.gitignore

 # Created by .gitignore support plugin (hsz.mobi)
 .idea/workspace.xml
-/out/
+test/data/out/
 /build
 /build_java9
 /bin

.travis.yml

+language: java
+before_cache:
+  - rm -f  $HOME/.gradle/caches/modules-2/modules-2.lock
+  - rm -fr $HOME/.gradle/caches/*/plugin-resolution/
+cache:
+  directories:
+    - $HOME/.gradle/caches/
+    - $HOME/.gradle/wrapper/
+jdk: openjdk10
+install:
+- ./gradlew -b build_java9.gradle assemble
+script:
+- ./gradlew -b build_java9.gradle check
+- jdk_switcher use openjdk8
+- ./gradlew compileJava
\ No newline at end of file

README.md

 # igv
+[![Build Status](https://travis-ci.org/igvteam/igv.svg?branch=master)](https://travis-ci.org/igvteam/igv)
 
 Integrative Genomics Viewer - dekstop genome visualization tool for Mac, Windows, and Linux.
 

build.gradle

@@ -179,6 +179,7 @@ tasks.withType(Test) {
     systemProperties['include.longrunning'] = 'false'
     systemProperties['ignore.ioexceptions'] = 'false'
     maxHeapSize = '2000m'
+    maxParallelForks = Runtime.runtime.availableProcessors().intdiv(2) ?: 1
 }
 
 task createDist(type: Copy, dependsOn: fullJar)  {

build_java9.gradle

@@ -109,6 +109,7 @@ tasks.withType(Test) {
     systemProperties['include.longrunning'] = 'false'
     systemProperties['ignore.ioexceptions'] = 'false'
     maxHeapSize = '2000m'
+    maxParallelForks = Runtime.runtime.availableProcessors().intdiv(2) ?: 1
 }
 
 compileTestJava {

debian/changelog

+igv (2.4.17+dfsg-1) unstable; urgency=medium
+
+  * New upstream version
+  * debhelper 12
+  * Standards-Version: 4.3.0
+
+ -- Andreas Tille <tille@debian.org>  Wed, 30 Jan 2019 14:45:04 +0100
+
 igv (2.4.16+dfsg-1) unstable; urgency=medium
 
   * New upstream version

debian/compat

-11
+12

debian/control

@@ -6,7 +6,7 @@ Section: non-free/science
 XS-Autobuild: yes
 Priority: optional
 Build-Depends: default-jdk,
-               debhelper (>= 11~),
+               debhelper (>= 12~),
                gradle-debian-helper,
                junit4,
                libbatik-java,
@@ -41,7 +41,7 @@ Build-Depends: default-jdk,
                libfest-util-java,
                libfest-reflect-java,
                ant
-Standards-Version: 4.2.1
+Standards-Version: 4.3.0
 Vcs-Browser: https://salsa.debian.org/med-team/igv
 Vcs-Git: https://salsa.debian.org/med-team/igv.git
 Homepage: http://www.broadinstitute.org/igv/

genomes/db/hg19/hg19_annotations.xml

@@ -39,8 +39,8 @@
         <!--<Resource name="COSMIC" resourceType="das" hyperlink="http://www.sanger.ac.uk/genetics/CGP/cosmic/"-->
                   <!--path="http://das.sanger.ac.uk/das/cosmic_mutations_GRCh37/features"-->
                   <!--trackLine="featureVisibilityWindow=0"/>-->
-        <Resource name="OMIM Genes" hyperlink="http://www.ncbi.nlm.nih.gov/omim"
-                  url="http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=$$"
+        <Resource name="OMIM Genes" hyperlink="https://omim.org/"
+                  url=" https://omim.org/entry/$$"
                   path="http://www.broadinstitute.org/igvdata/annotations/hg19/phenotype/hg19_omim_genes.bed.gz"/>
         <Resource name="GWAS Catalog" hyperlink="http://genome.ucsc.edu/cgi-bin/hgTrackUi?g=gwasCatalog"
                   url="http://genome.ucsc.edu/cgi-bin/hgc?g=gwasCatalog&amp;i=$$"

src/main/java/org/broad/igv/feature/genome/GenomeManager.java

@@ -101,7 +101,11 @@ public class GenomeManager {
     private static Logger log = Logger.getLogger(GenomeManager.class);
 
     private static final String ACT_USER_DEFINED_GENOME_LIST_FILE = "user-defined-genomes.txt";
-    public static final String TEST_USER_DEFINED_GENOME_LIST_FILE = "test-user-defined-genomes.txt";
+    
+    // Tacking on a timestamp & random number to avoid file collisions with parallel testing JVMs.  Not guaranteed unique
+    // but highly unlikely to be repeated.
+    public static final String TEST_USER_DEFINED_GENOME_LIST_FILE = "test-user-defined-genomes_" + 
+            System.currentTimeMillis() + "_" + Math.random() + ".txt";
 
     public static final GenomeListItem DEFAULT_GENOME = new GenomeListItem("Human hg19", "http://s3.amazonaws.com/igv.broadinstitute.org/genomes/hg19.genome", "hg19");
 

src/main/java/org/broad/igv/feature/genome/fasta/FastaIndexedSequence.java

@@ -49,7 +49,6 @@ public class FastaIndexedSequence implements Sequence {
 
     final FastaIndex index;
     final String path;
-    final long contentLength;
 
     private final ArrayList<String> chromoNamesList;
 
