why htsjdk SamReader query() not work?

Question

[wkk.215774]

l am using htsjdk package to handle my bam file, but it seems the SamReader query() method does not work for me. This is my program code:

SamReader reader=SamReaderFactory.makeDefault().open(new File(in_bam_file));
    SAMFileWriter outputstream=new SAMFileWriterFactory().makeSAMWriter(reader.getFileHeader(), true, new File(out_bam_file));
    SAMRecordIterator recordQuery=reader.query("chr1",1, 10000000,true);
    while(recordQuery.hasNext())
    System.out.println("query size is:\t"+recordQuery.next());

when l running this program, nothing print out. l have already read the htsjdk api doc, but l don't know why. Someone know this? l use htsjdk 2.9.1

[Pierre Lindenbaum]

1) are you sure there is a 'chr1' in your bam file ('chr1" , not '1' ). What the output of

samtools -c your.bam "chr1:1-10000000"

2) what's the point of this SAMFileWriter ?

[wkk.215774]

1) yes, pretty sure, cause l use "samtools view -H R7103052.bam" to check the header @SQ, it's chr1 not 1. 2) "SAMFileWriter" is just for testing.