Last commit

Filters a BAM using a java expression compiled in memory.


Usage: samjdk [options] Files
      Compression Level.
      Default: 5
      user's code is the whole body of the filter class, not just the 'apply' 
      Default: false
    -e, --expression
      java expression
    -X, --fail
      Save dicarded reads in that file
    -f, --file
      java file. Either option -e or -f is required.
    -h, --help
      print help and exit
      What kind of help. One of [usage,markdown,xml].
    -N, --limit
      limit to 'N' records (for debugging).
      Default: -1
       Don't show the generated code
      Default: false
    -o, --output
      Output file. Optional . Default: stdout
      [20171110] PAIR-MODE .The signature of java function is `public Object 
      apply(final List<SAMRecord> records)`. This function must return `true` 
      to accept the whole list, `false` to reject eveything, or another 
      `List<SAMRecord>`.Input MUST be sorted on query name using picard 
      SortSam (not `samtools sort` 
      https://github.com/samtools/hts-specs/issues/5 ).
      Default: false
    -R, --reference
      For reading CRAM. Indexed fasta Reference file. This file must be 
      indexed with samtools faidx and with picard CreateSequenceDictionary
      Sam output format.
      Default: SAM
      Possible Values: [BAM, SAM, CRAM]
      Save the generated java code in the following directory
      print version and exit


See also in Biostars


Requirements / Dependencies

Download and Compile

$ git clone "https://github.com/lindenb/jvarkit.git"
$ cd jvarkit
$ ./gradlew samjdk

The java jar file will be installed in the dist directory.

Creation Date


Source code


Unit Tests




The project is licensed under the MIT license.


Should you cite samjdk ? https://github.com/mr-c/shouldacite/blob/master/should-I-cite-this-software.md

The current reference is:


Filters a BAM using a java expression compiled at runtime.

About the script

The user code is a piece of java code that will be inserted as the method test, or as the body of a com.github.lindenb.jvarkit.tools.samjs.SamJdk.AbstractFilter class with implements java.util.function.Predicate<SAMRecord>:

At the time of writing the documentation, the parent class AbstractFilter is defined as:

public static class AbstractFilter
		implements Function<SAMRecord,Object>
		// hashmap, the user is free to use It 
		protected final Map<String,Object> userData = new HashMap<>();
		// input SAM header
		protected final SAMFileHeader header;
		protected AbstractFilter(final SAMFileHeader header) {
			this.header = header;
		public Object apply(final SAMRecord record) {
			throw new IllegalStateException("apply(record) for AbstractFilter is not implemented");


The user code will be inserted in the following java code:

 1  import java.util.*;
 2  import java.util.stream.*;
 3  import java.util.function.*;
 4  import htsjdk.samtools.*;
 5  import htsjdk.samtools.util.*;
 6  import javax.annotation.processing.Generated;
 7  @Generated(value="SamJdk",date="2017-08-07T14:48:39+0200")
 8  public class SamJdkCustom756098808 extends com.github.lindenb.jvarkit.tools.samjs.SamJdk.AbstractFilter {
 9    public SamJdkCustom756098808(final SAMFileHeader header) {
10    super(header);
11    }
12    @Override
13    public boolean test(final SAMRecord record) {
14     // user's code starts here 
15     return record.getContig()==null;
16     //user's code ends here 
17     }
18  }

When the option --body is set : the user’s code is the whole body (but the constructor) of the class

The program is then compiled in memory.

The method apply returns an object that can either:


Example 1

get a SAM where the read OR the mate is unmapped

java -jar dist/samjdk.jar  \
	-e "return record.getReadUnmappedFlag() || record.getMateUnmappedFlag();" \