@@ -60,7 +59,6 @@ public class FastaIndexedSequence implements Sequence {
     public FastaIndexedSequence(String path, String indexPath) throws IOException {
 
         this.path = path;
-        contentLength = ParsingUtils.getContentLength(path);
 
         if (indexPath == null) indexPath = path + ".fai";
 

src/main/java/org/broad/igv/maf/MAFIndex.java

@@ -235,7 +235,7 @@ public class MAFIndex {
                     String species = src;
                     String chr = src;
                     if (src.contains(".")) {
-                        String[] srcTokens = ParsingUtils.PERIOD_PATTERN.split(src);
+                        String[] srcTokens = ParsingUtils.PERIOD_PATTERN.split(src, 2);
                         species = srcTokens[0];
                         chr = srcTokens[1];
                     }

src/main/java/org/broad/igv/maf/MAFParser.java

@@ -108,7 +108,7 @@ public class MAFParser implements MAFReader {
 
         BufferedReader reader = new BufferedReader(new InputStreamReader(is), 256000);
 
-        List<MultipleAlignmentBlock> alignments = new ArrayList<MultipleAlignmentBlock>();
+        List<MultipleAlignmentBlock> alignments = new ArrayList<>();
 
         String line;
         while ((line = reader.readLine()) != null) {
@@ -239,7 +239,7 @@ public class MAFParser implements MAFReader {
                 String species = src;
                 String chr = src;
                 if (src.contains(".")) {
-                    String[] srcTokens = ParsingUtils.PERIOD_PATTERN.split(src);
+                    String[] srcTokens = ParsingUtils.PERIOD_PATTERN.split(src, 2);
                     species = srcTokens[0];
                     chr = srcTokens[1];
                 }

src/main/java/org/broad/igv/maf/MAFRenderer.java

@@ -67,9 +67,9 @@ public class MAFRenderer {
         double origin = context.getOrigin();
         double locScale = context.getScale();
 
-        if (locScale > 1) {
-            return;
-        }
+//        if (locScale > 1) {
+//            return;
+//        }
 
         for (MultipleAlignmentBlock.Gap gap : gaps) {
 
@@ -110,10 +110,6 @@ public class MAFRenderer {
         double origin = context.getOrigin();
         double locScale = context.getScale();
 
-        if (locScale > 1) {
-            return;
-        }
-
         double pixelStart = ((multipleAlignment.getStart() - origin) / locScale);
 
 
@@ -122,7 +118,6 @@ public class MAFRenderer {
         int y = (int) (trackRectangle.getY() + (trackRectangle.getHeight() - h) / 2);
         Rectangle rect = new Rectangle((int) pixelStart, y, w, h);
 
-        if (locScale < 1) {
 
         int pY = (int) rect.getY();
         int dY = (int) rect.getHeight();
@@ -161,21 +156,24 @@ public class MAFRenderer {
             Color color = nucleotideColors.get(charToDraw);
 
             if ((dX >= 8) && (dY >= 12) || charToDraw == '.') {
-
-                    // Graphics2D gBackground = context.getGraphic2DForColor(background);
-                    // gBackground.fillRect(pX0, pY, dX, dY);
                 if (charToDraw == '.') {
                     color = Color.LIGHT_GRAY;
                 } else if (color == null) {
                     color = Color.black;
                 }
-
                 g.setColor(color);
+
+                if(charToDraw == '-') {
+                    g.fillRect(pX0 + 2, pY + 4, dX - 4, dY - 4);
+                }
+                else {
                     drawCenteredText(g, new char[]{charToDraw}, pX0, pY + 2, dX, dY - 2);
+                }
             } else {
                 if (color != null) {
+                    int wb = Math.max(1, dX - 1);
                     g.setColor(color);
-                        g.fillRect(pX0, pY, dX - 1, dY);
+                    g.fillRect(pX0, pY, wb, dY);
                 }
 
             }
@@ -195,7 +193,7 @@ public class MAFRenderer {
             }
 
         }
-        }
+
     }
 
     private void drawCenteredText(Graphics2D g, char[] chars, int x, int y,

src/main/java/org/broad/igv/maf/MAFtoSAM.java

@@ -26,12 +26,10 @@
 
 package org.broad.igv.maf;
 
