Package org.broad.igv.feature.tribble

Examples of org.broad.igv.feature.tribble.IGVBEDCodec.decode()

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                String[] closest = Arrays.copyOfRange(tokens, numCols0, numCols0 + numCols1);
                //If not found, bedtools returns -1 for positions
                if (closest[1].trim().equalsIgnoreCase("-1")) {
                    continue;
                }
                feat = codec.decode(closest);
            } else if (operation == Operation.MULTIINTER) {
                //We only look at regions common to ALL inputs
                //Columns: chr \t start \t \end \t # of files which contained this feature \t comma-separated list files +many more
                int numRegions = Integer.parseInt(tokens[3]);
                if (numRegions < sources.length) {
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                int numRegions = Integer.parseInt(tokens[3]);
                if (numRegions < sources.length) {
                    continue;
                }
                String[] intersection = Arrays.copyOf(tokens, 3);
                feat = codec.decode(intersection);
            } else {
                feat = codec.decode(tokens);
            }
            featuresList.add(feat);
        }
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                    continue;
                }
                String[] intersection = Arrays.copyOf(tokens, 3);
                feat = codec.decode(intersection);
            } else {
                feat = codec.decode(tokens);
            }
            featuresList.add(feat);
        }

        in.close();
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        BufferedReader in = new BufferedReader(new InputStreamReader(is));
        int totalLines = 0;
        String val = "";
        AsciiFeatureCodec featureCodec = new IGVBEDCodec(genome);
        while ((val = in.readLine()) != null) {
            Feature feat = featureCodec.decode(val);
            checkFeatureIntegrity(feat, "chr2");
            totalLines += 1;
        }
        assertEquals(72, totalLines);
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