htsjdk的使用

写在前面

直接从htsjdk中掌握其使用，以掌握在没有教程的情况下，从api接口文档直接掌握依赖库的使用
官网API地址: https://samtools.github.io/htsjdk/javadoc/htsjdk/index.html

官方API文档

大概看了下文档之后，发现SAMReader可能是使用了我还是比较陌生的工厂模式，需要从一个SAMReaderFactory来获取

public abstract class SamReaderFactory
extends java.lang.Object
Describes the functionality for producing SamReader, and offers a handful of static generators.

     SamReaderFactory.makeDefault().open(new File("/my/bam.bam");
 
Example: Configure a factory

      final SamReaderFactory factory =
          SamReaderFactory.makeDefault()
              .enable(SamReaderFactory.Option.INCLUDE_SOURCE_IN_RECORDS, SamReaderFactory.Option.VALIDATE_CRC_CHECKSUMS)
              .validationStringency(ValidationStringency.SILENT);

 
Example: Open two bam files from different sources, using different options

     final SamReaderFactory factory =
          SamReaderFactory.makeDefault()
              .enable(SamReaderFactory.Option.INCLUDE_SOURCE_IN_RECORDS, SamReaderFactory.Option.VALIDATE_CRC_CHECKSUMS)
              .validationStringency(ValidationStringency.SILENT);

     // File-based bam
     final SamReader fileReader = factory.open(new File("/my/bam.bam"));

     // HTTP-hosted BAM with index from an arbitrary stream
     final SeekableStream myBamIndexStream = ...
     final SamInputResource resource =
          SamInputResource.of(new URL("http://example.com/data.bam")).index(myBamIndexStream);
     final SamReader complicatedReader = factory.open(resource);

简单的快速打开和遍历SAM文件

        SamReader sr = SamReaderFactory.makeDefault().enable(SamReaderFactory.Option.INCLUDE_SOURCE_IN_RECORDS).validationStringency(ValidationStringency.SILENT).open(new File("D:\\Tmp\\StructureScore\\merged.region.sorted.bam"));
        SAMRecordIterator samIterator = sr.iterator();
        while (samIterator.hasNext()) {
            SAMRecord curSAM = samIterator.next();
            System.err.println(curSAM.getReferenceIndex());
            System.err.println(curSAM.getReadName());
            System.err.println(curSAM.getReferenceName());
        }

打开并快速获取BAM文件的某个区域（使用了BAI）

        SamReader sr = SamReaderFactory.makeDefault().enable(SamReaderFactory.Option.INCLUDE_SOURCE_IN_RECORDS).validationStringency(ValidationStringency.SILENT).open(new File("D:\\Tmp\\StructureScore\\merged.region.sorted.bam"));
        SAMRecordIterator samIterator1 = sr.query("miRNA_6", 1116, 1117,true);
        while (samIterator1.hasNext()) {
            SAMRecord curSAM = samIterator1.next();
            System.err.println(curSAM.getReadName());
            System.err.println(curSAM.getReferenceName());
        }

其中miRNA_6是染色体ID，随后是 起始坐标和终止坐标。

有帮助的帖子 ，关于 htsjdk 索引的使用

https://www.biostars.org/p/214515/

如何做超过两个的分割面板

https://stackoverflow.com/questions/25593672/creating-jsplitpane-with-3-panels