Write free text comment with @CO in BAM file
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6 weeks ago
mhasa006 ▴ 50

I'm trying to add a free text while writing the reads in a BAM file. As the Java hstjdk samtool doc mentions, I can add a free text with @CO SAMTag. For example,

I'm adding the NM tag and MD tag using this code

record.setAttribute(htsjdk.samtools.SAMTag.MD.name(), "Value");
record.setAttribute(htsjdk.samtools.SAMTag.NM.name(), "Value");

But when I try to do the same for @CO tag

record.setAttribute(htsjdk.samtools.SAMTag.CO.name(), "Value");

I get the following error

cannot find symbol
symbol:   variable CO
location: class htsjdk.samtools.SAMTag

Can someone help me figure out how to add free text while writing a BAM file? Thanks in advance.

BAM hstjdk java • 715 views
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what is your version of htsjdk ?

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samtools 1.2 Using htslib 1.2.1

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Samtools is up to v.1.12 so consider updating.

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Can this be an issue because of the earlier version of samtools? I tried the

record.setAttribute("SO","value");

It runs through without error, but nothing was written in the BAM file

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but nothing was written in the BAM file

we cannot help without seeing the code.

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GenoMax htsjdk version is ~ not related to samtools or htslib.

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no, what is the version of htsjdk ? not samtools, not htslib. https://github.com/samtools/htsjdk/releases

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htsjdk version 1.133

Can the version cause this issue?

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htsjdk version 1.133 Can the version cause this issue?

yes. 1.333 is 7 years old. And CO was not defined then.

https://github.com/samtools/htsjdk/blob/3ed9b1d7681099ab77921916f7e6d0dd29f7d245/src/java/htsjdk/samtools/SAMTag.java

It's just too old. You shouldn't use this library. "951 commits to master since this release "

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Got it, Thanks for the help.

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6 weeks ago

use setAttribute(String,String) https://github.com/samtools/htsjdk/blob/master/src/main/java/htsjdk/samtools/SAMRecord.java#L1529

record.setAttribute("SO","value");
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