Hello Biostars Community,
I am a newbie to the bioinformatics world and need some help with a project I am working on!
I need to use htsjdk to extract every tlen value from a BAM file and have a few questions.
Sorry for all of the questions, I have been googling a lot and haven't found answers!
Any help is appreciated, thanks in advance!
•
written
by
Hakan.Erol.HE •
This may get you in the right direction:
// Open bam file
SamReader samReader= SamReaderFactory.
makeDefault().
validationStringency(ValidationStringency.SILENT).
open(new File("aln.bam"));
// Start iterating from start to end of chr7.
SAMRecordIterator iter = samReader.query("chr7", 0, 0, false);
while(iter.hasNext()){
// Iterate thorough each record and extract fragment size
SAMRecord rec= iter.next();
int tlen= rec.getInferredInsertSize();
System.out.println(tlen);
}
Get list of chromosomes/contig names from SamReader object:
List<SAMSequenceRecord> refSeqs= samReader.getFileHeader().getSequenceDictionary().getSequences();
for(SAMSequenceRecord ref : refSeqs){
System.out.println(ref.getSequenceName());
}
Ah thank you so much! getInferredInsertSize is what I was looking for, much appreciated!
Might you know how to start iterating from the start of a particular chromosome?
Hi- See edit. Have a look at the htsjdk docs for the meaning of the various method. Also make sure ValidationStringency.SILENT is ok for you.
Much appreciated. One more question, is there a function that returns the list of chromosomes/contigs so I can dynamically build that list?
The contig names do indeed work thank you. However, I am running into an issue with reading from a specific one using the query method.
I get this error: htsjdk.samtools.SAMException: No index is available for this BAM file. How do I provide the index file?
You can make the index with e.g. command line samtools samtools index aln.bam, the bam file needs to be sorted by position in order to be indexed (samtools sort aln.bam > sorted.bam). You can also sort and index within Java/htsdjk (I would have to look this up though.)
l'm using SamReader query method, but it doesn't work. Nothing print. l was wondering if you have this problem. My code:
SamReader reader=SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT).open(new File(in_bam_file));
SAMRecordIterator recordQuery=reader.query("chr3",179198825, 179199177,false);
while(recordQuery.hasNext()){
SAMRecord res=recordQuery.next();
System.out.println("query size is:\t"+res.getInferredInsertSize());
}
hi, l use SamReader query method, it doesn't work, l don't know why. My htsjdk version is 2.8.1.
SamReader reader=SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT).open(new File(in_bam_file));
SAMRecordIterator recordQuery=reader.query("chr3",179198825, 179199177,false);
while(recordQuery.hasNext()){
SAMRecord res=recordQuery.next();
System.out.println("query size is:\t"+res.getInferredInsertSize());
}
l am pretty sure, 'chr3' is right and the interval is also right. 'samtools view in.bam chr3:179198825-179199177' could print the results.
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