@HD	VN:1.4	SO:unsorted
@SQ	SN:seq1	LN:1575
@SQ	SN:seq2	LN:1584
B7_591:4:96:693:509	73	seq1	1	99	36M	*	0	0	CACTAGTGGCTCATTGTAAATGTGTGGTTTAACTCG	<<<<<<<<<<<<<<<;<<<<<<<<<5<<<<<;:<;7	H0:i:1	H1:i:0	MF:i:18	NM:i:0	UQ:i:0	Aq:i:73
EAS54_65:7:152:368:113	73	seq1	3	99	35M	*	0	0	CTAGTGGCTCATTGTAAATGTGTGGTTTAACTCGT	<<<<<<<<<<0<<<<655<<7<<<:9<<3/:<6):H0:i:1	H1:i:0	MF:i:18	NM:i:0	UQ:i:0	Aq:i:66
EAS51_64:8:5:734:57	137	seq1	5	99	35M	*	0	0	AGTGGCTCATTGTAAATGTGTGGTTTAACTCGTCC	<<<<<<<<<<<7;71<<;<;;<7;<<3;);3*8/5H0:i:1	H1:i:0	MF:i:18	NM:i:0	UQ:i:0	Aq:i:66
B7_591:1:289:587:906	137	seq1	6	63	36M	*	0	0	GTGGCTCATTGTAATTTTTTGTTTTAACTCTTCTCT	(-&----,----)-)-),'--)---',+-,),''*,	H0:i:0	H1:i:0	MF:i:130	NM:i:5	UQ:i:38	Aq:i:63
EAS56_59:8:38:671:758	137	seq1	9	99	35M	*	0	0	GCTCATTGTAAATGTGTGGTTTAACTCGTCCATGG	<<<<<<<<<<<<<<<;<;7<<<<<<<<7<<;:<5%H0:i:1	H1:i:0	MF:i:18	NM:i:0	UQ:i:0	Aq:i:72
EAS56_61:6:18:467:281	73	seq1	13	99	35M	*	0	0	ATTGTAAATGTGTGGTTTAACTCGTCCCTGGCCCA	<<<<<<<<;<<<8<<<<<;8:;6/686&;(16666H0:i:0	H1:i:1	MF:i:18	NM:i:1	UQ:i:5	Aq:i:39
EAS114_28:5:296:340:699	137	seq1	13	99	36M	*	0	0	ATTGTAAATGTGTGGTTTAACTCGTCCATGGCCCAG	<<<<<;<<<;<;<<<<<<<<<<<8<8<3<8;<;<0;	H0:i:1	H1:i:0	MF:i:18	NM:i:0	UQ:i:0	Aq:i:73
B7_597:6:194:894:408	73	seq1	15	99	35M	*	0	0	TGTAAATGTGTGGTTTAACTCGTCCATTGCCCAGC	<<<<<<<<<7<<;<<<<;<<<7;;<<<*,;;572<H0:i:0	H1:i:1	MF:i:18	NM:i:1	UQ:i:9	Aq:i:43
EAS188_4:8:12:628:973	89	seq1	18	75	35M	*	0	0	AAATGTGTGGTTTAACTCGTCCATGGCCCAGCATT	==;=:;:;;:====;=;===:=======;==;===H0:i:1	H1:i:0	MF:i:64	NM:i:0	UQ:i:0	Aq:i:0

Example 2

remove reads with indels:

java -jar dist/samjdk.jar -e 'if(record.getReadUnmappedFlag()) return false; Cigar cigar=record.getCigar();if(cigar==null) return false; for(int i=0;i< cigar.numCigarElements();++i) {if(cigar.getCigarElement(i).getOperator().isIndelOrSkippedRegion()) return false; } return true;' input.bam

Example 3

select unmappeds read or clipped reads

java -jar dist/samjdk.jar -o out.bam -e 'return record.getReadUnmappedFlag() || record.getCigar().getCigarElements().stream().anyMatch(C->C.getOperator().isClipping());'  in.bam

Example 4

check whether all BAM read contain defined read groups? ( https://bioinformatics.stackexchange.com/questions/2590/ )

java -jar dist/samjdk.jar -e 'return record.getReadGroup()==null;'  input.bam

Example 5

select chimeric reads virus/host

java -jar dist/samjdk.jar -e '
    final Set<String> virus_chrom = new HashSet<>(Arrays.asList("viral_seg1", "viral_seg2"));
    if(record.getReadUnmappedFlag()) return false;
    if(record.getReadPairedFlag() && !record.getMateUnmappedFlag())
        if( virus_chrom.contains(record.getReferenceName()) !=
            return true;
    for(final SAMRecord other: SAMUtils.getOtherCanonicalAlignments(record))
        if( virus_chrom.contains(record.getReferenceName()) !=
            return true;
    return false;' input.bam


cigar string with deletion >= 1kb

$ java -jar dist/samjdk.jar -e 'return !record.getReadUnmappedFlag() && record.getCigar().getCigarElements().stream().anyMatch(C->C.getLength()>=1000 && (C.getOperator()==CigarOperator.N || C.getOperator()==CigarOperator.D));'  in.bam


in PAIRED mode find some pairs of reads where at least one read startsWith AAAAAAG. See https://bioinformatics.stackexchange.com/questions/2812.

java -jar picard.jar SortSam I=S1.bam O=/dev/stdout  SO=queryname |\
java -jar dist/samjdk.jar --samoutputformat BAM --pair -e 'return records.stream().anyMatch(R->R.getReadString().startsWith("AAAAAAG"));' |\
samtools sort -T tmp - | samtools view -h - 


