-
Notifications
You must be signed in to change notification settings - Fork 133
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
https://github.com/lindenb/jvarkit/issues/257
- Loading branch information
Showing
6 changed files
with
22 additions
and
179 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,171 +0,0 @@ | ||
| # TViewCmd | ||
|
|
||
|  | ||
|
|
||
| equivalent of samtools tview | ||
|
|
||
|
|
||
| ## Usage | ||
|
|
||
| ``` | ||
| Usage: tview [options] Files | ||
| Options: | ||
| --clip | ||
| Show clip | ||
| Default: false | ||
| --coverage, --depth | ||
| Number of rows for coverage (hide:<=0) | ||
| Default: 10 | ||
| --filter | ||
| A filter expression. Reads matching the expression will be filtered-out. | ||
| Empty String means 'filter out nothing/Accept all'. See https://github.com/lindenb/jvarkit/blob/master/src/main/resources/javacc/com/github/lindenb/jvarkit/util/bio/samfilter/SamFilterParser.jj | ||
| for a complete syntax. 'default' is 'mapqlt(1) || Duplicate() || | ||
| FailsVendorQuality() || NotPrimaryAlignment() || | ||
| SupplementaryAlignment()' | ||
| Default: mapqlt(1) || Duplicate() || FailsVendorQuality() || NotPrimaryAlignment() || SupplementaryAlignment() | ||
| --groupby | ||
| Group Reads by. Data partitioning using the SAM Read Group (see | ||
| https://gatkforums.broadinstitute.org/gatk/discussion/6472/ ) . It can | ||
| be any combination of sample, library.... | ||
| Default: sample | ||
| Possible Values: [readgroup, sample, library, platform, center, sample_by_platform, sample_by_center, sample_by_platform_by_center, any] | ||
| -h, --help | ||
| print help and exit | ||
| --helpFormat | ||
| What kind of help. One of [usage,markdown,xml]. | ||
| --hideBases | ||
| Hide bases | ||
| Default: false | ||
| --hideHomRef | ||
| Hide HOM_REF variations | ||
| Default: false | ||
| --hideNoCall | ||
| Hide NO_CALL variations | ||
| Default: false | ||
| --insert | ||
| Show insertions | ||
| Default: false | ||
| -layout, --layout | ||
| Layout reads | ||
| Default: pileup | ||
| Possible Values: [pileup, name] | ||
| -left, --leftmargin | ||
| left margin width | ||
| Default: 15 | ||
| -maxrows, --maxrowss | ||
| maximum number of rows per read group. -1 == all | ||
| Default: -1 | ||
| --noconsensus | ||
| Hide Consensus line | ||
| Default: false | ||
| --nodefaultinterval | ||
| if no interval was provided, don't try to create a default one. | ||
| Default: false | ||
| -o, --out | ||
| Output file. Optional . Default: stdout | ||
| --format, --outputformat | ||
| Output format | ||
| Default: tty | ||
| Possible Values: [tty, plain, html] | ||
| --readName | ||
| Show read name | ||
| Default: false | ||
| -R, --reference | ||
| Indexed fasta Reference file. This file must be indexed with samtools | ||
| faidx and with picard CreateSequenceDictionary | ||
| -r, --region | ||
| Interval list | ||
| Default: [] | ||
| -V, --variant, --variants, --vcf | ||
| Variant file. if filename ends with '.list' it is interpreted as a list | ||
| of file (one file per line) | ||
| --version | ||
| print version and exit | ||
| -width, --width | ||
| default screen width | ||
| Default: -1 | ||
| ``` | ||
|
|
||
|
|
||
| ## Keywords | ||
|
|
||
| * sam | ||
| * bam | ||
| * visualization | ||
| * terminal | ||
|
|
||
|
|
||
| ## Compilation | ||
|
|
||
| ### Requirements / Dependencies | ||
|
|
||
| * java [compiler SDK 11](https://jdk.java.net/11/). Please check that this java is in the `${PATH}`. Setting JAVA_HOME is not enough : (e.g: https://github.com/lindenb/jvarkit/issues/23 ) | ||
|
|
||
|
|
||
| ### Download and Compile | ||
|
|
||
| ```bash | ||
| $ git clone "https://github.com/lindenb/jvarkit.git" | ||
| $ cd jvarkit | ||
| $ ./gradlew tview | ||
| ``` | ||
|
|
||
| The java jar file will be installed in the `dist` directory. | ||
|
|
||
| ## Source code | ||
|
|
||
| [https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/tview/TViewCmd.java](https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/tview/TViewCmd.java) | ||
|
|
||
| ### Unit Tests | ||
|
|
||
| [https://github.com/lindenb/jvarkit/tree/master/src/test/java/com/github/lindenb/jvarkit/tools/tview/TViewCmdTest.java](https://github.com/lindenb/jvarkit/tree/master/src/test/java/com/github/lindenb/jvarkit/tools/tview/TViewCmdTest.java) | ||
|
|
||
|
|
||
| ## Contribute | ||
|
|
||
| - Issue Tracker: [http://github.com/lindenb/jvarkit/issues](http://github.com/lindenb/jvarkit/issues) | ||
| - Source Code: [http://github.com/lindenb/jvarkit](http://github.com/lindenb/jvarkit) | ||
|
|
||
| ## License | ||
|
|
||
| The project is licensed under the MIT license. | ||
|
|
||
| ## Citing | ||
|
|
||
| Should you cite **tview** ? [https://github.com/mr-c/shouldacite/blob/master/should-I-cite-this-software.md](https://github.com/mr-c/shouldacite/blob/master/should-I-cite-this-software.md) | ||
|
|
||
| The current reference is: | ||
|
|
||
| [http://dx.doi.org/10.6084/m9.figshare.1425030](http://dx.doi.org/10.6084/m9.figshare.1425030) | ||
|
|
||
| > Lindenbaum, Pierre (2015): JVarkit: java-based utilities for Bioinformatics. figshare. | ||
| > [http://dx.doi.org/10.6084/m9.figshare.1425030](http://dx.doi.org/10.6084/m9.figshare.1425030) | ||
|
|
||
| ## Example | ||
|
|
||
| ``` | ||
| $ java -jar dist/tview.jar -R toy.fa toy.bam --clip --groupby sample --insert --plain | ||
| ref:1-61 | ||
| POS: 1.......^^..11..^^^^....^^..21........31...^.....41........51 | ||
| REF: AGCATGTT**AGATAA****GATA**GCTGTGCTAGTAGGCAG*TCAGCGCCATNNNNNNN | ||
| ndefined_sample TT**AGATAAAGAGGATA**-CTG cagcgccat | ||
| AAAAGATAAGG**GATAAA NNNNNNtaggc | ||
| NNNNN**AGCTAA | ||
| ATA**GCT--------------CTCAGC | ||
| ample CONSENSUS TTAAAGNTAANGAGGATAAAGCTG TAGGC CTCAGCGCCAT | ||
| efined_sample 3 ******** **** ** **** | ||
| ******** **** ** **** | ||
| ******** **** ** **** | ||
| ************************ ***** *********** | ||
| ************************ ***** *********** | ||
| ************************ ***** *********** | ||
| ****************************************************** | ||
| ****************************************************** | ||
| ****************************************************** | ||
| 0 ****************************************************** | ||
| ``` | ||
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters