
+`SAM`, `BAM`, `BOWTIE`, `BAMPE`, or `BEDPE`. Default is `AUTO` which
+will allow MACS to decide the format automatically. `AUTO` is also
+useful when you combine different formats of files. Note that MACS
+can't detect `BAMPE` or `BEDPE` format with `AUTO`, and you have to
+implicitly specify the format for `BAMPE` and `BEDPE`.
+Nowadays, the most common formats are `BED` or `BAM` (including
+`BEDPE` and `BAMPE`). Our recommendation is to convert your data to
+`BED` or `BAM` first.
+Also, MACS2 can detect and read gzipped file. For example, `.bed.gz`
+file can be directly used without being uncompressed with `--format
+BED`.
+Here are detailed explanation of the recommanded formats:
+###### `BED`
+The BED format can be found at [UCSC genome browser
+website](http://genome.ucsc.edu/FAQ/FAQformat#format1).
+The essential columns in BED format input are the 1st column
+`chromosome name`, the 2nd `start position`, the 3rd `end position`,
+and the 6th, `strand`.
+Note that, for `BED` format, the 6th column of strand information is
+required by MACS. And please pay attention that the coordinates in BED
+format are zero-based and half-open. See more detail at
+[UCSC site](http://genome.ucsc.edu/FAQ/FAQtracks#tracks1).
+###### `BAM`/`SAM`
+If the format is `BAM`/`SAM`, please check the definition in
+(http://samtools.sourceforge.net/samtools.shtml).  If the `BAM` file is
+generated for paired-end data, MACS will only keep the left mate(5'
+end) tag. However, when format `BAMPE` is specified, MACS will use the
+real fragments inferred from alignment results for reads pileup.
+###### `BEDPE` or `BAMPE`
+A special mode will be triggered while the format is specified as
+`BAMPE` or `BEDPE`. In this way, MACS2 will process the `BAM` or `BED`
+files as paired-end data. Instead of building a bimodal distribution
+of plus and minus strand reads to predict fragment size, MACS2 will
+use actual insert sizes of pairs of reads to build fragment pileup.
+The `BAMPE` format is just a `BAM` format containing paired-end alignment
+information, such as those from `BWA` or `BOWTIE`.
+The `BEDPE` format is a simplified and more flexible `BED` format,
+which only contains the first three columns defining the chromosome
+name, left and right position of the fragment from Paired-end
+sequencing. Please note, this is NOT the same format used by
+`BEDTOOLS`, and the `BEDTOOLS` version of `BEDPE` is actually not in a
+standard `BED` format. You can use MACS2 subcommand `randsample` to
+convert a `BAM` file containing paired-end information to a `BEDPE`
+format file:
+```
+macs2 randsample -i the_BAMPE_file.bam -f BAMPE -p 100 -o the_BEDPE_file.bed
+```
+##### `-g`/`--gsize`
+PLEASE assign this parameter to fit your needs!
+It's the mappable genome size or effective genome size which is
+defined as the genome size which can be sequenced. Because of the
+repetitive features on the chromosomes, the actual mappable genome
+size will be smaller than the original size, about 90% or 70% of the
+genome size. The default *hs* -- 2.7e9 is recommended for human
+genome. Here are all precompiled parameters for effective genome size:
+ * hs: 2.7e9
+ * mm: 1.87e9
+ * ce: 9e7
+ * dm: 1.2e8
+Users may want to use k-mer tools to simulate mapping of Xbps long
+reads to target genome, and to find the ideal effective genome
+size. However, usually by taking away the simple repeats and Ns from
+the total genome, one can get an approximate number of effective
+genome size. A slight difference in the number won't cause a big
+difference of peak calls, because this number is used to estimate a
+genome-wide noise level which is usually the least significant one
+compared with the *local biases* modeled by MACS.
+##### `-s`/`--tsize`
+The size of sequencing tags. If you don't specify it, MACS will try to
+use the first 10 sequences from your input treatment file to determine
+the tag size. Specifying it will override the automatically determined
+tag size.
+##### `-q`/`--qvalue`
+The q-value (minimum FDR) cutoff to call significant regions. Default
+is 0.05. For broad marks, you can try 0.05 as the cutoff. Q-values are
+calculated from p-values using the Benjamini-Hochberg procedure.
+##### `-p`/`--pvalue`
+The p-value cutoff. If `-p` is specified, MACS2 will use p-value instead
+of q-value.
+##### `--min-length`, `--max-gap`
+These two options can be used to fine-tune the peak calling behavior
+by specifying the minimum length of a called peak and the maximum
+allowed a gap between two nearby regions to be merged. In other words,
+a called peak has to be longer than `min-length`, and if the distance
+between two nearby peaks is smaller than `max-gap` then they will be
+merged as one. If they are not set, MACS2 will set the DEFAULT value
+for `min-length` as the predicted fragment size `d`, and the DEFAULT
+value for `max-gap` as the detected read length. Note, if you set a
+`min-length` value smaller than the fragment size, it may have NO
+effect on the result. For broad peak calling with `--broad` option
+set, the DEFAULT `max-gap` for merging nearby stronger peaks will be
+the same as narrow peak calling, and 4 times of the `max-gap` will be
+used to merge nearby weaker (broad) peaks. You can also use
+`--cutoff-analysis` option with the default setting, and check the
+column `avelpeak` under different cutoff values to decide a reasonable
+`min-length` value.
+##### `--nolambda`
+With this flag on, MACS will use the background lambda as local
+lambda. This means MACS will not consider the local bias at peak
+candidate regions.
+##### `--slocal`, `--llocal`
+These two parameters control which two levels of regions will be
+checked around the peak regions to calculate the maximum lambda as
+local lambda. By default, MACS considers 1000bp for small local
+region(`--slocal`), and 10000bps for large local region(`--llocal`)
+which captures the bias from a long-range effect like an open
+chromatin domain. You can tweak these according to your
+project. Remember that if the region is set too small, a sharp spike
+in the input data may kill a significant peak.
+##### `--nomodel`
+While on, MACS will bypass building the shifting model.
+##### `--extsize`
+While `--nomodel` is set, MACS uses this parameter to extend reads in
+5'->3' direction to fix-sized fragments. For example, if the size of
+the binding region for your transcription factor is 200 bp, and you
+want to bypass the model building by MACS, this parameter can be set
+as 200. This option is only valid when `--nomodel` is set or when MACS
+fails to build model and `--fix-bimodal` is on.
+##### `--shift`
+Note, this is NOT the legacy `--shiftsize` option which is replaced by
+`--extsize`! You can set an arbitrary shift in bp here. Please Use
+discretion while setting it other than the default value (0). When
+`--nomodel` is set, MACS will use this value to move cutting ends (5')
+then apply `--extsize` from 5' to 3' direction to extend them to
+fragments. When this value is negative, ends will be moved toward
+3'->5' direction, otherwise 5'->3' direction. Recommended to keep it
+as default 0 for ChIP-Seq datasets, or -1 * half of *EXTSIZE* together
+with `--extsize` option for detecting enriched cutting loci such as
+certain DNAseI-Seq datasets. Note, you can't set values other than 0
+if the format is BAMPE or BEDPE for paired-end data. The default is 0.
+Here are some examples for combining `--shift` and `--extsize`:
+1. To find enriched cutting sites such as some DNAse-Seq datasets. In
+this case, all 5' ends of sequenced reads should be extended in both
+directions to smooth the pileup signals. If the wanted smoothing
+window is 200bps, then use `--nomodel --shift -100 --extsize 200`.
+2. For certain nucleosome-seq data, we need to pile up the centers of
+nucleosomes using a half-nucleosome size for wavelet analysis
+(e.g. NPS algorithm). Since the DNA wrapped on nucleosome is about
+147bps, this option can be used: `--nomodel --shift 37 --extsize 73`.
+##### `--keep-dup`
+It controls the MACS behavior towards duplicate tags at the exact same
+location -- the same coordination and the same strand. The default
+`auto` option makes MACS calculate the maximum tags at the exact same
+location based on binomial distribution using 1e-5 as p-value cutoff;
+and the `all` option keeps every tag.  If an integer is given, at most
+this number of tags will be kept at the same location. The default is
+to keep one tag at the same location. Default: 1
+##### `--broad`
+When this flag is on, MACS will try to composite broad regions in
+BED12 ( a gene-model-like format ) by putting nearby highly enriched
+regions into a broad region with loose cutoff. The broad region is
+controlled by another cutoff through `--broad-cutoff`. Please note
+that, the `max-gap` value for merging nearby weaker/broad peaks is 4
+times of `max-gap` for merging nearby stronger peaks. The later one
+can be controlled by `--max-gap` option, and by default it is the
+average fragment/insertion length in the PE data. DEFAULT: False
+##### `--broad-cutoff`
+Cutoff for the broad region. This option is not available unless
+`--broad` is set. If `-p` is set, this is a p-value cutoff, otherwise,
+it's a q-value cutoff.  DEFAULT: 0.1
+##### `--scale-to <large|small>`
+When set to `large`, linearly scale the smaller dataset to the same
+depth as the larger dataset. By default or being set as `small`, the
+larger dataset will be scaled towards the smaller dataset. Beware, to
+scale up small data would cause more false positives.
