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replace java BiojavaAdamContext with scala BiojavaAdamContext
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‎README.md‎

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# biojava-adam
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BioJava and ADAM integration.
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[Biojava](http://biojava.org) and ADAM integration.
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### Hacking biojava-adam
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@@ -38,37 +38,58 @@ Type :help for more information.
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scala> import org.biojava.nbio.adam.BiojavaAdamContext
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import org.biojava.nbio.adam.BiojavaAdamContext
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scala> val biojavaContext = new BiojavaAdamContext(sc)
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biojavaContext: org.biojava.nbio.adam.BiojavaAdamContext = org.biojava.nbio.adam.BiojavaAdamContext@1e041848
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scala> val bc = BiojavaAdamContext(sc)
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bc: org.biojava.nbio.adam.BiojavaAdamContext = org.biojava.nbio.adam.BiojavaAdamContext@4f8900b0
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scala> val reads = biojavaContext.loadFastqReads("fastq_sample1.fq")
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reads: org.bdgenomics.adam.rdd.sequence.ReadRDD = ReadRDD(MapPartitionsRDD[1] at map at BiojavaAdamContext.java:180,SequenceDictionary{
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H06HDADXX130110:1:2103:11970:57672/2->250
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H06HDADXX130110:2:2116:3345:91806/2->250
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H06HDADXX130110:1:2103:11970:57672/1->250
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H06HDADXX130110:2:2116:3345:91806/1->250
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H06JUADXX130110:1:1108:6424:55322/1->250
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H06JUADXX130110:1:1108:6424:55322/2->250})
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scala> val reads = bc.loadFastqReads("src/test/resources/org/biojava/nbio/adam/bqsr.0.fq")
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reads: org.bdgenomics.adam.rdd.read.ReadRDD = RDDBoundReadRDD with 0 reference sequences
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scala> reads.rdd.first
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res0: org.bdgenomics.formats.avro.Read = {"name": "H06HDADXX130110:2:2116:3345:91806/1", "description":
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"H06HDADXX130110:2:2116:3345:91806/1", "alphabet": "DNA", "sequence": "GTTAGGGTTAGGGTTGGGTTAGGGTTAGGGTT
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AGGGTTAGGGGTAGGGTTAGGGTTAGGGGTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGGTAGGGCTAGGGTTAAGGGTAGGGTTAGCGAAAGGGCTG
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GGGTTAGGGGTGCGGGTACGCGTAGCATTAGGGCTAGAAGTAGGATCTGCAGTGCCTGACCGCGTCTGCGCGGCGACTGCCCAAAGCCTGGGGCCGACTCCAG
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GCTGAAGCTCAT", "length": 250, "qualityScores": ">=<=???>?>???=??>>8<?><=2=<===1194<?;:?>>?#3==>########
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#######################################################################################################
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############################################################################################",
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"qualityScoreVariant": "FASTQ_SANGER"}
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scala> val sequences = biojavaContext.loadGenbankDna("SCU49845.gb")
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sequences: org.bdgenomics.adam.rdd.sequence.SequenceRDD = SequenceRDD(MapPartitionsRDD[7] at map at BiojavaAdamContext.java:244,SequenceDictionary{
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U49845->5028})
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scala> sequences.rdd.first
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res1: org.bdgenomics.formats.avro.Sequence = {"name": "U49845", "description": "Saccharomyces cerevisiae
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res0: org.bdgenomics.formats.avro.Read = {"name": "SRR062634.10022079/1", "description":
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"SRR062634.10022079/1", "alphabet": "DNA", "sequence": "AATTCAAAACCAGCCTGGCCAATATGGTGAAACCTCATCTCTACTAAAAA
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TACAAAAATTAGCCAGGCATGGTGGTGCGTGCGTGTAGTCCCAGCTACTT", "length": 100, "qualityScores": "?-DDBEEB=EEEDDEDEEEA
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:D?5?E?CEBE5ED?D:AEDEDEDED-B,BC0AC,BB6@CDBDEC?BCBAA@5,=8CA-?A>?2:&048<BB5BE#####", "qualityScoreVariant":
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"FASTQ_SANGER", "attributes": {}}
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scala> val dna = bc.loadBiojavaFastaDna("src/test/resources/org/biojava/nbio/adam/hla_gen.0.fa")
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dna: org.bdgenomics.adam.rdd.sequence.SequenceRDD = RDDBoundSequenceRDD with 0 reference sequences
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scala> dna.rdd.first
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res0: org.bdgenomics.formats.avro.Sequence = {"name": "HLA:HLA00001 A*01:01:01:01 3503 bp",
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"description": null, "alphabet": "DNA", "sequence": "CAGGAGCAGAGGGGTCAGGGCGAAGTCCCAGGGCCCCAGGCGTGGCTCTCAG
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GGTCTCAGGCCCCGAAGGCGGTGTATGGATTGGGGAGTCCCAGCCTTGGGGATTCCCCAACTCCGCAGTTTCTTTTCTCCCTCTCCCAACCTACGTAGGGTCCTT
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CATCCTGGATACTCACGACGCGGACCCAGTTCTCACTCCCATTGGGTGTCGGGTTTCCAGAGAAGCCAATCAGTGTCGTCGCGGTCGCTGTTCTAAAGTCCGCAC
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...
