Fixing @PG tag uniqueness issue
The Problem: ------------ the SAM spec does not allow multiple @PG tags with the same id. Our @PG tag writing routines were allowing that to happen with the boolean parameter "keep_all_pg_records". How this fixes it: ------------------ This commit removes that option from all the utility functions and cleans up the code around the classes that used these methods off-spec. Summarized changes: ------------------- * Remove keep_all_pg_records option from setupWriter utility methos in Util * Update all walkers to now replace the last @PG tag of the same walker (if it already exists) * Cleanup NWaySamFileWriter now that it doesn't need to keep track of the keep_all_pg_records variable * Simplify the multiple implementations to setupWriter Bamboo: ------- http://gsabamboo.broadinstitute.org/browse/GSAUNSTABLE-PARALLEL31 Issue Tracker: -------------- [fixes 47100885]
This commit is contained in:
Mauricio Carneiro
parent
f42bdaee3c
commit
ec475a46b1
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@ -123,7 +123,7 @@ public class ReduceReads extends ReadWalker<ObjectArrayList<GATKSAMRecord>, Redu
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* The number of bases to keep around mismatches (potential variation)
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*/
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@Argument(fullName = "context_size", shortName = "cs", doc = "", required = false)
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private int contextSize = 10;
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public int contextSize = 10;
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/**
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* The minimum mapping quality to be considered for the consensus synthetic read. Reads that have
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@ -131,7 +131,7 @@ public class ReduceReads extends ReadWalker<ObjectArrayList<GATKSAMRecord>, Redu
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* towards variable regions.
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*/
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@Argument(fullName = "minimum_mapping_quality", shortName = "minmap", doc = "", required = false)
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private int minMappingQuality = 20;
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public int minMappingQuality = 20;
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/**
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* The minimum base quality to be considered for the consensus synthetic read. Reads that have
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@ -139,14 +139,14 @@ public class ReduceReads extends ReadWalker<ObjectArrayList<GATKSAMRecord>, Redu
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* towards variable regions.
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*/
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@Argument(fullName = "minimum_base_quality_to_consider", shortName = "minqual", doc = "", required = false)
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private byte minBaseQual = 20;
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public byte minBaseQual = 20;
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/**
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* Reads have notoriously low quality bases on the tails (left and right). Consecutive bases with quality
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* lower than this threshold will be hard clipped off before entering the reduce reads algorithm.
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*/
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@Argument(fullName = "minimum_tail_qualities", shortName = "mintail", doc = "", required = false)
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private byte minTailQuality = 2;
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public byte minTailQuality = 2;
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/**
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* Any number of VCF files representing known SNPs to be used for the experimental polyploid-based reduction.
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@ -161,21 +161,21 @@ public class ReduceReads extends ReadWalker<ObjectArrayList<GATKSAMRecord>, Redu
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* and read group).
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*/
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@Argument(fullName = "dont_simplify_reads", shortName = "nosimplify", doc = "", required = false)
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private boolean DONT_SIMPLIFY_READS = false;
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public boolean DONT_SIMPLIFY_READS = false;
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/**
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* Do not hard clip adaptor sequences. Note: You don't have to turn this on for reads that are not mate paired.
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* The program will behave correctly in those cases.
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*/
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@Argument(fullName = "dont_hardclip_adaptor_sequences", shortName = "noclip_ad", doc = "", required = false)
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private boolean DONT_CLIP_ADAPTOR_SEQUENCES = false;
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public boolean DONT_CLIP_ADAPTOR_SEQUENCES = false;
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/**
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* Do not hard clip the low quality tails of the reads. This option overrides the argument of minimum tail
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* quality.
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*/
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@Argument(fullName = "dont_hardclip_low_qual_tails", shortName = "noclip_tail", doc = "", required = false)
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private boolean DONT_CLIP_LOW_QUAL_TAILS = false;
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public boolean DONT_CLIP_LOW_QUAL_TAILS = false;
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/**
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* Do not use high quality soft-clipped bases. By default, ReduceReads will hard clip away any low quality soft clipped
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@ -183,7 +183,7 @@ public class ReduceReads extends ReadWalker<ObjectArrayList<GATKSAMRecord>, Redu
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* regions. The minimum quality for soft clipped bases is the same as the minimum base quality to consider (minqual)
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*/
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@Argument(fullName = "dont_use_softclipped_bases", shortName = "no_soft", doc = "", required = false)
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private boolean DONT_USE_SOFTCLIPPED_BASES = false;
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public boolean DONT_USE_SOFTCLIPPED_BASES = false;
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/**
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* Do not compress read names. By default, ReduceReads will compress read names to numbers and guarantee
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@ -191,55 +191,55 @@ public class ReduceReads extends ReadWalker<ObjectArrayList<GATKSAMRecord>, Redu
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* there is no guarantee that read name uniqueness will be maintained -- in this case we recommend not compressing.
