$ mvn install 

$ spark-shell \ --conf spark.serializer=org.apache.spark.serializer.KryoSerializer \ --conf spark.kryo.registrator=org.biojava.nbio.adam.BiojavaKryoRegistrator \ --jars target/biojava-adam-$VERSION.jar,$PATH_TO_ADAM_ASSEMBLY_JAR Welcome to ____ __ / __/__ ___ _____/ /__ _\ \/ _ \/ _ `/ __/ '_/ /___/ .__/\_,_/_/ /_/\_\ version 3.2.1 /_/ Using Scala version 2.12.15 (Java HotSpot(TM) 64-Bit Server VM, Java 1.8.0_191) Type in expressions to have them evaluated. Type :help for more information. scala> import org.biojava.nbio.adam.BiojavaAdamContext import org.biojava.nbio.adam.BiojavaAdamContext scala> val bc = BiojavaAdamContext(sc) bc: org.biojava.nbio.adam.BiojavaAdamContext = org.biojava.nbio.adam.BiojavaAdamContext@4f8900b0 scala> val reads = bc.loadFastqReads("src/test/resources/org/biojava/nbio/adam/bqsr.0.fq") reads: org.bdgenomics.adam.rdd.read.ReadRDD = RDDBoundReadRDD with 0 reference sequences scala> reads.rdd.first res0: org.bdgenomics.formats.avro.Read = {"name": "SRR062634.10022079/1", "description": "SRR062634.10022079/1", "alphabet": "DNA", "sequence": "AATTCAAAACCAGCCTGGCCAATATGGTGAAACCTCATCTCTACTAAAA ATACAAAAATTAGCCAGGCATGGTGGTGCGTGCGTGTAGTCCCAGCTACTT", "length": 100, "qualityScores": "?-DDBEEB=EEEDDEDEE EA:D?5?E?CEBE5ED?D:AEDEDEDED-B,BC0AC,BB6@CDBDEC?BCBAA@5,=8CA-?A>?2:&048<BB5BE#####", "qualityScoreVariant": "FASTQ_SANGER", "attributes": {}} scala> val dna = bc.loadBiojavaFastaDna("src/test/resources/org/biojava/nbio/adam/hla_gen.0.fa") dna: org.bdgenomics.adam.rdd.sequence.SequenceRDD = RDDBoundSequenceRDD with 0 reference sequences scala> dna.rdd.first res0: org.bdgenomics.formats.avro.Sequence = {"name": "HLA:HLA00001 A*01:01:01:01 3503 bp", "description": null, "alphabet": "DNA", "sequence": "CAGGAGCAGAGGGGTCAGGGCGAAGTCCCAGGGCCCCAGGCGTGGCTCTCAG GGTCTCAGGCCCCGAAGGCGGTGTATGGATTGGGGAGTCCCAGCCTTGGGGATTCCCCAACTCCGCAGTTTCTTTTCTCCCTCTCCCAACCTACGTAGGGTCCTT CATCCTGGATACTCACGACGCGGACCCAGTTCTCACTCCCATTGGGTGTCGGGTTTCCAGAGAAGCCAATCAGTGTCGTCGCGGTCGCTGTTCTAAAGTCCGCAC ... scala> val prot = bc.loadBiojavaFastaProtein("src/test/resources/org/biojava/nbio/adam/hla_prot.0.fa") prot: org.bdgenomics.adam.rdd.sequence.SequenceRDD = RDDBoundSequenceRDD with 0 reference sequences scala> prot.rdd.first res2: org.bdgenomics.formats.avro.Sequence = {"name": "HLA:HLA00001 A*01:01:01:01 365 bp", "description": null, "alphabet": "PROTEIN", "sequence": "MAVMAPRTLLLLLSGALALTQTWAGSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSD AASQKMEPRAPWIEQEGPEYWDQETRNMKAHSQTDRANLGTLRGYYNQSEDGSHTIQIMYGCDVGPDGRFLRGYRQDAYDGKDYIALNEDLRSWTAADMAAQITK RKWEAVHAAEQRRVYLEGRCVDGLRRYLENGKETLQRTDPPKTHMTHHPISDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDGTFQKWAAVVV PSGEEQRYTCHVQHEGLPKPLTLRWELSSQPTIPIVGIIAGLVLLGAVITGAVVAAVMWRRKSSDRKGGSYTQAASSDSAQGSDVSLTACKV", "length": 365, "attributes": {}} scala> val genbankDna = bc.loadGenbankDna("src/test/resources/org/biojava/nbio/adam/SCU49845.gb") genbankDna: org.bdgenomics.adam.rdd.sequence.SequenceRDD = RDDBoundSequenceRDD with 0 reference sequences scala> genbankDna.rdd.first res4: org.bdgenomics.formats.avro.Sequence = {"name": "U49845", "description": "Saccharomyces cerevisiae TCP1-beta gene, partial cds; and Axl2p\n(AXL2) and Rev7p (REV7) genes, complete cds.", "alphabet": "DNA", "sequence": "GATCCTCCATATACAACGGTATCTCCACCTCAGGTTTAGATCTCAACAACGGAACCATTGCCGACATGAGACAGTTAGGTATCGTCGAGAGT TACAAGCTAAAACGAGCAGTAGTCAGCTCTGCATCTGAAGCCGCTGAAGTTCTACTAAGGGTGGATAACATCATCCGTGCAAGACCAAGAACCGCCAATAGACAA CATATGTAACATATTTAGGATATACCTCGAAAATAATAAACCGCCACACTGTCATTATTATAATTAGAAACAGAACGCAAAAATTATCCACTATATAATTCAAAG ... scala> val features = bc.loadGenbankDnaFeatures("src/test/resources/org/biojava/nbio/adam/SCU49845.gb") features: org.bdgenomics.adam.rdd.feature.FeatureRDD = RDDBoundFeatureRDD with 0 reference sequences scala> features.rdd.first res5: org.bdgenomics.formats.avro.Feature = {"featureId": null, "name": "source", "source": null, "featureType": null, "contigName": "U49845", "start": 0, "end": 5028, "strand": "FORWARD", "phase": null, "frame": null, "score": null, "geneId": null, "transcriptId": null, "exonId": null, "aliases": [], "parentIds": [], "target": null, "gap": null, "derivesFrom": null, "notes": [], "dbxrefs": [], "ontologyTerms": [], "circular": null, "attributes": {}} 

$ INPUT=Homo_sapiens.GRCh38.96.chromosome.21.dat.gz \ OUTPUT=Homo_sapiens.GRCh38.96.chromosome.21.sequences.adam \ spark-shell \ --conf spark.serializer=org.apache.spark.serializer.KryoSerializer \ --conf spark.kryo.registrator=org.biojava.nbio.adam.BiojavaKryoRegistrator \ --jars target/biojava-adam-$VERSION.jar,$PATH_TO_ADAM_ASSEMBLY_JAR -i scripts/loadGenbankDna.scala