Source code analysis of RNA-SeQC.jar package 2

4. Initialize the RNASeqMetrics object

   main code

        metrics.prepareOptionsFromCommandLine(cl);

  

    The main task is to inject the input parameters into the RNASeqMetrics object and create an output directory (according to the -o parameter).

    Generate refGene.txt file according to gtf

    Generate rRNA_intervals.txt file if there is no rRNA parameter

   SAMPLE_FILE attribute is bam file

   TRANSCRIPT_MODEL is a gtf file

   REF_GENOME is fasta file

 5. Read in the analysis file

    main code

   private void prepareFiles()

 

   

   read in bam file

      

this.bams = MetricSample.readInSamples(this.SAMPLE_FILE, this.OUT_DIR);

 

 

      looking for contig names in reference fai file--read into the fai file, that is, the index of fasta

     

ArrayList contigs = getOrderedContigsFAI(REF_GENOME);

   

     Load gtf file transcripts as transcript list

   

   TranscriptList transcripts = TranscriptList.loadGTF(TRANSCRIPT_GTF, transcriptTypeField);

   Generate data in refGene.txt file based on replica list and fasta index data contigs.

   List replicas in configs order

 

generation

Transcript.transcriptsToRefGeneFile(contigs, transcripts, refGeneFile);

    Among them, the rna type is written into rRNA_intervals.txt

  

   transcripts.toRRNAIntervalList(rRNAIntervalFile);