@HD	VN:1.5	GO:none	SO:coordinate
@SQ	SN:rotavirus	LN:1074
@PG	ID:bwa	PN:bwa	VN:0.7.12-r1044	CL:../bwa/bwa mem -R @RG\tID:S1\tSM:S1 ref.fa S1_01_R1.fq.gz S1_01_R2.fq.gz
@PG	ID:bwa.1	PN:bwa	VN:0.7.12-r1044	CL:../bwa/bwa mem -R @RG\tID:S1\tSM:S1 ref.fa S1_02_R1.fq.gz S1_02_R2.fq.gz
@PG	ID:bwa.2	PN:bwa	VN:0.7.12-r1044	CL:../bwa/bwa mem -R @RG\tID:S1\tSM:S1 ref.fa S1_03_R1.fq.gz S1_03_R2.fq.gz
rotavirus_34_627_6:0:0_4:0:0_b6	99	rotavirus	34	60	70M	=	558	594	GATGGATTCTCCTCAGCAGATGGTAAGGTCTATTATAAAACCTTCTTTTGAAGCTGCAGTTGTTGCTGCT	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	MD:Z:6G3A16C8T2T0A29	RG:Z:S1	NM:i:6	AS:i:40	XS:i:0
rotavirus_40_627_9:0:0_3:0:0_ab	99	rotavirus	40	42	61M9S	=	558	588	GTCTACTCAGCAGATTGTAATCTCTCTTAATCATACTTCATTTGAAGCTGCCGTTGTTGCTTCTCCTTCA	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	MD:Z:15G4G4A3T1A7T11A9	RG:Z:S1	NM:i:7	AS:i:26	XS:i:19
rotavirus_52_627_5:0:0_5:0:0_2f8	163	rotavirus	52	60	70M	=	558	576	GATTGTAAGCTCTAATATTAAAACTTCTTTAGAAGGTGCAGTTGTTGCTGCTACTTCAACATTAGAATTA	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	MD:Z:3G10T6T8T4C34	RG:Z:S1	NM:i:5	AS:i:46	XS:i:0
rotavirus_132_627_6:0:0_6:0:0_1ee	163	rotavirus	132	60	70M	=	558	496	AATATGATTACAATGAAGTCTTTACCAGAGTTAAAAGTAAATATGCTTATGTGCTGTAAGACTCTGGTGT	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	MD:Z:19A22T2A7A2G1T11	RG:Z:S1	NM:i:6	AS:i:40	XS:i:0
rotavirus_160_646_2:0:0_6:0:0_2e2	99	rotavirus	160	60	70M	=	577	487	AGTTAAAAGTAAATTTGATTCTGTGATGGATGACACTGGTGTTAAAAACAATCTTTTGGGTAAAGCTATA	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	MD:Z:20A13T35	RG:Z:S1	NM:i:2	AS:i:60	XS:i:0
rotavirus_239_683_6:0:0_4:0:0_a7	163	rotavirus	239	60	64M6S	=	614	445	CAGGCGTTAAATGGAAAGATTAGCTCAGCTATAAGAAATAGCAATTGGATGAGTGATTCTAAAAGGGTAG	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	MD:Z:18T13T8A10C11	RG:Z:S1	NM:i:4	AS:i:44	XS:i:0
rotavirus_132_627_6:0:0_6:0:0_1ee	83	rotavirus	558	60	70M	=	132	-496	AAAAAAGATTTGAATAACTATAACAGAGGGTTATTGACAAATACAATTCGTGGGTACAAAAAGCGAAGAA	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	MD:Z:15C4A12A3G9A1T20	RG:Z:S1	NM:i:6	AS:i:40	XS:i:0
rotavirus_34_627_6:0:0_4:0:0_b6	147	rotavirus	558	60	70M	=	34	-594	AAAAAAGATTTGAATCACTAAAACTGAGGGTTAATGAGAAATACAATACGTCGGTACATAAAGCGAAGAA	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	MD:Z:24A24T1G6A11	RG:Z:S1	NM:i:4	AS:i:50	XS:i:0
rotavirus_40_627_9:0:0_3:0:0_ab	147	rotavirus	558	60	70M	=	40	-588	AAAAAAGATTTGAATCACTAATACAGAGGGTTAATGAGATATACAATACTTGGGTACAAAAACCGAAGAA	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	MD:Z:21A17A22G7	RG:Z:S1	NM:i:3	AS:i:55	XS:i:0
rotavirus_52_627_5:0:0_5:0:0_2f8	83	rotavirus	558	60	70M	=	52	-576	AAAAAAGATTTGAATCACGATAACAGAGGGTGAATGAGAAATACATTACTTCGGTACAAAAAGCGAAGAA	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	MD:Z:18T1A10T13A5G18	RG:Z:S1	NM:i:5	AS:i:45	XS:i:0
rotavirus_160_646_2:0:0_6:0:0_2e2	147	rotavirus	577	60	70M	=	160	-487	AAAAAAGAGGGGTTATGAGTAATACAATACTTGGGTACAAAAAGAGATGAAAGTAAATGAAAATATGTAC	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	MD:Z:4C6T1A5A24C2A22	RG:Z:S1	NM:i:6	AS:i:41	XS:i:0
rotavirus_239_683_6:0:0_4:0:0_a7	83	rotavirus	614	60	70M	=	239	-445	AAAAAAGCGAAGAAAGTAAATGTAAATAGGTACTCTCTTCAGAATGTTATCTCACAACAGCAAAAACAAA	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	MD:Z:0C21A5T36C4	RG:Z:S1	NM:i:4	AS:i:54	XS:i:0