-import htsjdk.samtools.*;
 import org.broad.igv.Globals;
 import org.broad.igv.feature.genome.ChromosomeNameComparator;
 import org.broad.igv.tools.sort.SAMSorter;
 import org.broad.igv.tools.sort.Sorter;
-import org.broad.igv.tools.sort.SorterFactory;
 import org.broad.igv.util.ParsingUtils;
 
 import java.io.*;
@@ -69,7 +67,7 @@ public class MAFtoSAM {
 
     public static void convert(String path, String outputPath, boolean noSATag) throws IOException {
 
-        File unsortedOutput = new File(outputPath + ".unsorted.sam");
+        File unsortedOutput = new File(outputPath + ".unsorted");
         File outputFile = new File(outputPath);
 
         BufferedReader reader = ParsingUtils.openBufferedReader(path);
@@ -87,144 +85,12 @@ public class MAFtoSAM {
         reader.close();
 
         // Insert header and  SA tags
-        addSATags(unsortedOutput, outputFile, sequenceDictionary);
-
+        addHeaderAndSort(unsortedOutput, outputFile, sequenceDictionary);
 
         unsortedOutput.deleteOnExit();
 
     }
 
-    private static void addSATags(File inputFile, File outputFile, Map<String, Integer> sequenceDictionary) throws IOException {
-
-        String groupedOutput = inputFile.getAbsolutePath() + ".grouped.sam";
-        Sorter sorter = SorterFactory.getSorter(inputFile, new File(groupedOutput));
-        sorter.setComparator(SAMSorter.ReadNameComparator);
-        sorter.run();
-
-        // Get Sam file reader, output header, then iterate through sam records combining those with like read names
-
-        BufferedReader reader = new BufferedReader(new FileReader(groupedOutput));
-        PrintWriter out = new PrintWriter(new BufferedWriter(new FileWriter(outputFile)));
-        outputHeader(sequenceDictionary, out);
-
-
-        String line;
-        String[] lastRecord = null;
-
-        List<String[]> chimericAlignments = new ArrayList<>();
-
-        // Records should now be sorted by read name
-        while ((line = reader.readLine()) != null) {
-            if (line.startsWith("@")) {
-                out.println(line);
-            } else {
-                String[] record = Globals.tabPattern.split(line);
-
-                if (lastRecord == null || lastRecord[0].equals(record[0])) {
-                    chimericAlignments.add(record);
-                } else {
-                    if (chimericAlignments.size() > 0) {
-                        printChimericAlignments(out, chimericAlignments);
-                    }
-                    chimericAlignments.clear();
-                    chimericAlignments.add(record);
-                }
-                lastRecord = record;
-            }
-        }
-
-        // Last one
-        if (chimericAlignments.size() > 0) {
-            printChimericAlignments(out, chimericAlignments);
-        }
-
-        out.flush();
-        out.close();
-
-        (new File(groupedOutput)).deleteOnExit();
-
-    }
-
-    private static void printChimericAlignments(PrintWriter out, List<String[]> chimericAlignments) {
-
-        if (chimericAlignments.size() == 1) {
-            // Not chimeric, just print
-            printRecord(out, chimericAlignments.get(0));
-            out.println();
-        } else {
-
-            // Mark all but one alignment in the list as primary
-            int primaryRecordIndex = 0;
-            int longestSequence = chimericAlignments.get(0)[9].length();
-            for(int i=1; i<chimericAlignments.size(); i++) {
-                String[] thisRecord = chimericAlignments.get(i);
-                int seqLength = thisRecord[9].length();
-                if(seqLength > longestSequence) {
-                    longestSequence = seqLength;
-                    primaryRecordIndex = i;
-                }
-            }
-
-            for(int i=0; i<chimericAlignments.size(); i++) {
-                if(i == primaryRecordIndex) continue;
-                String[] thisRecord = chimericAlignments.get(i);
-                thisRecord[1] = String.valueOf(Integer.parseInt(thisRecord[1]) | NOT_PRIMARY_ALIGNMENT_FLAG);
-            }
-
-            for (int i = 0; i < chimericAlignments.size(); i++) {
-
-                String[] thisRecord = chimericAlignments.get(i);
-
-                StringBuffer saTag = new StringBuffer("SA:Z:");
-
-
-                // Build up the SA string -- essentially a list of the other parts of this chmeric alignment.
-                for (int j = 0; j < chimericAlignments.size(); j++) {
-
-                    if (j == i) continue;
-
-                    String[] supRecord = chimericAlignments.get(j);
-
-                    // This is fragile, but we control the order
-                    String nm;
-                    String nmString = supRecord[11];
-                    if (nmString.startsWith("NM:i:")) {
-                        nm = nmString.substring(5);
-                    } else {
-                        nm = "0";
-                    }
-
-                    boolean isNegativeStrand = (Integer.parseInt(supRecord[1]) & READ_STRAND_FLAG) != 0;
-
-                    saTag.append(supRecord[2] + "," + supRecord[3] + "," + (isNegativeStrand ? "-," : "+,") +
-                            supRecord[5] + "," + supRecord[4] + "," + nm + ";");
-                }
-
-                if (i > 0) {
-                    int flags = Integer.parseInt(thisRecord[1]) | SUPPLEMENTARY_FLAG;
-                    thisRecord[1] = Integer.toString(flags);
-                }
-
-                printRecord(out, thisRecord);
-
-                out.print("\t" + saTag.toString());
-
-                out.println();
-
-
-            }
-        }
-
-    }
-
-    private static void printRecord(PrintWriter out, String[] record) {
-        out.print(record[0]);
-        for (int i = 1; i < record.length; i++) {
-            out.print("\t" + record[i]);
-        }
-    }
-
-
     private static void parseBlock(BufferedReader reader, PrintWriter out, Map<String, Integer> sequenceDictionary) throws IOException {
 
