基因数据处理42之mango问题_seqdict.avro不存在解决

参考【1】中问题解决
问题分析：这是新版本的问题：adam0.19.1目前在maven中心仓库没有

解决办法：

package org.gcdss.testimport java.io.Fileimport java.nio.file.Filesimport org.apache.parquet.hadoop.metadata.CompressionCodecNameimport org.apache.spark.{SparkContext, SparkConf}import org.bdgenomics.adam.rdd.{ADAMSaveAnyArgs}import org.bdgenomics.adam.rdd.ADAMContext._/**  * Created by xubo on 2016/5/30.  */object fastqSaveAdam0191 {  def resourcePath(path: String) = ClassLoader.getSystemClassLoader.getResource(path).getFile  def tmpFile(path: String) = Files.createTempDirectory("").toAbsolutePath.toString + "/" + path  def main(args: Array[String]) {    val conf = new SparkConf().setMaster("local[4]").setAppName(this.getClass().getSimpleName().filter(!_.equals('$')))    val sc = new SparkContext(conf)    //    val fastqFile = "hs38DHL1F10Len10.fq"    //    val fastqFile = "mouse_chrM.bam"F    val fastqFile = " datatest2.sort.bam"    //    val fastqLoad = sc.loadAlignments(resourcePath(fastqFile))    val fastqLoad = sc.loadAlignments(fastqFile)    //    fastqLoad.rdd.take(10).foreach(println)    //    fastqLoad.rdd.adamParquetSave("adam")    def tempLocation(suffix: String = ".adam"): String = {      val tempFile = File.createTempFile("ADAMContextSuite", "")      val tempDir = tempFile.getParentFile      new File(tempDir, tempFile.getName + suffix).getAbsolutePath    }    val loc = tempLocation()    println(loc)    fastqLoad.rdd.saveAsParquet(TestSaveArgs(loc), fastqLoad.sequences, fastqLoad.recordGroups)    //    fastqLoad.    println("end")    sc.stop  }}case class TestSaveArgs(var outputPath: String) extends ADAMSaveAnyArgs {  var sortFastqOutput = false  var asSingleFile = false  var blockSize = 128 * 1024 * 1024  var pageSize = 1 * 1024 * 1024  var compressionCodec = CompressionCodecName.GZIP  var logLevel = "SEVERE"  var disableDictionaryEncoding = false}

pom配置：

<?xml version="1.0" encoding="UTF-8"?><project xmlns="http://maven.apache.org/POM/4.0.0"         xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"         xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">    <modelVersion>4.0.0</modelVersion>    <groupId>org.gcdss</groupId>    <artifactId>GCDSS</artifactId>    <version>1.0-SNAPSHOT</version>    <properties>        <adam.version>0.19.1-SNAPSHOT</adam.version>        <scala.version>2.10.4</scala.version>        <scala.version.prefix>2.10</scala.version.prefix>        <scalatra.version>2.4.+</scalatra.version>        <spark.version>1.5.2</spark.version>        <parquet.version>1.8.1</parquet.version>    </properties>    <repositories>        <repository>            <id>central</id>            <url>http://repo1.maven.org/maven2/</url>        </repository>        <repository>            <id>Sonatype</id>            <url>http://oss.sonatype.org/content/repositories/snapshots/</url>        </repository>        <repository>            <id>Apache</id>            <url>http://people.apache.org/repo/m2-snapshot-repository</url>        </repository>        <repository>            <id>SparkPackagesRepo</id>            <url>http://dl.bintray.com/spark-packages/maven</url>        </repository>    </repositories>    <build>        <plugins>            <plugin>                <groupId>org.scalatest</groupId>                <artifactId>scalatest-maven-plugin</artifactId>                <configuration>                    <reportsDirectory>${project.build.directory}/surefire-reports</reportsDirectory>                    <junitxml>.</junitxml>                    <filereports>ADAMTestSuite.txt</filereports>                    <!--                        As explained here: http://stackoverflow.com/questions/1660441/java-flag-to-enable-extended-serialization-debugging-info                        The second option allows us better debugging for serialization-based errors.                    -->                    <argLine>-Xmx1024m -Dsun.io.serialization.extendedDebugInfo=true</argLine>                </configuration>                <executions>                    <execution>                        <id>test</id>                        <goals>                            <goal>test</goal>                        </goals>                    </execution>                </executions>            </plugin>        </plugins>    </build>    <dependencies>        <!--<dependency>-->        <!--<groupId>org.bdgenomics.utils</groupId>-->        <!--<artifactId>utils-misc_2.10</artifactId>-->        <!--<type>test-jar</type>-->        <!--<scope>test</scope>-->        <!--</dependency>-->        <!--<dependency>-->        <!--<groupId>org.bdgenomics.bdg-formats</groupId>-->        <!--<artifactId>bdg-formats</artifactId>-->        <!--</dependency>-->        <dependency>            <groupId>org.bdgenomics.adam</groupId>            <artifactId>adam-core_2.10</artifactId>            <version>${adam.version}</version>        </dependency>        <dependency>            <groupId>org.bdgenomics.adam</groupId>            <artifactId>adam-core_2.10</artifactId>            <version>${adam.version}</version>            <type>test-jar</type>            <scope>test</scope>        </dependency>        <dependency>            <groupId>org.bdgenomics.adam</groupId>            <artifactId>adam-cli_2.10</artifactId>            <version>${adam.version}</version>        </dependency>        <!--<dependency>-->        <!--<groupId>org.scalatest</groupId>-->        <!--<artifactId>scalatest_2.10</artifactId>-->        <!--<scope>test</scope>-->        <!--</dependency>-->    </dependencies></project>

结果：

hadoop@Master:~/xubo/data/mango$ unzip ADAMContextSuite5309214740546591997.adam.zip Archive:  ADAMContextSuite5309214740546591997.adam.zip   creating: ADAMContextSuite5309214740546591997.adam/ extracting: ADAMContextSuite5309214740546591997.adam/._SUCCESS.crc   extracting: ADAMContextSuite5309214740546591997.adam/._common_metadata.crc   extracting: ADAMContextSuite5309214740546591997.adam/._metadata.crc   extracting: ADAMContextSuite5309214740546591997.adam/._rgdict.avro.crc   extracting: ADAMContextSuite5309214740546591997.adam/._seqdict.avro.crc   extracting: ADAMContextSuite5309214740546591997.adam/.part-r-00000.gz.parquet.crc   extracting: ADAMContextSuite5309214740546591997.adam/_SUCCESS    inflating: ADAMContextSuite5309214740546591997.adam/_common_metadata    inflating: ADAMContextSuite5309214740546591997.adam/_metadata    inflating: ADAMContextSuite5309214740546591997.adam/_rgdict.avro    inflating: ADAMContextSuite5309214740546591997.adam/_seqdict.avro    inflating: ADAMContextSuite5309214740546591997.adam/part-r-00000.gz.parquet  

运行环境为idea

参考：
【1】 http://blog.csdn.net/xubo245/article/details/51537256
【2】https://github.com/bigdatagenomics/adam/blob/master/adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/AlignmentRecordRDDFunctions.scala
【3】https://github.com/bigdatagenomics/adam/blob/master/adam-core/src/main/scala/org/bdgenomics/adam/rdd/ADAMContext.scala