Question: “How to extract reads with a known variant form a bam file”

Searching for a base ‘T’ on ‘rotavirus’ at 1044.

final String contig= "rotavirus";
final int mutpos = 1044;
final char mutbase='T';
if(record.getReadUnmappedFlag()) return false;
if(!record.getContig().equals(contig)) return false;
if(record.getEnd() < mutpos) return false;
if(record.getStart() > mutpos) return false;
int readpos = record.getReadPositionAtReferencePosition(mutpos);
if(readpos<1) return false;
final byte[]    bases= record.getReadBases();
if(bases[readpos]==mutbase) return true;
return false;


Remove Double clipped reads

java -jar dist/samjdk.jar -e 'if(record.getReadUnmappedFlag()) return true;final Cigar c=record.getCigar();if(c==null || c.numCigarElements()<2) return true; return !(c.getFirstCigarElement().getOperator().isClipping() && c.getLastCigarElement().getOperator().isClipping()) ;' input.bam


get discordant reads

$ java -jar dist/samjdk.jar -e 'return record.getReadPairedFlag() && !record.getReadUnmappedFlag() && !record.getMateUnmappedFlag() && !record.getReferenceName().equals(record.getMateReferenceName());'  in.bam


exclude clipped reads:

java -jar dist/samjdk.jar -e 'return record.getReadUnmappedFlag() || record.getCigar()==null || !record.getCigar().isClipped();'


BAM file for reads that map 100% identity

java -jar  dist/samjdk.jar -e 'return !record.getReadUnmappedFlag() && record.getCigarString().equals("100M") &&  (record.getIntegerAttribute("NM")==null || record.getIntegerAttribute("NM").intValue()==0);' in.bam


.. modify the vcf so that a snp that is detected where the read depth is more than the average read depth at the sample will change to the reference allele.

VariantContextBuilder vcb=new VariantContextBuilder(variant);
final double avgdp = variant.getGenotypes().stream().filter(G->G.hasDP()).mapToInt(G->G.getDP()).average().getAsDouble();
        if(!G.isCalled()) return G;
        if(!G.hasDP()) return G;
        if((double)G.getDP()> avgdp) return G;
        final List<Allele> aL=new ArrayList<>();
        while(aL.size()<G.getPloidy()) aL.add(variant.getReference());
        return new GenotypeBuilder(G).alleles(aL).make();
return vcb.make();



Subset smaller BAM to contain several thousand rows from multiple chromosomes

$ java -jar dist/samjdk.jar --body -e \
  'Map<String,Integer> c=new HashMap<>(); public Object apply(SAMRecord r) {int n=c.getOrDefault(r.getContig(),0);if(n>=5000) return false; c.put(r.getContig(),n+1); return r;}' \


getting a list of alignment with a particular bam tag from a bam file

$ java -jar dist/samjdk.jar --body \
     -e 'Set<String> xc = null;  public Object apply( SAMRecord R) { if(xc==null) try {xc=new HashSet<>(IOUtil.slurpLines(new java.io.File("needed.txt")));} catch(Exception e) {throw new RuntimeIOException(e);} String att= R.getStringAttribute("XC"); return att!=null && xc.contains(att);}' \


remove reads where clipping > 33%

$ java -jar dist/samjdk.jar -e 'return record.getReadUnmappedFlag() || record.getCigar()==null || record.getCigar().getCigarElements().stream().filter(C->C.getOperator().isClipping()).mapToInt(C->C.getLength()).sum() / (double)record.getCigar().getReadLength() < 0.33;' input.bam