Migrate default and GATK arguments over to new attribute system in preparation for conversion.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@600 348d0f76-0448-11de-a6fe-93d51630548a
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hanna
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@ -15,10 +15,9 @@ 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.Utils;
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import org.broadinstitute.sting.utils.cmdLine.CommandLineProgram;
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import org.broadinstitute.sting.utils.cmdLine.Argument;
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import java.io.File;
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import java.io.FileNotFoundException;
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import java.io.PrintStream;
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import java.util.ArrayList;
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import java.util.List;
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@ -26,23 +25,50 @@ public class GenomeAnalysisTK extends CommandLineProgram {
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public static GenomeAnalysisTK Instance = null;
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// parameters and their defaults
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@Argument(fullName="input_file",shortName="I",doc="SAM or BAM file(s)",required=false)
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public List<File> INPUT_FILES = null;
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@Argument(fullName="maximum_reads",shortName="M",doc="Maximum number of reads to process before exiting",required=false)
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public String MAX_READS_ARG = "-1";
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public String STRICTNESS_ARG = "strict";
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public File REF_FILE_ARG = null;
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public String DEBUGGING_STR = null;
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public String REGION_STR = null;
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public String Analysis_Name = null;
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public String DBSNP_FILE = null;
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public String HAPMAP_FILE = null;
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public String HAPMAP_CHIP_FILE = null;
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public Boolean ENABLED_THREADED_IO = false;
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public Boolean UNSAFE = false;
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public String MAX_ON_FLY_SORTS = null;
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public String DOWNSAMPLE_FRACTION = null;
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public String DOWNSAMPLE_COVERAGE = null;
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public String INTERVALS_FILE = null;
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@Argument(fullName="validation_strictness",shortName="S",doc="How strict should we be with validation (LENIENT|SILENT|STRICT)",required=false)
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public String STRICTNESS_ARG = "strict";
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@Argument(fullName="reference_sequence", shortName="R",doc="Reference sequence file",required=false)
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public File REF_FILE_ARG = null;
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@Argument(fullName="genome_region", shortName="L", doc="Genome region to operation on: from chr:start-end",required=false)
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public String REGION_STR = null;
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@Argument(fullName="analysis_type", shortName="T", doc="Type of analysis to run")
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public String Analysis_Name = null;
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@Argument(fullName="DBSNP",shortName="D",doc="DBSNP file",required=false)
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public String DBSNP_FILE = null;
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@Argument(fullName="hapmap",shortName="H",doc="Hapmap file",required=false)
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public String HAPMAP_FILE = null;
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@Argument(fullName="hapmap_chip",shortName="hc",doc="Hapmap chip file",required=false)
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public String HAPMAP_CHIP_FILE = null;
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@Argument(fullName="threaded_IO",shortName="P",doc="If set, enables threaded I/O operations",required=false)
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public Boolean ENABLED_THREADED_IO = false;
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@Argument(fullName="unsafe",shortName="U",doc="If set, enables unsafe operations, nothing will be checked at runtime.",required=false)
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public Boolean UNSAFE = false;
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@Argument(fullName="sort_on_the_fly",shortName="sort",doc="Maximum number of reads to sort on the fly",required=false)
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public String MAX_ON_FLY_SORTS = null;
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@Argument(fullName="downsample_to_fraction",shortName="dfrac",doc="Fraction [0.0-1.0] of reads to downsample to",required=false)
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public String DOWNSAMPLE_FRACTION = null;
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@Argument(fullName="downsample_to_coverage",shortName="dcov",doc="Coverage [integer] to downsample to",required=false)
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public String DOWNSAMPLE_COVERAGE = null;
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@Argument(fullName="intervals_file",shortName="V",doc="File containing list of genomic intervals to operate on. line := <contig> <start> <end>",required=false)
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public String INTERVALS_FILE = null;
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// our walker manager
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private WalkerManager walkerManager = null;
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@ -50,27 +76,35 @@ public class GenomeAnalysisTK extends CommandLineProgram {
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public String pluginPathName = null;
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private TraversalEngine engine = null;
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public boolean DEBUGGING = false;
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@Argument(fullName="all_loci",shortName="A",doc="Should we process all loci, not just those covered by reads",required=false)
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public Boolean WALK_ALL_LOCI = false;
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@Argument(fullName="disablethreading",shortName="dt",doc="Disable experimental threading support.",required=false)
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public Boolean DISABLE_THREADING = false;
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/**
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* An output file presented to the walker.