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*/
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@Argument(fullName = "dont_compress_read_names", shortName = "nocmp_names", doc = "", required = false)
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private boolean DONT_COMPRESS_READ_NAMES = false;
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public boolean DONT_COMPRESS_READ_NAMES = false;
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/**
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* Optionally hard clip all incoming reads to the desired intervals. The hard clips will happen exactly at the interval
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* border.
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*/
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@Argument(fullName = "hard_clip_to_interval", shortName = "clip_int", doc = "", required = false)
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private boolean HARD_CLIP_TO_INTERVAL = false;
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public boolean HARD_CLIP_TO_INTERVAL = false;
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/**
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* Minimum proportion of mismatches in a site to trigger a variant region. Anything below this will be
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* considered consensus.
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*/
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@Argument(fullName = "minimum_alt_proportion_to_trigger_variant", shortName = "minvar", doc = "", required = false)
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private double minAltProportionToTriggerVariant = 0.05;
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public double minAltProportionToTriggerVariant = 0.05;
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/**
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* Minimum proportion of indels in a site to trigger a variant region. Anything below this will be
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* considered consensus.
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*/
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@Argument(fullName = "minimum_del_proportion_to_trigger_variant", shortName = "mindel", doc = "", required = false)
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private double minIndelProportionToTriggerVariant = 0.05;
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public double minIndelProportionToTriggerVariant = 0.05;
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/**
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* Downsamples the coverage of a variable region approximately (guarantees the minimum to be equal to this).
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* A value of 0 turns downsampling off.
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*/
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@Argument(fullName = "downsample_coverage", shortName = "ds", doc = "", required = false)
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private int downsampleCoverage = 250;
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public int downsampleCoverage = 250;
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@Hidden
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@Argument(fullName = "nwayout", shortName = "nw", doc = "", required = false)
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private boolean nwayout = false;
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public boolean nwayout = false;
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@Hidden
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@Argument(fullName = "", shortName = "dl", doc = "", required = false)
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private int debugLevel = 0;
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public int debugLevel = 0;
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@Hidden
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@Argument(fullName = "", shortName = "dr", doc = "", required = false)
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private String debugRead = "";
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public String debugRead = "";
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@Hidden
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@Argument(fullName = "downsample_strategy", shortName = "dm", doc = "", required = false)
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private DownsampleStrategy downsampleStrategy = DownsampleStrategy.Normal;
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public DownsampleStrategy downsampleStrategy = DownsampleStrategy.Normal;
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@Hidden
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@Argument(fullName = "no_pg_tag", shortName = "npt", doc ="", required = false)
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private boolean NO_PG_TAG = false;
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public boolean NO_PG_TAG = false;
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public enum DownsampleStrategy {
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Normal,
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@ -282,7 +282,6 @@ public class ReduceReads extends ReadWalker<ObjectArrayList<GATKSAMRecord>, Redu
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final boolean preSorted = true;
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final boolean indexOnTheFly = true;
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final boolean keep_records = true;
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final SAMFileHeader.SortOrder sortOrder = SAMFileHeader.SortOrder.coordinate;
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if (nwayout) {
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SAMProgramRecord programRecord = NO_PG_TAG ? null : Utils.createProgramRecord(toolkit, this, PROGRAM_RECORD_NAME);
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@ -292,7 +291,7 @@ public class ReduceReads extends ReadWalker<ObjectArrayList<GATKSAMRecord>, Redu
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writerToUse = out;
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out.setPresorted(false);
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if (!NO_PG_TAG) {
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Utils.setupWriter(out, toolkit, toolkit.getSAMFileHeader(), !preSorted, keep_records, this, PROGRAM_RECORD_NAME);
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Utils.setupWriter(out, toolkit, toolkit.getSAMFileHeader(), !preSorted, this, PROGRAM_RECORD_NAME);
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}
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}
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}
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@ -38,7 +38,6 @@ import org.broadinstitute.sting.gatk.iterators.ReadTransformer;
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import org.broadinstitute.sting.gatk.iterators.ReadTransformersMode;
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import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
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import org.broadinstitute.sting.gatk.walkers.*;
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import org.broadinstitute.sting.utils.GenomeLoc;
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import org.broadinstitute.sting.utils.SampleUtils;
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import org.broadinstitute.sting.utils.Utils;
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import org.broadinstitute.sting.utils.baq.BAQ;
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@ -151,7 +150,7 @@ public class PrintReads extends ReadWalker<GATKSAMRecord, SAMFileWriter> impleme
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@Hidden
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@Argument(fullName = "no_pg_tag", shortName = "npt", doc ="", required = false)
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private boolean NO_PG_TAG = false;
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public boolean NO_PG_TAG = false;
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List<ReadTransformer> readTransformers = Collections.emptyList();
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private TreeSet<String> samplesToChoose = new TreeSet<String>();
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@ -166,7 +165,6 @@ public class PrintReads extends ReadWalker<GATKSAMRecord, SAMFileWriter> impleme
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* The initialize function.