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scala> val prot = bc.loadBiojavaFastaProtein("src/test/resources/org/biojava/nbio/adam/hla_prot.0.fa")
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prot: org.bdgenomics.adam.rdd.sequence.SequenceRDD = RDDBoundSequenceRDD with 0 reference sequences
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scala> prot.rdd.first
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res2: org.bdgenomics.formats.avro.Sequence = {"name": "HLA:HLA00001 A*01:01:01:01 365 bp", "description":
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null, "alphabet": "PROTEIN", "sequence": "MAVMAPRTLLLLLSGALALTQTWAGSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSD
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AASQKMEPRAPWIEQEGPEYWDQETRNMKAHSQTDRANLGTLRGYYNQSEDGSHTIQIMYGCDVGPDGRFLRGYRQDAYDGKDYIALNEDLRSWTAADMAAQITK
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RKWEAVHAAEQRRVYLEGRCVDGLRRYLENGKETLQRTDPPKTHMTHHPISDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDGTFQKWAAVVV
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PSGEEQRYTCHVQHEGLPKPLTLRWELSSQPTIPIVGIIAGLVLLGAVITGAVVAAVMWRRKSSDRKGGSYTQAASSDSAQGSDVSLTACKV", "length":
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365, "attributes": {}}
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scala> val genbankDna = bc.loadGenbankDna("src/test/resources/org/biojava/nbio/adam/SCU49845.gb")
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genbankDna: org.bdgenomics.adam.rdd.sequence.SequenceRDD = RDDBoundSequenceRDD with 0 reference sequences
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scala> genbankDna.rdd.first
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res4: org.bdgenomics.formats.avro.Sequence = {"name": "U49845", "description": "Saccharomyces cerevisiae
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TCP1-beta gene, partial cds; and Axl2p\n(AXL2) and Rev7p (REV7) genes, complete cds.", "alphabet": "DNA",
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"sequence": "GATCCTCCATATACAACGGTATCTCCACCTCAGGTTTAGATCTCAACAACGGAACCATTGCCGACATGAGACAGTTAGGTATCGTCGAGAGT
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TACAAGCTAAAACGAGCAGTAGTCAGCTCTGCATCTGAAGCCGCTGAAGTTCTACTAAGGGTGGATAACATCATCCGTGCAAGACCAAGAACCGCCAATAGACAA
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CATATGTAACATATTTAGGATATACCTCGAAAATAATAAACCGCCACACTGTCATTATTATAATTAGAAACAGAACGCAAAAATTATCCACTATATAATTCAAAG
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...
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scala> val features = bc.loadGenbankDnaFeatures("src/test/resources/org/biojava/nbio/adam/SCU49845.gb")
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features: org.bdgenomics.adam.rdd.feature.FeatureRDD = RDDBoundFeatureRDD with 0 reference sequences
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scala> features.rdd.first
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res5: org.bdgenomics.formats.avro.Feature = {"featureId": null, "name": "source", "source": null,
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"featureType": null, "contigName": "U49845", "start": 0, "end": 5028, "strand": "FORWARD", "phase":
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null, "frame": null, "score": null, "geneId": null, "transcriptId": null, "exonId": null, "aliases":
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[], "parentIds": [], "target": null, "gap": null, "derivesFrom": null, "notes": [], "dbxrefs": [],
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"ontologyTerms": [], "circular": null, "attributes": {}}
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```

‎pom.xml‎

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<?xml version="1.0" encoding="ISO-8859-1"?>
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<!--
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biojava-adam BioJava and ADAM integration.
