Extract the SAM File header section

Question

[mhasa006]

How can I extract the header section of the SAM File with htsjdk package? Below is an example of a SAM File

@HD     VN:1.3  SO:coordinate
@SQ     SN:chr1 LN:248956422
@SQ     SN:chr10        LN:133797422
@SQ     SN:chr11        LN:135086622
XXX:111:312:1312     99      chr1    10349   1       56M44S  =       10349   56      CCCTAACCTAACCCTAACCCTAA EEEEEEEEEEEEEEEEEEEEEEEE
XXX:111:312:1312     99      chr1    10349   1       56M44S  =       10349   56      CCCTAACCTAACCCTAACCCTAA EEEEEEEEEEEEEEEEEEEEEEEE

I want to extract only

    @HD     VN:1.3  SO:coordinate
    @SQ     SN:chr1 LN:248956422
    @SQ     SN:chr10        LN:133797422
    @SQ     SN:chr11        LN:135086622

How to do that with htsjdk?

Answer 1

[Pierre Lindenbaum]

a minimal code. Don't do this in production (static method, streams are not closed,...)

import htsjdk.samtools.*;
import java.io.*;

class Biostar327241 {
public static void main(final String args[]) throws Exception {
 new SAMTextHeaderCodec().encode(
    new PrintWriter(System.out),
    SamReaderFactory.makeDefault().open(new File(args[0])).getFileHeader(),
    true
    );
  }
}

compile:

javac -cp "/path/to/com/github/samtools/htsjdk/2.15.0/htsjdk-2.15.0.jar:/path/to/commons-logging/commons-logging/1.1.1/commons-logging-1.1.1.jar:/path/to/gov/nih/nlm/ncbi/ngs-java/1.2.4/ngs-java-1.2.4.jar:/path/to/org/apache/commons/commons-compress/1.4.1/commons-compress-1.4.1.jar:/path/to/org/apache/commons/commons-jexl/2.1.1/commons-jexl-2.1.1.jar:/path/to/org/tukaani/xz/1.5/xz-1.5.jar:/path/to/org/xerial/snappy/snappy-java/1.1.4/snappy-java-1.1.4.jar"  Biostar327241.java

execute (don't forget the '.' alone at the end of the classpath):

java -cp "/path/to/com/github/samtools/htsjdk/2.15.0/htsjdk-2.15.0.jar:/path/to/commons-logging/commons-logging/1.1.1/commons-logging-1.1.1.jar:/path/to/gov/nih/nlm/ncbi/ngs-java/1.2.4/ngs-java-1.2.4.jar:/path/to/org/apache/commons/commons-compress/1.4.1/commons-compress-1.4.1.jar:/path/to/org/apache/commons/commons-jexl/2.1.1/commons-jexl-2.1.1.jar:/path/to/org/tukaani/xz/1.5/xz-1.5.jar:/path/to/org/xerial/snappy/snappy-java/1.1.4/snappy-java-1.1.4.jar:."  Biostar327241 S1.bam


@HD VN:1.3  SO:coordinate
@SQ SN:RF01 LN:3302
@SQ SN:RF02 LN:2687
@SQ SN:RF03 LN:2592
@SQ SN:RF04 LN:2362
@SQ SN:RF05 LN:1579
@SQ SN:RF06 LN:1356
@SQ SN:RF07 LN:1074
@SQ SN:RF08 LN:1059
@SQ SN:RF09 LN:1062
@SQ SN:RF10 LN:751
@SQ SN:RF11 LN:666
@RG ID:S1   SM:S1   LB:L1   CN:Nantes