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*/
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public void initialize() {
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final boolean keep_records = true;
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final GenomeAnalysisEngine toolkit = getToolkit();
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if ( platform != null )
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@ -192,7 +190,7 @@ public class PrintReads extends ReadWalker<GATKSAMRecord, SAMFileWriter> impleme
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final boolean preSorted = true;
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if (getToolkit() != null && getToolkit().getArguments().BQSR_RECAL_FILE != null && !NO_PG_TAG ) {
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Utils.setupWriter(out, toolkit, toolkit.getSAMFileHeader(), !preSorted, keep_records, this, PROGRAM_RECORD_NAME);
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Utils.setupWriter(out, toolkit, toolkit.getSAMFileHeader(), !preSorted, this, PROGRAM_RECORD_NAME);
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}
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}
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@ -29,7 +29,6 @@ import com.google.java.contract.Ensures;
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import com.google.java.contract.Requires;
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import net.sf.samtools.SAMFileHeader;
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import net.sf.samtools.SAMProgramRecord;
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import net.sf.samtools.util.StringUtil;
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import org.apache.log4j.Logger;
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import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
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import org.broadinstitute.sting.gatk.io.StingSAMFileWriter;
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@ -87,9 +86,7 @@ public class Utils {
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* @return True if the two objects are equal, false otherwise.
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*/
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public static boolean equals(Object lhs, Object rhs) {
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if (lhs == null && rhs == null) return true;
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else if (lhs == null) return false;
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else return lhs.equals(rhs);
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return lhs == null && rhs == null || lhs != null && lhs.equals(rhs);
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}
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public static <T> List<T> cons(final T elt, final List<T> l) {
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@ -128,35 +125,6 @@ public class Utils {
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logger.warn(String.format("* %s", builder));
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}
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public static ArrayList<Byte> subseq(char[] fullArray) {
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byte[] fullByteArray = new byte[fullArray.length];
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StringUtil.charsToBytes(fullArray, 0, fullArray.length, fullByteArray, 0);
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return subseq(fullByteArray);
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}
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public static ArrayList<Byte> subseq(byte[] fullArray) {
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return subseq(fullArray, 0, fullArray.length - 1);
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}
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public static ArrayList<Byte> subseq(byte[] fullArray, int start, int end) {
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assert end < fullArray.length;
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ArrayList<Byte> dest = new ArrayList<Byte>(end - start + 1);
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for (int i = start; i <= end; i++) {
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dest.add(fullArray[i]);
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}
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return dest;
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}
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public static String baseList2string(List<Byte> bases) {
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byte[] basesAsbytes = new byte[bases.size()];
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int i = 0;
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for (Byte b : bases) {
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basesAsbytes[i] = b;
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i++;
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}
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return new String(basesAsbytes);
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}
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/**
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* join the key value pairs of a map into one string, i.e. myMap = [A->1,B->2,C->3] with a call of:
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* joinMap("-","*",myMap) -> returns A-1*B-2*C-3
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@ -255,7 +223,6 @@ public class Utils {
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* Create a new list that contains the elements of left along with elements elts
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* @param left a non-null list of elements
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* @param elts a varargs vector for elts to append in order to left
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* @param <T>
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* @return A newly allocated linked list containing left followed by elts
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*/
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public static <T> List<T> append(final List<T> left, T ... elts) {
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@ -267,9 +234,9 @@ public class Utils {
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/**
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* Returns a string of the values in joined by separator, such as A,B,C
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*
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* @param separator
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* @param doubles
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* @return
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* @param separator separator character
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* @param doubles the array with values
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* @return a string with the values separated by the separator
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*/
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public static String join(String separator, double[] doubles) {
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if ( doubles == null || doubles.length == 0)
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@ -486,7 +453,7 @@ public class Utils {
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return rcbases;
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}
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static public final <T> List<T> reverse(final List<T> l) {
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static public <T> List<T> reverse(final List<T> l) {
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final List<T> newL = new ArrayList<T>(l);
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Collections.reverse(newL);
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return newL;
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@ -525,10 +492,8 @@ public class Utils {
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/**
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* Helper utility that calls into the InetAddress system to resolve the hostname. If this fails,
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* unresolvable gets returned instead.
