Up: Component summary
Up: Component summary
Component
GetReadsVisualizes reads that are aligned to a given position.
| Version | 1.0 |
|---|---|
| Bundle | sequencing |
| Categories | |
| Authors | Sirkku Karinen (sirkku.karinen@helsinki.fi) |
| Issue tracker | View/Report issues |
| Requires | picard-1.62.jar (jar) ; sam-1.32.jar (jar) ; installer (bash) |
| Source files | component.xml |
| Usage | Example with default values |
Inputs| Name | Type | Mandatory | Description |
|---|---|---|---|
| alignment | BAM | Optional | A bam or sam file |
| array | Array<BAM> | Optional | An array of bam or sam files |
Outputs| Name | Type | Description |
|---|---|---|
| reads | TextFile | Reads in the given position |
Parameters| Name | Type | Default | Description |
|---|---|---|---|
| chromosome | string | (no default) | |
| position | int | (no default) |
Test cases| Test case | Parameters▼ | IN alignment |
IN array |
OUT reads |
||
|---|---|---|---|---|---|---|
| case1 | properties | alignment | (missing) | reads | ||
|
chromosome=chr21, |
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| case2 | properties | (missing) | array | (missing) | ||
|
chromosome=chr21, |
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| case3 | properties | alignment | (missing) | reads | ||
|
chromosome=chr21, |
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