Add a new interval list scatter mode (#1786)

* Add a new interval list scatter mode to avoid issue of giant final list
in large joint genotyping scatters

src/main/java/picard/util/IntervalList/IntervalListScatterMode.java

@@ -75,6 +75,16 @@ public enum IntervalListScatterMode implements CommandLineParser.ClpEnum {
      * rather than the base level, for example CNV calling.
      */
     INTERVAL_COUNT(IntervalListScattererByIntervalCount::new, "Scatter the interval list into similarly sized interval lists " +
+            "(by interval count, not by base count). " +
+            "Resulting interval lists will contain the same number of intervals except for the last, which contains the remainder."),
+
+    /***
+     * A scatter by interval **count** which attempts to fill each resulting interval list with approximately equal numbers
+     * of intervals, disregarding the base count. This approach distributes the remainder intervals across the initial interval lists.
+     * This is the preferred mode for whole genome joint calling and other scenarios where the interval list to be split
+     * contains a large number of intervals that should be distributed equally by count.
+     */
+    INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER(IntervalListScattererByIntervalCountWithDistributedRemainder::new, "Scatter the interval list into similarly sized interval lists " +
             "(by interval count, not by base count). " +
             "Resulting interval lists will contain similar number of intervals.");
 

src/main/java/picard/util/IntervalList/IntervalListScattererByIntervalCountWithDistributedRemainder.java

@@ -0,0 +1,23 @@
+package picard.util.IntervalList;
+
+import htsjdk.samtools.util.Interval;
+import htsjdk.samtools.util.IntervalList;
+
+import java.util.Arrays;
+import java.util.List;
+
+/**
+ * Scatters {@link IntervalList} by into `interval count` shards so that resulting {@link IntervalList}'s have
+ * approximately same number of intervals in them. The "remainder" intervals are distributed over the last lists.
+ */
+public class IntervalListScattererByIntervalCountWithDistributedRemainder extends IntervalListScattererByIntervalCount {
+
+    @Override
+    public List<Interval> takeSome(final Interval interval, final long idealSplitWeight, final long currentSize, final double projectSizeOfRemaining) {
+        if (projectSizeOfRemaining > currentSize) {
+            return Arrays.asList(interval, null);
+        } else {
+            return Arrays.asList(null, interval);
+        }
+    }
+}

src/main/java/picard/util/IntervalListTools.java

@@ -455,7 +455,7 @@ protected int doWork() {
 
         if (SCATTER_CONTENT != null) {
             final long listSize = SUBDIVISION_MODE.make().listWeight(output);
-            SCATTER_COUNT = (int) listSize / SCATTER_CONTENT;
+            SCATTER_COUNT = (int)Math.round((double) listSize / SCATTER_CONTENT);
             LOG.info(String.format("Using SCATTER_CONTENT = %d and an interval of size %d, attempting to scatter into %s intervals.", SCATTER_CONTENT, listSize, SCATTER_COUNT));
         }
 

src/test/java/picard/util/IntervalListScattererTest.java

@@ -33,6 +33,7 @@
 
 import java.io.File;
 import java.util.*;
+import java.util.stream.Collectors;
 
 /**
  * Basic test for scatter functionality in IntervalListTools
@@ -43,6 +44,12 @@ public class IntervalListScattererTest {
     private static final File INTERVAL_FILE = new File(TEST_DATA_DIR, "scatterable.interval_list");
     private static final IntervalList LIST_TO_SCATTER = IntervalList.fromFile(INTERVAL_FILE);
 
+    static final File LARGER_INTERVAL_FILE = new File(TEST_DATA_DIR, "test.hg38.200.interval_list");
+    private static final List<File> LARGER_INTERVAL_EXPECTEDS = Arrays.asList(new File(TEST_DATA_DIR, "largeScatters").listFiles());
+    static final List<IntervalList> LARGER_EXPECTED_LISTS = LARGER_INTERVAL_EXPECTEDS.stream().sorted().flatMap(l -> Arrays.asList(l.listFiles()).stream().map(f -> IntervalList.fromFile(f))).collect(Collectors.toList());
+    private static final List<File> LARGER_INTERVAL_NO_REMAINDER_EXPECTEDS = Arrays.asList(new File(TEST_DATA_DIR, "largeScattersNoRemainder").listFiles());
+    static final List<IntervalList> LARGER_NO_REMAINDER_EXPECTED_LISTS = LARGER_INTERVAL_NO_REMAINDER_EXPECTEDS.stream().sorted().flatMap(l -> Arrays.asList(l.listFiles()).stream().map(f -> IntervalList.fromFile(f))).collect(Collectors.toList());
+
     private static final File INTERVAL_WITH_OVERFLOW_FILE = new File(TEST_DATA_DIR, "scatterable_with_overflow.interval_list");
     private static final IntervalList LIST_TO_SCATTER_WITH_OVERFLOW = IntervalList.fromFile(INTERVAL_WITH_OVERFLOW_FILE);
 
