Package org.broadinstitute.gatk.utils.commandline

Examples of org.broadinstitute.gatk.utils.commandline.Tags.containsKey()

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        final Tags tags = rodBinding.getTags();
        final String name = rodBinding.getName();

        // Parse the tags to decide which tracks have which properties
        if( tags != null ) {
            isKnown = tags.containsKey("known") && tags.getValue("known").equals("true");
            isTraining = tags.containsKey("training") && tags.getValue("training").equals("true");
            isAntiTraining = tags.containsKey("bad") && tags.getValue("bad").equals("true");
            isTruth = tags.containsKey("truth") && tags.getValue("truth").equals("true");
            isConsensus = tags.containsKey("consensus") && tags.getValue("consensus").equals("true");
            prior = ( tags.containsKey("prior") ? Double.parseDouble(tags.getValue("prior")) : prior );
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        final String name = rodBinding.getName();

        // Parse the tags to decide which tracks have which properties
        if( tags != null ) {
            isKnown = tags.containsKey("known") && tags.getValue("known").equals("true");
            isTraining = tags.containsKey("training") && tags.getValue("training").equals("true");
            isAntiTraining = tags.containsKey("bad") && tags.getValue("bad").equals("true");
            isTruth = tags.containsKey("truth") && tags.getValue("truth").equals("true");
            isConsensus = tags.containsKey("consensus") && tags.getValue("consensus").equals("true");
            prior = ( tags.containsKey("prior") ? Double.parseDouble(tags.getValue("prior")) : prior );
        }
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        // Parse the tags to decide which tracks have which properties
        if( tags != null ) {
            isKnown = tags.containsKey("known") && tags.getValue("known").equals("true");
            isTraining = tags.containsKey("training") && tags.getValue("training").equals("true");
            isAntiTraining = tags.containsKey("bad") && tags.getValue("bad").equals("true");
            isTruth = tags.containsKey("truth") && tags.getValue("truth").equals("true");
            isConsensus = tags.containsKey("consensus") && tags.getValue("consensus").equals("true");
            prior = ( tags.containsKey("prior") ? Double.parseDouble(tags.getValue("prior")) : prior );
        }
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        // Parse the tags to decide which tracks have which properties
        if( tags != null ) {
            isKnown = tags.containsKey("known") && tags.getValue("known").equals("true");
            isTraining = tags.containsKey("training") && tags.getValue("training").equals("true");
            isAntiTraining = tags.containsKey("bad") && tags.getValue("bad").equals("true");
            isTruth = tags.containsKey("truth") && tags.getValue("truth").equals("true");
            isConsensus = tags.containsKey("consensus") && tags.getValue("consensus").equals("true");
            prior = ( tags.containsKey("prior") ? Double.parseDouble(tags.getValue("prior")) : prior );
        }

        // Report back to the user which tracks were found and the properties that were detected
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        if( tags != null ) {
            isKnown = tags.containsKey("known") && tags.getValue("known").equals("true");
            isTraining = tags.containsKey("training") && tags.getValue("training").equals("true");
            isAntiTraining = tags.containsKey("bad") && tags.getValue("bad").equals("true");
            isTruth = tags.containsKey("truth") && tags.getValue("truth").equals("true");
            isConsensus = tags.containsKey("consensus") && tags.getValue("consensus").equals("true");
            prior = ( tags.containsKey("prior") ? Double.parseDouble(tags.getValue("prior")) : prior );
        }

        // Report back to the user which tracks were found and the properties that were detected
        if( !isConsensus && !isAntiTraining ) {
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            isKnown = tags.containsKey("known") && tags.getValue("known").equals("true");
            isTraining = tags.containsKey("training") && tags.getValue("training").equals("true");
            isAntiTraining = tags.containsKey("bad") && tags.getValue("bad").equals("true");
            isTruth = tags.containsKey("truth") && tags.getValue("truth").equals("true");
            isConsensus = tags.containsKey("consensus") && tags.getValue("consensus").equals("true");
            prior = ( tags.containsKey("prior") ? Double.parseDouble(tags.getValue("prior")) : prior );
        }

        // Report back to the user which tracks were found and the properties that were detected
        if( !isConsensus && !isAntiTraining ) {
            logger.info( String.format( "Found %s track: \tKnown = %s \tTraining = %s \tTruth = %s \tPrior = Q%.1f", name, isKnown, isTraining, isTruth, prior) );
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