Re: [igv-help] Load and access TDF file

James Robinson

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Aug 1, 2017, 12:07:04 AM8/1/17

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There is no library per se, but you could download igvtools and use "igvtools.jar" as a library. There is no documentation, because again this is not really a libary, but see org.broad.igv.tdfTDFDataSourceTest as an example to get started.

On Mon, Jul 31, 2017 at 7:43 PM, Tjioe Marvin Christian <t.marvin....@gmail.com> wrote:

Hi,

Just wondering, is there any way to load and access TDF file in my own code?

Thank you

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James Robinson

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Aug 1, 2017, 12:08:22 AM8/1/17

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I should add that bigwig is probably a better format in that it is more widely used and supported by more tools. The two formats were developed independently at around the same time, and for most purposes are equivalent.

Tjioe Marvin Christian

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Aug 2, 2017, 6:39:35 AM8/2/17

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Thanks for your answer.

Just wondering when I look at here: https://github.com/igvteam/igv/blob/8b4fa74fc51d20f91c467f123f6e8b8bf23698e5/test/src/org/broad/igv/tdf/TDFDataSourceTest.java#L64

the "genome" variable, where it comes from? I realize, to get the score I need that but I couldn't find how to declare it.

And also thanks for your suggestion for bigwig format, I'll have a look at that

Cheers!

On Tuesday, August 1, 2017 at 2:07:04 PM UTC+10, Jim Robinson wrote:

There is no library per se, but you could download igvtools and use "igvtools.jar" as a library. There is no documentation, because again this is not really a libary, but see org.broad.igv.tdfTDFDataSourceTest as an example to get started.

On Mon, Jul 31, 2017 at 7:43 PM, Tjioe Marvin Christian <t.marvin....@gmail.com> wrote:

Hi,

Just wondering, is there any way to load and access TDF file in my own code?

Thank you

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James Robinson

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Aug 2, 2017, 2:06:11 PM8/2/17

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The genome parameter can be null. Its only used to do chromosome aliasing, for example 1<->chr1.

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Tjioe Marvin Christian

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Aug 2, 2017, 8:52:51 PM8/2/17

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Thank you. but it seems I can't use exactly same like the example because the function "getSummaryScores()" is protected and not public. There's no way I can't access it.

If I used the function "getSummaryScoresForRange()" and put null for the genome variable. It gives me null exception.

Do you have any idea about this one?

Thanks again

On Thursday, August 3, 2017 at 4:06:11 AM UTC+10, Jim Robinson wrote:

The genome parameter can be null. Its only used to do chromosome aliasing, for example 1<->chr1.

On Wed, Aug 2, 2017 at 3:39 AM, Tjioe Marvin Christian <t.marvin....@gmail.com> wrote:

Thanks for your answer.

Just wondering when I look at here: https://github.com/igvteam/igv/blob/8b4fa74fc51d20f91c467f123f6e8b8bf23698e5/test/src/org/broad/igv/tdf/TDFDataSourceTest.java#L64

the "genome" variable, where it comes from? I realize, to get the score I need that but I couldn't find how to declare it.

And also thanks for your suggestion for bigwig format, I'll have a look at that

Cheers!

On Tuesday, August 1, 2017 at 2:07:04 PM UTC+10, Jim Robinson wrote:
There is no library per se, but you could download igvtools and use "igvtools.jar" as a library. There is no documentation, because again this is not really a libary, but see org.broad.igv.tdfTDFDataSourceTest as an example to get started.

On Mon, Jul 31, 2017 at 7:43 PM, Tjioe Marvin Christian <t.marvin....@gmail.com> wrote:
Hi,

Just wondering, is there any way to load and access TDF file in my own code?

Thank you

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James Robinson

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Aug 2, 2017, 8:58:38 PM8/2/17

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Sorry not specifically. Its not designed to be a library of course, to make it work as such will likely require some code changes. I'll entertain pull requests in this regard.

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Tjioe Marvin Christian

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Aug 2, 2017, 10:27:51 PM8/2/17

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No problem, I just need a good way to count the read depth so I try to use TDF file.

I can use htsjdk to count that, but it's pretty slow because I repeat it several times.

Thank you

James Robinson

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Aug 2, 2017, 10:52:25 PM8/2/17

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You can output a wig file instead of "tdf" by just using a ".wig" extension instead of ".tdf". This can then be converted to bigwig, if you wish.

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Tjioe Marvin Christian

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Aug 8, 2017, 11:37:34 AM8/8/17

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I just curious about this:

https://github.com/igvteam/igv/blob/8b4fa74fc51d20f91c467f123f6e8b8bf23698e5/test/src/org/broad/igv/tdf/TDFDataSourceTest.java#L64

Previously you said I can use null for the genome variable, but still it didn't work at all.

Is there any way to load it?

Thank you

On Tuesday, August 1, 2017 at 2:07:04 PM UTC+10, Jim Robinson wrote:

There is no library per se, but you could download igvtools and use "igvtools.jar" as a library. There is no documentation, because again this is not really a libary, but see org.broad.igv.tdfTDFDataSourceTest as an example to get started.

On Mon, Jul 31, 2017 at 7:43 PM, Tjioe Marvin Christian <t.marvin....@gmail.com> wrote:

Hi,

Just wondering, is there any way to load and access TDF file in my own code?

Thank you

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James Robinson

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Aug 8, 2017, 11:56:26 AM8/8/17

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You'll just have to step through and debug it, I can't guess what the problem is with no details.

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Tjioe Marvin Christian

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Aug 8, 2017, 8:12:34 PM8/8/17

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Sorry forgot to put the detail. From what I knew, it will pop up error in this part:

https://github.com/igvteam/igv/blob/af98ed0138b433976a8edf6373ede1d53847ffb4/src/org/broad/igv/tdf/TDFDataSource.java#L519

It came from this part:

https://github.com/igvteam/igv/blob/af98ed0138b433976a8edf6373ede1d53847ffb4/src/org/broad/igv/tdf/TDFDataSource.java#L198

from this function getSummaryScores

Thanks

On Wednesday, August 9, 2017 at 1:56:26 AM UTC+10, Jim Robinson wrote:

You'll just have to step through and debug it, I can't guess what the problem is with no details.

On Tue, Aug 8, 2017 at 8:37 AM, Tjioe Marvin Christian <t.marvin....@gmail.com> wrote:

I just curious about this:
https://github.com/igvteam/igv/blob/8b4fa74fc51d20f91c467f123f6e8b8bf23698e5/test/src/org/broad/igv/tdf/TDFDataSourceTest.java#L64

Previously you said I can use null for the genome variable, but still it didn't work at all.
Is there any way to load it?

Thank you

On Tuesday, August 1, 2017 at 2:07:04 PM UTC+10, Jim Robinson wrote:
There is no library per se, but you could download igvtools and use "igvtools.jar" as a library. There is no documentation, because again this is not really a libary, but see org.broad.igv.tdfTDFDataSourceTest as an example to get started.

On Mon, Jul 31, 2017 at 7:43 PM, Tjioe Marvin Christian <t.marvin....@gmail.com> wrote:
Hi,

Just wondering, is there any way to load and access TDF file in my own code?

Thank you

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James Robinson

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Aug 9, 2017, 12:00:36 AM8/9/17

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Yes, I don't think you'll be able to use TDFDataSource directly as it's too dependent on IGV. You can use it as a model for your own class that uses TDFReader directly. But as I stated earlier I think you would be better off using wig and bigWig.

Jim

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Tjioe Marvin Christian

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Aug 9, 2017, 8:57:09 AM8/9/17

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Okay thank you so much for your help.

Cheers!

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