+##### `-B`/`--bdg`
+If this flag is on, MACS will store the fragment pileup, control
+lambda in bedGraph files. The bedGraph files will be stored in the
+current directory named `NAME_treat_pileup.bdg` for treatment data,
+`NAME_control_lambda.bdg` for local lambda values from control.
+##### `--call-summits`
+MACS will now reanalyze the shape of signal profile (p or q-score
+depending on the cutoff setting) to deconvolve subpeaks within each
+peak called from the general procedure. It's highly recommended to
+detect adjacent binding events. While used, the output subpeaks of a
+big peak region will have the same peak boundaries, and different
+scores and peak summit positions.
+##### `--buffer-size`
+MACS uses a buffer size for incrementally increasing internal array
+size to store reads alignment information for each chromosome or
+contig. To increase the buffer size, MACS can run faster but will
+waste more memory if certain chromosome/contig only has very few
+reads. In most cases, the default value 100000 works fine. However, if
+there are a large number of chromosomes/contigs in your alignment and
+reads per chromosome/contigs are few, it's recommended to specify a
+smaller buffer size in order to decrease memory usage (but it will
+take longer time to read alignment files). Minimum memory requested
+for reading an alignment file is about # of CHROMOSOME * BUFFER_SIZE *
+8 Bytes. DEFAULT: 100000
+#### Output files
+1. `NAME_peaks.xls` is a tabular file which contains information about
+   called peaks. You can open it in excel and sort/filter using excel
+   functions. Information include:
+    - chromosome name
+    - start position of peak
+    - end position of peak
+    - length of peak region
+    - absolute peak summit position
+    - pileup height at peak summit
+    - -log10(pvalue) for the peak summit (e.g. pvalue =1e-10, then
+      this value should be 10)
+    - fold enrichment for this peak summit against random Poisson
+      distribution with local lambda,
+    - -log10(qvalue) at peak summit
+   Coordinates in XLS is 1-based which is different from BED
+   format. When `--broad` is enabled for broad peak calling, the
+   pileup, p-value, q-value, and fold change in the XLS file will be
+   the mean value across the entire peak region, since peak summit
+   won't be called in broad peak calling mode.
+2. `NAME_peaks.narrowPeak` is BED6+4 format file which contains the
+   peak locations together with peak summit, p-value, and q-value. You
+   can load it to the UCSC genome browser. Definition of some specific
+   columns are:
+   - 5th: integer score for display. It's calculated as
+     `int(-10*log10pvalue)` or `int(-10*log10qvalue)` depending on
+     whether `-p` (pvalue) or `-q` (qvalue) is used as score
+     cutoff. Please note that currently this value might be out of the
+     [0-1000] range defined in [UCSC ENCODE narrowPeak
+     format](https://genome.ucsc.edu/FAQ/FAQformat.html#format12). You
+     can let the value saturated at 1000 (i.e. p/q-value = 10^-100) by
+     using the following 1-liner awk: `awk -v OFS="\t"
+     '{$5=$5>1000?1000:$5} {print}' NAME_peaks.narrowPeak`
+   - 7th: fold-change at peak summit
+   - 8th: -log10pvalue at peak summit
+   - 9th: -log10qvalue at peak summit
+   - 10th: relative summit position to peak start
+   The file can be loaded directly to the UCSC genome browser. Remove
+   the beginning track line if you want to analyze it by other tools.
+3. `NAME_summits.bed` is in BED format, which contains the peak
+   summits locations for every peak. The 5th column in this file is
+   the same as what is in the `narrowPeak` file. If you want to find
+   the motifs at the binding sites, this file is recommended. The file
+   can be loaded directly to the UCSC genome browser. Remove the
+   beginning track line if you want to analyze it by other tools.
+4. `NAME_peaks.broadPeak` is in BED6+3 format which is similar to
+   `narrowPeak` file, except for missing the 10th column for
+   annotating peak summits. This file and the `gappedPeak` file will
+   only be available when `--broad` is enabled. Since in the broad
+   peak calling mode, the peak summit won't be called, the values in
+   the 5th, and 7-9th columns are the mean value across all positions
+   in the peak region. Refer to `narrowPeak` if you want to fix the
+   value issue in the 5th column.
+5. `NAME_peaks.gappedPeak` is in BED12+3 format which contains both
+   the broad region and narrow peaks. The 5th column is the score for
+   showing grey levels on the UCSC browser as in `narrowPeak`. The 7th
+   is the start of the first narrow peak in the region, and the 8th
+   column is the end. The 9th column should be RGB color key, however,
+   we keep 0 here to use the default color, so change it if you
+   want. The 10th column tells how many blocks including the starting
+   1bp and ending 1bp of broad regions. The 11th column shows the
+   length of each block and 12th for the start of each block. 13th:
+   fold-change, 14th: *-log10pvalue*, 15th: *-log10qvalue*. The file can
+   be loaded directly to the UCSC genome browser. Refer to
+   `narrowPeak` if you want to fix the value issue in the 5th column.