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*
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* @return
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*/
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public static final String resolveHostname() {
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public static String resolveHostname() {
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try {
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return InetAddress.getLocalHost().getCanonicalHostName();
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}
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@ -555,17 +520,15 @@ public class Utils {
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* Creates a program record for the program, adds it to the list of program records (@PG tags) in the bam file and sets
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* up the writer with the header and presorted status.
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*
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* @param toolkit the engine
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* @param originalHeader original header
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* @param KEEP_ALL_PG_RECORDS whether or not to keep all the other program records already existing in this BAM file
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* @param programRecord the program record for this program
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*/
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public static SAMFileHeader setupWriter(GenomeAnalysisEngine toolkit, SAMFileHeader originalHeader, boolean KEEP_ALL_PG_RECORDS, SAMProgramRecord programRecord) {
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SAMFileHeader header = originalHeader.clone();
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List<SAMProgramRecord> oldRecords = header.getProgramRecords();
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List<SAMProgramRecord> newRecords = new ArrayList<SAMProgramRecord>(oldRecords.size()+1);
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public static SAMFileHeader setupWriter(final SAMFileHeader originalHeader, final SAMProgramRecord programRecord) {
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final SAMFileHeader header = originalHeader.clone();
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final List<SAMProgramRecord> oldRecords = header.getProgramRecords();
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final List<SAMProgramRecord> newRecords = new ArrayList<SAMProgramRecord>(oldRecords.size()+1);
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for ( SAMProgramRecord record : oldRecords )
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if ( (programRecord != null && !record.getId().startsWith(programRecord.getId())) || KEEP_ALL_PG_RECORDS )
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if ( (programRecord != null && !record.getId().startsWith(programRecord.getId())))
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newRecords.add(record);
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if (programRecord != null) {
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@ -580,14 +543,13 @@ public class Utils {
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* the new header to be added to the BAM writer.
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*
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* @param toolkit the engine
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* @param KEEP_ALL_PG_RECORDS whether or not to keep all the other program records already existing in this BAM file
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* @param walker the walker object (so we can extract the command line)
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* @param PROGRAM_RECORD_NAME the name for the PG tag
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* @return a pre-filled header for the bam writer
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*/
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public static SAMFileHeader setupWriter(GenomeAnalysisEngine toolkit, SAMFileHeader originalHeader, boolean KEEP_ALL_PG_RECORDS, Object walker, String PROGRAM_RECORD_NAME) {
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public static SAMFileHeader setupWriter(final GenomeAnalysisEngine toolkit, final SAMFileHeader originalHeader, final Object walker, final String PROGRAM_RECORD_NAME) {
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final SAMProgramRecord programRecord = createProgramRecord(toolkit, walker, PROGRAM_RECORD_NAME);
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return setupWriter(toolkit, originalHeader, KEEP_ALL_PG_RECORDS, programRecord);
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return setupWriter(originalHeader, programRecord);
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}
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/**
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@ -597,12 +559,11 @@ public class Utils {
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* @param writer BAM file writer
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* @param toolkit the engine
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* @param preSorted whether or not the writer can assume reads are going to be added are already sorted
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* @param KEEP_ALL_PG_RECORDS whether or not to keep all the other program records already existing in this BAM file
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* @param walker the walker object (so we can extract the command line)
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* @param PROGRAM_RECORD_NAME the name for the PG tag
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*/
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public static void setupWriter(StingSAMFileWriter writer, GenomeAnalysisEngine toolkit, SAMFileHeader originalHeader, boolean preSorted, boolean KEEP_ALL_PG_RECORDS, Object walker, String PROGRAM_RECORD_NAME) {
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SAMFileHeader header = setupWriter(toolkit, originalHeader, KEEP_ALL_PG_RECORDS, walker, PROGRAM_RECORD_NAME);
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public static void setupWriter(StingSAMFileWriter writer, GenomeAnalysisEngine toolkit, SAMFileHeader originalHeader, boolean preSorted, Object walker, String PROGRAM_RECORD_NAME) {
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SAMFileHeader header = setupWriter(toolkit, originalHeader, walker, PROGRAM_RECORD_NAME);
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writer.writeHeader(header);
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writer.setPresorted(preSorted);
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}
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@ -629,23 +590,11 @@ public class Utils {
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return programRecord;
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}
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public static <E> Collection<E> makeCollection(Iterable<E> iter) {
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Collection<E> list = new ArrayList<E>();
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for (E item : iter) {
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list.add(item);
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}
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return list;
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}
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/**
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* Returns the number of combinations represented by this collection
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* of collection of options.