@@ -64,7 +71,7 @@ public String toString() {
                     '}';
         }
 
-        private Testcase(final File file, final int scatterWidth, final IntervalListScatterMode mode, final List<IntervalList> expectedScatter) {
+        Testcase(final File file, final int scatterWidth, final IntervalListScatterMode mode, final List<IntervalList> expectedScatter) {
             this.source = IntervalList.fromFile(file);
             this.file = file;
             this.expectedScatter = expectedScatter;
@@ -73,8 +80,32 @@ private Testcase(final File file, final int scatterWidth, final IntervalListScat
         }
     }
 
-    @DataProvider
-    public static Iterator<Object[]> testScatterTestcases() {
+    /**
+     * These are split out separately and private because the treatment of remainders causes different behavior whether
+     * scatter count is specified (as similated here) versus whether scatter *content* is specified, as in in the IntervalListTools
+     * integration tests
+     * @return test cases with expected behavior for distributed remainder mode given a specified number of output lists
+     */
+    private static List<Testcase> getRemainderTestcases() {
+        final List<Testcase> testCases = new ArrayList<>();
+        testCases.add(new Testcase(
+                LARGER_INTERVAL_FILE, 60, IntervalListScatterMode.INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER,
+                LARGER_EXPECTED_LISTS
+        ));
+
+        testCases.add(new Testcase(
+                LARGER_INTERVAL_FILE, 20, IntervalListScatterMode.INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER,
+                LARGER_NO_REMAINDER_EXPECTED_LISTS
+        ));
+        return testCases;
+    }
+
+    /**
+     * These test cases for modes not including INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER have the same behavior
+     *
+     * @return
+     */
+    public static List<Testcase> getScatterTestcases() {
         final List<Testcase> testCases = new ArrayList<>();
         Assert.assertEquals(LIST_TO_SCATTER.getUniqueBaseCount(), 200, "Wrong unique base count");
         Assert.assertEquals(LIST_TO_SCATTER_MANY.getUniqueBaseCount(), 32 * 2, "Wrong unique base count");
@@ -393,7 +424,14 @@ public static Iterator<Object[]> testScatterTestcases() {
                                 IntervalList.overlaps(LIST_TO_SCATTER_MANY, secondThird))
                         ))))));
 
-        return testCases.stream().map(tc -> new Object[]{tc}).iterator();
+        return testCases;
+    }
+
+    @DataProvider
+    public static Iterator<Object[]> testScatterTestcases() {
+        final List<Testcase> testcases = new ArrayList<>(getScatterTestcases());
+        testcases.addAll(getRemainderTestcases());
+        return testcases.stream().map(tc -> new Object[]{tc}).iterator();
     }
 
     @Test(dataProvider = "testScatterTestcases")

src/test/java/picard/util/IntervalListToolsTest.java

@@ -30,6 +30,7 @@
 import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
 import picard.cmdline.CommandLineProgramTest;
+import picard.util.IntervalList.IntervalListScatterMode;
 import picard.util.IntervalList.IntervalListScatterer;
 
 import java.io.File;
@@ -40,21 +41,25 @@
 import java.util.List;
 import java.util.Objects;
 import java.util.Scanner;
+import java.util.stream.Collectors;
 import java.util.stream.Stream;
 