+6. `NAME_model.r` is an R script which you can use to produce a PDF
+   image of the model based on your data. Load it to R by:
+   `$ Rscript NAME_model.r`
+   Then a pdf file `NAME_model.pdf` will be generated in your current
+   directory. Note, R is required to draw this figure.
+7. The `NAME_treat_pileup.bdg` and `NAME_control_lambda.bdg` files are
+   in bedGraph format which can be imported to the UCSC genome browser
+   or be converted into even smaller bigWig files. The
+   `NAME_treat_pielup.bdg` contains the pileup signals (normalized
+   according to `--scale-to` option) from ChIP/treatment sample. The
+   `NAME_control_lambda.bdg` contains local biases estimated for each
+   genomic location from the control sample, or from treatment sample
+   when the control sample is absent. The subcommand `bdgcmp` can be
+   used to compare these two files and make a bedGraph file of scores
+   such as p-value, q-value, log-likelihood, and log fold changes.
+## Other useful links
+ * [Cistrome](http://cistrome.org/ap/)
+ * [bedTools](http://code.google.com/p/bedtools/)
+ * [UCSC toolkits](http://hgdownload.cse.ucsc.edu/admin/exe/)
+## Tips of fine-tuning peak calling
+There are several subcommands within MACSv2 package to fine-tune or
+customize your analysis:
+1. `bdgcmp` can be used on `*_treat_pileup.bdg` and
+   `*_control_lambda.bdg` or bedGraph files from other resources to
+   calculate the score track.
+2. `bdgpeakcall` can be used on `*_treat_pvalue.bdg` or the file
+   generated from bdgcmp or bedGraph file from other resources to call
+   peaks with given cutoff, maximum-gap between nearby mergeable peaks
+   and a minimum length of peak. bdgbroadcall works similarly to
+   bdgpeakcall, however, it will output `_broad_peaks.bed` in BED12
+   format.
+3. Differential calling tool -- `bdgdiff`, can be used on 4 bedGraph
+   files which are scores between treatment 1 and control 1, treatment
+   2 and control 2, treatment 1 and treatment 2, treatment 2 and
+   treatment 1. It will output consistent and unique sites according
+   to parameter settings for minimum length, the maximum gap and
+   cutoff.
+4. You can combine subcommands to do a step-by-step peak calling. Read
+   detail at [MACS2
+   wikipage](https://github.com/taoliu/MACS/wiki/Advanced%3A-Call-peaks-using-MACS2-subcommands)
+
+%prep
+%autosetup -n MACS2-2.2.7.1
+
+%build
+%py3_build
+
+%install
+%py3_install
+install -d -m755 %{buildroot}/%{_pkgdocdir}
+if [ -d doc ]; then cp -arf doc %{buildroot}/%{_pkgdocdir}; fi
+if [ -d docs ]; then cp -arf docs %{buildroot}/%{_pkgdocdir}; fi
+if [ -d example ]; then cp -arf example %{buildroot}/%{_pkgdocdir}; fi
+if [ -d examples ]; then cp -arf examples %{buildroot}/%{_pkgdocdir}; fi
+pushd %{buildroot}
+if [ -d usr/lib ]; then
+	find usr/lib -type f -printf "/%h/%f\n" >> filelist.lst
+fi
+if [ -d usr/lib64 ]; then
+	find usr/lib64 -type f -printf "/%h/%f\n" >> filelist.lst
+fi
+if [ -d usr/bin ]; then
+	find usr/bin -type f -printf "/%h/%f\n" >> filelist.lst
+fi
+if [ -d usr/sbin ]; then
+	find usr/sbin -type f -printf "/%h/%f\n" >> filelist.lst
+fi
+touch doclist.lst
+if [ -d usr/share/man ]; then
+	find usr/share/man -type f -printf "/%h/%f.gz\n" >> doclist.lst
+fi
+popd
+mv %{buildroot}/filelist.lst .
+mv %{buildroot}/doclist.lst .
+
+%files -n python3-MACS2 -f filelist.lst
+%dir %{python3_sitelib}/*
+
+%files help -f doclist.lst
+%{_docdir}/*
+
+%changelog
+* Wed May 10 2023 Python_Bot <Python_Bot@openeuler.org> - 2.2.7.1-1
+- Package Spec generated
diff --git a/sources b/sources
new file mode 100644
index 0000000..b5a45ee
--- /dev/null
+++ b/sources
@@ -0,0 +1 @@
+cfdac500a0d4f51e24864364e0025738  MACS2-2.2.7.1.tar.gz