windowSplitter.py $input $size $out_file1 ${wintype.choice} ${wintype.offset} -l ${input.metadata.chromCol},${input.metadata.startCol},${input.metadata.endCol},${input.metadata.strandCol}
.. class:: infomark
**What it does**
This tool splits the intervals in the input file into smaller intervals based on the specified window-size and window type.
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.. class:: warningmark
**Note**
The positions at the end of the input interval which do not fit into the last window or a new window of required size, will be omitted from the output.
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.. class:: infomark
**About formats**
**BED format** Browser Extensible Data format was designed at UCSC for displaying data tracks in the Genome Browser. It has three required fields and several additional optional ones:
The first three BED fields (required) are::
1. chrom - The name of the chromosome (e.g. chr1, chrY_random).
2. chromStart - The starting position in the chromosome. (The first base in a chromosome is numbered 0.)
3. chromEnd - The ending position in the chromosome, plus 1 (i.e., a half-open interval).
The additional BED fields (optional) are::
4. name - The name of the BED line.
5. score - A score between 0 and 1000.
6. strand - Defines the strand - either '+' or '-'.
7. thickStart - The starting position where the feature is drawn thickly at the Genome Browser.
8. thickEnd - The ending position where the feature is drawn thickly at the Genome Browser.
9. reserved - This should always be set to zero.
10. blockCount - The number of blocks (exons) in the BED line.
11. blockSizes - A comma-separated list of the block sizes. The number of items in this list should correspond to blockCount.
12. blockStarts - A comma-separated list of block starts. All of the blockStart positions should be calculated relative to chromStart. The number of items in this list should correspond to blockCount.
13. expCount - The number of experiments.
14. expIds - A comma-separated list of experiment ids. The number of items in this list should correspond to expCount.
15. expScores - A comma-separated list of experiment scores. All of the expScores should be relative to expIds. The number of items in this list should correspond to expCount.
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**Example**
- For the following query::
chr22 1000 4700 NM_174568 0 +
- running this tool with **Window size as 1000**, will return::
chr22 1000 2000 NM_174568 0 +
chr22 2000 3000 NM_174568 0 +
chr22 3000 4000 NM_174568 0 +
- running this tool to make **Sliding windows** of **size 1000** and **offset 500**, will return::
chr22 1000 2000 NM_174568 0 +
chr22 1500 2500 NM_174568 0 +
chr22 2000 3000 NM_174568 0 +
chr22 2500 3500 NM_174568 0 +
chr22 3000 4000 NM_174568 0 +
chr22 3500 4500 NM_174568 0 +