 /**
  * Created by farjoun on 10/22/17.
  */
 
 public class IntervalListToolsTest extends CommandLineProgramTest {
-    private final File TEST_DATA_DIR = new File("testdata/picard/util/");
+    private static final File TEST_DATA_DIR = new File("testdata/picard/util/");
     private final File scatterable = new File(TEST_DATA_DIR, "scatterable.interval_list");
     private final File scatterableStdin = new File(TEST_DATA_DIR, "scatterable_stdin");
     private final File secondInput = new File(TEST_DATA_DIR, "secondInput.interval_list");
     private final File largeScatterable = new File(TEST_DATA_DIR, "large_scatterable.interval_list");
     private final File abutting = new File(TEST_DATA_DIR, "abutting.interval_list");
     private final File abutting_combined = new File(TEST_DATA_DIR, "abutting_combined.interval_list");
     private final File abutting_notcombined = new File(TEST_DATA_DIR, "abutting_notcombined.interval_list");
+    private static final List<File> LARGER_EXPECTED_WITH_REMAINDER_FILES = Arrays.asList(new File(TEST_DATA_DIR, "largeScattersWithRemainder").listFiles());
+    private static final List<IntervalList> LARGER_EXPECTED_WITH_REMAINDER_LISTS = LARGER_EXPECTED_WITH_REMAINDER_FILES.stream().sorted().flatMap(l -> Arrays.asList(l.listFiles()).stream().map(f -> IntervalList.fromFile(f))).collect(Collectors.toList());
+
 
     @Test
     public void testSecondInputValidation() {
@@ -293,10 +298,32 @@ private long testerCountOutput(IntervalListTools.Action action, IntervalListTool
         return reader.nextLong();
     }
 
+    /**
+     * These are split out separately and private because the treatment of remainders causes different behavior whether
+     * scatter count is specified (as similated here) versus whether scatter *content* is specified, as in in the IntervalListTools
+     * integration tests
+     * @return test cases with expected behavior for distributed remainder mode given a specified number of output lists
+     */
+    private static List<IntervalListScattererTest.Testcase> getRemainderTestcases() {
+        final List<IntervalListScattererTest.Testcase> testCases = new ArrayList<>();
+        testCases.add(new IntervalListScattererTest.Testcase(
+                IntervalListScattererTest.LARGER_INTERVAL_FILE, 67, IntervalListScatterMode.INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER,
+                LARGER_EXPECTED_WITH_REMAINDER_LISTS
+        ));
+
+        testCases.add(new IntervalListScattererTest.Testcase(
+                IntervalListScattererTest.LARGER_INTERVAL_FILE, 20, IntervalListScatterMode.INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER,
+                IntervalListScattererTest.LARGER_NO_REMAINDER_EXPECTED_LISTS
+        ));
+        return testCases;
+    }
+
     // test scatter with different kinds of balancing.
     @DataProvider
     public static Iterator<Object[]> testScatterTestcases() {
-        return IntervalListScattererTest.testScatterTestcases();
+        final List<IntervalListScattererTest.Testcase> testcases = new ArrayList<>(IntervalListScattererTest.getScatterTestcases());
+        testcases.addAll(getRemainderTestcases());
+        return testcases.stream().map(tc -> new Object[]{tc}).iterator();
     }
 
     private final List<File> dirsToDelete = new ArrayList<>();
@@ -381,7 +408,7 @@ public void testScatterByContent(final IntervalListScattererTest.Testcase tc) th
             args.add("OUTPUT=" + ilOutDir);
         }
 
-        args.add("SCATTER_CONTENT=" + tc.mode.make().listWeight(tc.source) / tc.expectedScatter.size());
+        args.add("SCATTER_CONTENT=" + (int)Math.round((double)tc.mode.make().listWeight(tc.source) / tc.expectedScatter.size()));
 
         Assert.assertEquals(runPicardCommandLine(args), 0);
 

testdata/picard/util/largeScatters/temp_0001_of_60/scattered.interval_list

@@ -0,0 +1,7 @@
+@HD	VN:1.6	SO:coordinate
+@SQ	SN:chr1	LN:248956422	M5:6aef897c3d6ff0c78aff06ac189178dd	AS:38	UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta	SP:Homo sapiens
+@PG	ID:1	CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScatters --SCATTER_COUNT 60 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false	PN:IntervalListTools
+chr1	1	195878	+	target_1
+chr1	195879	391754	+	target_2
+chr1	391755	606302	+	target_3
+chr1	606303	820848	+	target_4

