Usage of SAM-JDK

[Bruins]

Hi all,

I am having trouble understanding how to use SAM-JDK.

For example. My Java class needs to filter an input SAM or BAM file to remove all unaligned reads. Commandline, I would use:

ViewSam.jar ALIGNMENT_STATUS=Aligned I=alignment.bam

But how do I do this directly in my class?

I have been looking at the docs (http://picard.sourceforge.net/javadoc/) and browsed the mailing list archives and this forum (and I have seen the code example here). However I still have no idea where to start.

Does anyone have any idea how to address this? Is there some more documentation, or an experienced user to help me on my way?

Many thanks,

Wil

[drio]

Hi all,

I am having trouble understanding how to use SAM-JDK.

For example. My Java class needs to filter an input SAM or BAM file to remove all unaligned reads. Commandline, I would use:

ViewSam.jar ALIGNMENT_STATUS=Aligned I=alignment.bam

But how do I do this directly in my class?

I have been looking at the docs (http://picard.sourceforge.net/javadoc/) and browsed the mailing list archives and this forum (and I have seen the code example here). However I still have no idea where to start.

Does anyone have any idea how to address this? Is there some more documentation, or an experienced user to help me on my way?

Many thanks,

Wil

Does this help?

http://picard.sourceforge.net/command-line-overview.shtml

[Bruins]

I'm sorry, no. Thanks for the quick reply though. The page you gave me has already helped me a lot but explains only how to use the executable jars from the commandline.

To clarify what I am looking for, here a very minimal code example.

public class FilterAndSort {

    [...]

    // the method: filter all unaligned reads from a SAM or BAM file
    // @param bamfile the location of a BAM or SAM file as a string
    // @return filteredBamfile the location of the new filtered BAM or SAM file as a string
    private String reportAlignedReads(String bamfile) {

This is the point where I would like to utilise the ViewSam.jar functionality, but without having to make a commandline call from within my class. Luckily, SAM-JDK exists.

The code example (this one) shows how to access a SAM or BAM file. I am unsure how to use it and the other classes and methods available in the javadoc (both net.sf.picard and net.sf.samtools) to filter out the unaligned reads - I don't know where to start.

For example. The javadoc shows that the ViewSam class has constructor ViewSam() and two methods: a main method and a method called doWork() that 'does work after command line has been parsed'. Something tells me I am not supposed to use this class. But what other class...

        return filteredBamfile;
    }
}

I hope I'm not asking anything completely obvious... if so please tell me... because I get the feeling that I am mixing up things here, the Picard commandline tools and SAM-JDK.

Many thanks,
Wil

*** edit
Read the thread on the quality of posts (here). I was already unsure whether asking this question was inappropriate or not... So here how I feel about my own question:
- very sorry if it's silly
- I am very fond of SAMtools, don't get me wrong!
- I'd rather not bother the developers with this if it does turn out to be a very silly question. That is why I turn to this forum.
- and most importantly: a major thanks to all who take the time to read my questions, think about them and reply to them!