Examples of filterAlignment()

Examples of org.broad.igv.sam.reader.ReadGroupFilter.filterAlignment()

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                if (!record.isMapped() || (!showDuplicates && record.isDuplicate()) ||
                        (filterFailedReads && record.isVendorFailedRead()) ||
                        (filterSecondaryAlignments && !record.isPrimary()) ||
                        (filterSupplementaryAlignments && record.isSupplementary()) ||
                        record.getMappingQuality() < qualityThreshold ||
                        (filter != null && filter.filterAlignment(record))) {
                    continue;
                }

                t.addRecord(record);
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Examples of org.broad.igv.sam.reader.ReadGroupFilter.filterAlignment()

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            boolean showDuplicates = PreferenceManager.getInstance().getAsBoolean(PreferenceManager.SAM_SHOW_DUPLICATES);
            int qualityThreshold = PreferenceManager.getInstance().getAsInt(PreferenceManager.SAM_QUALITY_THRESHOLD);
            if (!rec.isMapped() || (!showDuplicates && rec.isDuplicate()) ||
                    (filterFailedReads && rec.isVendorFailedRead()) ||
                    rec.getMappingQuality() < qualityThreshold ||
                    (filter != null && filter.filterAlignment(rec))) {
                continue;
            }

            expectedResult.add(rec);
            //System.out.println("name: " + rec.getReadName() + "strt: " + rec.getStart() + " end: " + rec.getEnd());
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