package org.snpsift.testCases.unit;

import org.junit.jupiter.api.Test;
import org.snpeff.util.Gpr;
import org.snpeff.util.Log;
import org.snpsift.SnpSift;
import org.snpsift.SnpSiftCmdSplit;

import java.io.File;

import static org.junit.jupiter.api.Assertions.assertEquals;

/**
 * SnpSift 'split' test cases
 *
 * @author pcingola
 */
public class TestCasesSplit {

    public static boolean debug = false;
    public static boolean verbose = false;

    /**
     * Split by chromosome
     */
    @Test
    public void test_01() {
        Log.debug("Test");
        String file = "test/test_split_01.vcf";

        // Delete old files
        (new File("test/test_split_01.Y.vcf")).delete();
        (new File("test/test_split_01.19.vcf")).delete();

        // Run command
        String[] args = {"split", file};
        SnpSift snpSift = new SnpSift(args);
        SnpSiftCmdSplit cmd = (SnpSiftCmdSplit) snpSift.cmd();
        cmd.setVerbose(verbose);
        cmd.setDebug(debug);
        cmd.run();

        // Check output
        String expected = Gpr.readFile("test/test_split_01.Y.expected.vcf");
        String actual = Gpr.readFile("test/test_split_01.Y.vcf");
        assertEquals(expected, actual);

        expected = Gpr.readFile("test/test_split_01.19.expected.vcf");
        actual = Gpr.readFile("test/test_split_01.19.vcf");
        assertEquals(expected, actual);
    }

    /**
     * Split by number
     */
    @Test
    public void test_02() {
        Log.debug("Test");

        int numLines = 2;
        String file = "test/test_split_01.vcf";

        // Run command
        String[] args = {"split", "-l", numLines + "", file};
        SnpSift snpSift = new SnpSift(args);
        SnpSiftCmdSplit cmd = (SnpSiftCmdSplit) snpSift.cmd();
        cmd.setVerbose(verbose);
        cmd.setDebug(debug);
        cmd.run();

        // Check output
        for (String splitFile : cmd.getFileNames()) {
            int n = Gpr.countLines(splitFile);
            if (debug) Log.debug("Checking file '" + splitFile + "'\tnumber of lines: " + n);
            assertEquals(numLines + 1, n); // We expect 'numLines' + 1 header line
        }
    }

    /**
     * Split and join
     */
    @Test
    public void test_03() {
        Log.debug("Test");

        //---
        // Split
        //---
        String file = "test/test_split_01.vcf";
        String originalFile = Gpr.readFile(file);

        // Delete old files
        (new File("test/test_split_01.Y.vcf")).delete();
        (new File("test/test_split_01.19.vcf")).delete();

        // Run command
        String[] args = {"split", file};
        SnpSift snpSift = new SnpSift(args);
        SnpSiftCmdSplit cmd = (SnpSiftCmdSplit) snpSift.cmd();
        cmd.setVerbose(verbose);
        cmd.setDebug(debug);
        cmd.run();

        //---
        // Join
        //---
        String[] argsJoin = {"split", "-j", "test/test_split_01.Y.vcf", "test/test_split_01.19.vcf"};
        snpSift = new SnpSift(argsJoin);
        cmd = (SnpSiftCmdSplit) snpSift.cmd();
        cmd.setVerbose(true);
        cmd.setDebug(debug);
        String joinedFile = cmd.join(true);

        assertEquals(originalFile, joinedFile);

    }

}
