Adam学习16之SAM/BAM在Adam中的初始存储格式AlignmentRecord

最新推荐文章于 2021-01-24 21:23:18 发布

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最新推荐文章于 2021-01-24 21:23:18 发布

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1.SAM/BAM和Fastq一样的Avro，不详细就写了

2，数据：

{"readNum": 0, "contig": {"contigName": "chrUn_KN707606v1_decoy", "contigLength": 2200, "contigMD5": null, "referenceURL": null, "assembly": null, "species": null, "referenceIndex": 0}, "start": 1203, "oldPosition": null, "end": 1213, "mapq": 37, "readName": "chrUn_KN707606v1_decoy_1204_1728_0:0:0_1:0:0_0", "sequence": "CTCCTCGCCA", "qual": "2222222222", "cigar": "10M", "oldCigar": null, "basesTrimmedFromStart": 0, "basesTrimmedFromEnd": 0, "readPaired": false, "properPair": false, "readMapped": true, "mateMapped": false, "failedVendorQualityChecks": false, "duplicateRead": false, "readNegativeStrand": false, "mateNegativeStrand": false, "primaryAlignment": true, "secondaryAlignment": false, "supplementaryAlignment": false, "mismatchingPositions": "10", "origQual": null, "attributes": "XT:A:U\tXO:i:0\tXM:i:0\tNM:i:0\tXG:i:0\tX1:i:0\tX0:i:1", "recordGroupName": null, "recordGroupSequencingCenter": null, "recordGroupDescription": null, "recordGroupRunDateEpoch": null, "recordGroupFlowOrder": null, "recordGroupKeySequence": null, "recordGroupLibrary": null, "recordGroupPredictedMedianInsertSize": null, "recordGroupPlatform": null, "recordGroupPlatformUnit": null, "recordGroupSample": null, "mateAlignmentStart": null, "mateAlignmentEnd": null, "mateContig": null, "inferredInsertSize": null}

3.代码：

package org.bdgenomics.adamLocal.algorithms.test

import org.bdgenomics.formats.avro.AlignmentRecord
import org.bdgenomics.adam.models.SequenceRecord
import org.bdgenomics.formats.avro.Contig

object SAMFormat {
  def main(args: Array[String]) {
    val builder: AlignmentRecord.Builder = AlignmentRecord.newBuilder
    //    builder.setContig(SequenceRecord.toADAMContig(rec))
    val contig = Contig.newBuilder
    builder.setContig(contig.build)
    val sam = builder.build()
    println(sam);
  }
}

结果：

{"readNum": 0, "contig": {"contigName": null, "contigLength": null, "contigMD5": null, "referenceURL": null, "assembly": null, "species": null, "referenceIndex": null}, "start": null, "oldPosition": null, "end": null, "mapq": null, "readName": null, "sequence": null, "qual": null, "cigar": null, "oldCigar": null, "basesTrimmedFromStart": 0, "basesTrimmedFromEnd": 0, "readPaired": false, "properPair": false, "readMapped": false, "mateMapped": false, "failedVendorQualityChecks": false, "duplicateRead": false, "readNegativeStrand": false, "mateNegativeStrand": false, "primaryAlignment": false, "secondaryAlignment": false, "supplementaryAlignment": false, "mismatchingPositions": null, "origQual": null, "attributes": null, "recordGroupName": null, "recordGroupSequencingCenter": null, "recordGroupDescription": null, "recordGroupRunDateEpoch": null, "recordGroupFlowOrder": null, "recordGroupKeySequence": null, "recordGroupLibrary": null, "recordGroupPredictedMedianInsertSize": null, "recordGroupPlatform": null, "recordGroupPlatformUnit": null, "recordGroupSample": null, "mateAlignmentStart": null, "mateAlignmentEnd": null, "mateContig": null, "inferredInsertSize": null}