testdata/picard/util/largeScatters/temp_0002_of_60/scattered.interval_list

@@ -0,0 +1,7 @@
+@HD	VN:1.6	SO:coordinate
+@SQ	SN:chr1	LN:248956422	M5:6aef897c3d6ff0c78aff06ac189178dd	AS:38	UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta	SP:Homo sapiens
+@PG	ID:1	CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScatters --SCATTER_COUNT 60 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false	PN:IntervalListTools
+chr1	820849	910849	+	target_5
+chr1	910850	1000848	+	target_6
+chr1	1000849	1112599	+	target_7
+chr1	1112600	1224349	+	target_8

testdata/picard/util/largeScatters/temp_0003_of_60/scattered.interval_list

@@ -0,0 +1,7 @@
+@HD	VN:1.6	SO:coordinate
+@SQ	SN:chr1	LN:248956422	M5:6aef897c3d6ff0c78aff06ac189178dd	AS:38	UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta	SP:Homo sapiens
+@PG	ID:1	CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScatters --SCATTER_COUNT 60 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false	PN:IntervalListTools
+chr1	1224350	1348642	+	target_9
+chr1	1348643	1472934	+	target_10
+chr1	1472935	1584197	+	target_11
+chr1	1584198	1695459	+	target_12

testdata/picard/util/largeScatters/temp_0004_of_60/scattered.interval_list

@@ -0,0 +1,7 @@
+@HD	VN:1.6	SO:coordinate
+@SQ	SN:chr1	LN:248956422	M5:6aef897c3d6ff0c78aff06ac189178dd	AS:38	UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta	SP:Homo sapiens
+@PG	ID:1	CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScatters --SCATTER_COUNT 60 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false	PN:IntervalListTools
+chr1	1695460	1815724	+	target_13
+chr1	1815725	1935987	+	target_14
+chr1	1935988	2030188	+	target_15
+chr1	2030189	2124387	+	target_16

testdata/picard/util/largeScatters/temp_0005_of_60/scattered.interval_list

@@ -0,0 +1,7 @@
+@HD	VN:1.6	SO:coordinate
+@SQ	SN:chr1	LN:248956422	M5:6aef897c3d6ff0c78aff06ac189178dd	AS:38	UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta	SP:Homo sapiens
+@PG	ID:1	CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScatters --SCATTER_COUNT 60 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false	PN:IntervalListTools
+chr1	2124388	2261379	+	target_17
+chr1	2261380	2398369	+	target_18
+chr1	2398370	2662724	+	target_19
+chr1	2662725	2927077	+	target_20

testdata/picard/util/largeScatters/temp_0006_of_60/scattered.interval_list

@@ -0,0 +1,7 @@
+@HD	VN:1.6	SO:coordinate
+@SQ	SN:chr1	LN:248956422	M5:6aef897c3d6ff0c78aff06ac189178dd	AS:38	UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta	SP:Homo sapiens
+@PG	ID:1	CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScatters --SCATTER_COUNT 60 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false	PN:IntervalListTools
+chr1	2927078	3044965	+	target_21
+chr1	3044966	3162852	+	target_22
+chr1	3162853	3261512	+	target_23
+chr1	3261513	3360170	+	target_24

testdata/picard/util/largeScatters/temp_0007_of_60/scattered.interval_list

@@ -0,0 +1,7 @@
+@HD	VN:1.6	SO:coordinate
+@SQ	SN:chr1	LN:248956422	M5:6aef897c3d6ff0c78aff06ac189178dd	AS:38	UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta	SP:Homo sapiens
+@PG	ID:1	CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScatters --SCATTER_COUNT 60 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false	PN:IntervalListTools
+chr1	3360171	3481821	+	target_25
+chr1	3481822	3603470	+	target_26
+chr1	3603471	3720976	+	target_27
+chr1	3720977	3838480	+	target_28

testdata/picard/util/largeScatters/temp_0008_of_60/scattered.interval_list

@@ -0,0 +1,7 @@
+@HD	VN:1.6	SO:coordinate
+@SQ	SN:chr1	LN:248956422	M5:6aef897c3d6ff0c78aff06ac189178dd	AS:38	UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta	SP:Homo sapiens
+@PG	ID:1	CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScatters --SCATTER_COUNT 60 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false	PN:IntervalListTools
+chr1	3838481	3931034	+	target_29
+chr1	3931035	4023586	+	target_30
+chr1	4023587	4132844	+	target_31
+chr1	4132845	4242101	+	target_32