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Copyright (c) 2017 held jointly by the individual authors.
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biojava-adam Biojava and ADAM integration.
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Copyright (c) 2017-2018 held jointly by the individual authors.
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This library is free software; you can redistribute it and/or modify it
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under the terms of the GNU Lesser General Public License as published
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<packaging>jar</packaging>
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<name>biojava-adam</name>
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<version>5.0.0-SNAPSHOT</version>
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<description>BioJava and ADAM integration.</description>
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<description>Biojava and ADAM integration.</description>
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<url>http://www.biojava.org</url>
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<inceptionYear>2017</inceptionYear>
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<scm>
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<maven.enforcer.jdk-version>[1.8,)</maven.enforcer.jdk-version>
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<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
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<project.build.targetEncoding>UTF-8</project.build.targetEncoding>
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<scala.version>2.11.8</scala.version>
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<scala-guice.version>4.1.0</scala-guice.version>
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<scala.version>2.11.12</scala.version>
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<scala.version.prefix>2.11</scala.version.prefix>
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<slf4j.version>1.7.25</slf4j.version>
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<spark.version>2.2.1</spark.version>
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<artifactId>junit</artifactId>
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<version>${junit.version}</version>
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</dependency>
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<dependency>
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<groupId>net.codingwell</groupId>
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<artifactId>scala-guice_${scala.version.prefix}</artifactId>
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<version>${scala-guice.version}</version>
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</dependency>
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<dependency>
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<groupId>org.apache.spark</groupId>
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<artifactId>spark-core_2.11</artifactId>
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<artifactId>spark-core_${scala.version.prefix}</artifactId>
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<version>${spark.version}</version>
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</dependency>
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<dependency>
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<groupId>org.apache.spark</groupId>
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<artifactId>spark-sql_2.11</artifactId>
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<artifactId>spark-sql_${scala.version.prefix}</artifactId>
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<version>${spark.version}</version>
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</dependency>
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<dependency>
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<groupId>org.bdgenomics.adam</groupId>
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<artifactId>adam-core-spark2_2.11</artifactId>
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<artifactId>adam-core-spark2_${scala.version.prefix}</artifactId>
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<version>${adam.version}</version>
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<exclusions>
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<exclusion>
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<artifactId>slf4j-log4j12</artifactId>
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<version>${slf4j.version}</version>
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</dependency>
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<dependency>
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<groupId>net.codingwell</groupId>
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<artifactId>scala-guice_${scala.version.prefix}</artifactId>
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<version>4.1.0</version>
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</dependency>
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</dependencies>
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</dependencyManagement>
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<dependencies>
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<artifactId>junit</artifactId>
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<scope>test</scope>
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</dependency>
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<dependency>
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<groupId>net.codingwell</groupId>
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<artifactId>scala-guice_${scala.version.prefix}</artifactId>
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<scope>compile</scope>
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</dependency>
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<dependency>
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<groupId>org.apache.spark</groupId>
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<artifactId>spark-core_2.11</artifactId>
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<artifactId>spark-core_${scala.version.prefix}</artifactId>
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<scope>provided</scope>
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</dependency>
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<dependency>
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<groupId>org.apache.spark</groupId>
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<artifactId>spark-sql_2.11</artifactId>
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<artifactId>spark-sql_${scala.version.prefix}</artifactId>
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<scope>provided</scope>
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</dependency>
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<dependency>
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<groupId>org.bdgenomics.adam</groupId>
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<artifactId>adam-core-spark2_2.11</artifactId>
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<artifactId>adam-core-spark2_${scala.version.prefix}</artifactId>
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<scope>compile</scope>
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</dependency>
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<dependency>
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<artifactId>slf4j-log4j12</artifactId>
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<scope>test</scope>
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</dependency>
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<dependency>
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<groupId>net.codingwell</groupId>
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<artifactId>scala-guice_${scala.version.prefix}</artifactId>
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<scope>compile</scope>
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</dependency>
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</dependencies>
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<profiles>
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<profile>

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