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*
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* For example, if this is [[A, B], [C, D], [E, F, G]] returns 2 * 2 * 3 = 12
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*
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* @param options
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* @param <T>
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* @return
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*/
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@Requires("options != null")
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public static <T> int nCombinations(final Collection<T>[] options) {
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@ -676,21 +625,18 @@ public class Utils {
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* if N = 1 => [[A], [B], [C]]
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* if N = 2 => [[A, A], [B, A], [C, A], [A, B], [B, B], [C, B], [A, C], [B, C], [C, C]]
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*
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* @param objects
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* @param n
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* @param <T>
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* @param objects list of objects
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* @param n size of each combination
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* @param withReplacement if false, the resulting permutations will only contain unique objects from objects
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* @return
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* @return a list with all combinations with size n of objects.
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*/
|
||||
public static <T> List<List<T>> makePermutations(final List<T> objects, final int n, final boolean withReplacement) {
|
||||
final List<List<T>> combinations = new ArrayList<List<T>>();
|
||||
|
||||
if ( n <= 0 )
|
||||
;
|
||||
else if ( n == 1 ) {
|
||||
if ( n == 1 ) {
|
||||
for ( final T o : objects )
|
||||
combinations.add(Collections.singletonList(o));
|
||||
} else {
|
||||
} else if (n > 1) {
|
||||
final List<List<T>> sub = makePermutations(objects, n - 1, withReplacement);
|
||||
for ( List<T> subI : sub ) {
|
||||
for ( final T a : objects ) {
|
||||
|
|
@ -738,9 +684,6 @@ public class Utils {
|
|||
|
||||
/**
|
||||
* Create a constant map that maps each value in values to itself
|
||||
* @param values
|
||||
* @param <T>
|
||||
* @return
|
||||
*/
|
||||
public static <T> Map<T, T> makeIdentityFunctionMap(Collection<T> values) {
|
||||
Map<T,T> map = new HashMap<T, T>(values.size());
|
||||
|
|
@ -756,9 +699,6 @@ public class Utils {
|
|||
* groupSize = 2
|
||||
* result = [[A, B], [C, D], [E]]
|
||||
*
|
||||
* @param list
|
||||
* @param groupSize
|
||||
* @return
|
||||
*/
|
||||
public static <T> List<List<T>> groupList(final List<T> list, final int groupSize) {
|
||||
if ( groupSize < 1 ) throw new IllegalArgumentException("groupSize >= 1");
|
||||
|
|
|
|||
|
|
@ -141,7 +141,7 @@ public class NWaySAMFileWriter implements SAMFileWriter {
|
|||
private void addWriter(SAMReaderID id , String outName, SAMFileHeader.SortOrder order, boolean presorted,
|
||||
boolean indexOnTheFly, boolean generateMD5, SAMProgramRecord programRecord) {
|
||||
File f = new File(outName);
|
||||
SAMFileHeader header = Utils.setupWriter(toolkit, toolkit.getSAMFileHeader(id), KEEP_ALL_PG_RECORDS, programRecord);
|
||||
SAMFileHeader header = Utils.setupWriter(toolkit.getSAMFileHeader(id), programRecord);
|
||||
SAMFileWriterFactory factory = new SAMFileWriterFactory();
|
||||
factory.setCreateIndex(indexOnTheFly);
|
||||
factory.setCreateMd5File(generateMD5);
|
||||
|
|
|
|||
Loading…
Reference in New Issue