/*
* The MIT License
*
* Copyright (c) 2011 The Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
package picard.analysis;
import picard.metrics.MultilevelMetrics;
/**
* Metrics about the alignment of RNA-seq reads within a SAM file to genes, produced by the CollectRnaSeqMetrics
* program and usually stored in a file with the extension ".rna_metrics".
*/
public class RnaSeqMetrics extends MultilevelMetrics {
/** The total number of PF bases including non-aligned reads. */
public long PF_BASES;
/**
* The total number of aligned PF bases. Non-primary alignments are not counted. Bases in aligned reads that
* do not correspond to reference (e.g. soft clips, insertions) are not counted.
*/
public long PF_ALIGNED_BASES;
/** Number of bases in primary aligments that align to ribosomal sequence. */
public Long RIBOSOMAL_BASES;
/** Number of bases in primary aligments that align to a non-UTR coding base for some gene, and not ribosomal sequence. */
public long CODING_BASES;
/** Number of bases in primary aligments that align to a UTR base for some gene, and not a coding base. */
public long UTR_BASES;
/** Number of bases in primary aligments that align to an intronic base for some gene, and not a coding or UTR base. */
public long INTRONIC_BASES;
/** Number of bases in primary aligments that do not align to any gene. */
public long INTERGENIC_BASES;
/**
* Number of primary alignments that map to a sequence specified on command-line as IGNORED_SEQUENCE. These are not
* counted in PF_ALIGNED_BASES, CORRECT_STRAND_READS, INCORRECT_STRAND_READS, or any of the base-counting metrics.
* These reads are counted in PF_BASES.
*/
public long IGNORED_READS;
/** Number of aligned reads that map to the correct strand. 0 if library is not strand-specific. */
public long CORRECT_STRAND_READS;
/** Number of aligned reads that map to the incorrect strand. 0 if library is not strand-specific. */
public long INCORRECT_STRAND_READS;
/** RIBOSOMAL_BASES / PF_ALIGNED_BASES */
public Double PCT_RIBOSOMAL_BASES;
/** CODING_BASES / PF_ALIGNED_BASES */
public double PCT_CODING_BASES;
/** UTR_BASES / PF_ALIGNED_BASES */
public double PCT_UTR_BASES;
/** INTRONIC_BASES / PF_ALIGNED_BASES */
public double PCT_INTRONIC_BASES;
/** INTERGENIC_BASES / PF_ALIGNED_BASES */
public double PCT_INTERGENIC_BASES;
/** PCT_UTR_BASES + PCT_CODING_BASES */
public double PCT_MRNA_BASES;
/** The percentage of bases mapping to mRNA divided by the total number of PF bases. */
public double PCT_USABLE_BASES;
/** CORRECT_STRAND_READS/(CORRECT_STRAND_READS + INCORRECT_STRAND_READS). 0 if library is not strand-specific. */
public double PCT_CORRECT_STRAND_READS;
/** The median CV of coverage of the 1000 most highly expressed transcripts. Ideal value = 0. */
public double MEDIAN_CV_COVERAGE;
/**
* The median 5 prime bias of the 1000 most highly expressed transcripts, where 5 prime bias is calculated per
* transcript as: mean coverage of the 5' most 100 bases divided by the mean coverage of the whole transcript.
*/
public double MEDIAN_5PRIME_BIAS;
/**
* The median 3 prime bias of the 1000 most highly expressed transcripts, where 3 prime bias is calculated per
* transcript as: mean coverage of the 3' most 100 bases divided by the mean coverage of the whole transcript.
*/
public double MEDIAN_3PRIME_BIAS;
/** The ratio of coverage at the 5' end of to the 3' end based on the 1000 most highly expressed transcripts. */
public double MEDIAN_5PRIME_TO_3PRIME_BIAS;
}