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*/
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@Argument(fullName="out",shortName="o",doc="An output file presented to the walker. Will overwrite contents if file exists.",required=false)
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public String outFileName = null;
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/**
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* An error output file presented to the walker.
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*/
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@Argument(fullName="err",shortName="e",doc="An error output file presented to the walker. Will overwrite contents if file exists.",required=false)
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public String errFileName = null;
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/**
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* A joint file for both 'normal' and error output presented to the walker.
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*/
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@Argument(fullName="outerr",shortName="oe",doc="A joint file for 'normal' and error output presented to the walker. Will overwrite contents if file exists.",required=false)
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public String outErrFileName = null;
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/**
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* How many threads should be allocated to this analysis.
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*/
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@Argument(fullName="numthreads",shortName="nt",doc="How many threads should be allocated to running this analysis.",required=false)
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public int numThreads = 1;
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/**
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@ -83,6 +117,7 @@ public class GenomeAnalysisTK extends CommandLineProgram {
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*/
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private static Logger logger = Logger.getLogger(GenomeAnalysisTK.class);
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@Argument(fullName="rodBind",shortName="B",doc="",required=false)
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public static ArrayList<String> ROD_BINDINGS = new ArrayList<String>();
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@ -93,7 +128,6 @@ public class GenomeAnalysisTK extends CommandLineProgram {
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*/
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protected void setupArgs() {
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m_parser.addOptionalArgList("input_file", "I", "SAM or BAM file", "INPUT_FILES");
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//m_parser.addRequiredArg("input_file", "I", "SAM or BAM file", "INPUT_FILE");
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m_parser.addOptionalArg("maximum_reads", "M", "Maximum number of reads to process before exiting", "MAX_READS_ARG");
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m_parser.addOptionalArg("validation_strictness", "S", "How strict should we be with validation (LENIENT|SILENT|STRICT)", "STRICTNESS_ARG");
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m_parser.addOptionalArg("reference_sequence", "R", "Reference sequence file", "REF_FILE_ARG");
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@ -295,7 +329,6 @@ public class GenomeAnalysisTK extends CommandLineProgram {
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logger.info("Strictness is " + strictness);
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engine.setStrictness(strictness);
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engine.setDebugging(!(DEBUGGING_STR == null || DEBUGGING_STR.toLowerCase().equals("true")));
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engine.setMaxReads(Integer.parseInt(MAX_READS_ARG));
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if (REGION_STR != null) {
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@ -5,7 +5,6 @@ import org.apache.log4j.*;
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import java.io.IOException;
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import java.text.DateFormat;
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import java.text.SimpleDateFormat;
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import java.text.ParseException;
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/**
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* User: aaron
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@ -39,22 +38,38 @@ public abstract class CommandLineProgram {
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/**
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* the default log level
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*/
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@Argument(fullName="logging_level",
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shortName="l",
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doc="Set the minimum level of logging, i.e. setting INFO get's you INFO up to FATAL, setting ERROR gets you ERROR and FATAL level logging. (DEBUG, INFO, WARN, ERROR, FATAL, OFF). ",
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required=false)
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public String logging_level = "ERROR";
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/**
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* where to send the output of our logger
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*/
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@Argument(fullName="log_to_file",
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shortName="log",
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doc="Set the logging location",
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required=false)
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public String toFile = null;
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/**
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* do we want to silence the command line output
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*/
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@Argument(fullName="quiet_output_mode",
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shortName="quiet",
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doc="Set the logging to quiet mode, no output to stdout",
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required=false)
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public Boolean quietMode = false;
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/**
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* do we want to generate debugging information with the logs
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*/
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@Argument(fullName="debug_mode",
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shortName="debug",
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doc="Set the logging file string to include a lot of debugging information (SLOW!)",
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required=false)
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public Boolean debugMode = false;
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@ -103,9 +118,9 @@ public abstract class CommandLineProgram {
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/**
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* this is used to indicate if they've asked for help
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*/
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@Argument(fullName="help",shortName="h",doc="Generate this help message",required=false)
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public Boolean help = false;
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/**
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* This function is called to start processing the command line, and kick
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* off the execute message of the program.
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