         String line;
@@ -253,13 +119,15 @@ public class MAFtoSAM {
             }
             if (line.startsWith("s")) {
 
+
+
                 if (null == referenceLine) {
                     referenceLine = parseSequenceLine(line);
                     refBytes = referenceLine.text.getBytes();
 
                     if (referenceLine.src.contains(".")) {
-                        int idx = referenceLine.src.lastIndexOf('.') + 1;
-                        chr = referenceLine.src.substring(idx);
+                        String[] srcTokens = ParsingUtils.PERIOD_PATTERN.split(referenceLine.src, 2);
+                        chr = srcTokens[1];
                     } else {
                         chr = referenceLine.src;
                     }
@@ -267,6 +135,8 @@ public class MAFtoSAM {
                 } else {
 
                     queryLine = parseSequenceLine(line);
+                    String[] srcTokens = ParsingUtils.PERIOD_PATTERN.split(queryLine.src, 2);
+                    String species = srcTokens[0];
 
                     int flags = queryLine.strand == '+' ? 0 : 16;
 
@@ -334,7 +204,7 @@ public class MAFtoSAM {
                     String qual = "*";
 
                     out.print(readName + "\t" + flags + "\t" + chr + "\t" + start + "\t" + mapq + "\t" + cigarString + "\t" +
-                            rnext + "\t" + pnext + "\t" + tlen + "\t" + seq + "\t" + qual + "\tNM:i:" + nm);
+                            rnext + "\t" + pnext + "\t" + tlen + "\t" + seq + "\t" + qual + "\tNM:i:" + nm + "\tRG:Z:" + species);
                     if (barcode != null) {
                         out.print("\tBC:Z:" + barcode);
                     }
@@ -349,6 +219,32 @@ public class MAFtoSAM {
         // Output SAN header
     }
 
+
+    private static void addHeaderAndSort(File inputFile, File outputFile, Map<String, Integer> sequenceDictionary) throws IOException {
+
+        String sortedOutput = inputFile.getAbsolutePath() + ".sam";
+        Sorter sorter = new SAMSorter(inputFile, new File(sortedOutput));
+        sorter.run();
+
+        // Get Sam file reader, output header, then iterate through sam records combining those with like read names
+
+        BufferedReader reader = new BufferedReader(new FileReader(sortedOutput));
+        PrintWriter out = new PrintWriter(new BufferedWriter(new FileWriter(outputFile)));
+        outputHeader(sequenceDictionary, out);
+
+
+        String line;
+        // Records should now be sorted by read name
+        while ((line = reader.readLine()) != null) {
+            out.println(line);
+        }
+
+        out.flush();
+        out.close();
+
+    }
+
+
     private static void outputHeader(Map<String, Integer> sequenceDictionary, PrintWriter out) {
 
         List<String> chrNames = new ArrayList<String>(sequenceDictionary.keySet());
@@ -416,5 +312,7 @@ public class MAFtoSAM {
         int srcSize;
         String text;
     }
+
+
 }
 

src/main/java/org/broad/igv/maf/MultipleAlignmentTrack.java

@@ -193,7 +193,7 @@ public class MultipleAlignmentTrack extends AbstractTrack {
         if (frame.getScale() > 1) return true;   // Zoomed out, nothing to pain
 
         String chr = frame.getChrName();
-        int start = (int) frame.getOrigin();
+        int start = Math.max(0, (int) frame.getOrigin());
         int end = (int) frame.getEnd();
         return loadedAlignments != null && loadedAlignments.contains(chr, start, end);
     }
@@ -205,7 +205,7 @@ public class MultipleAlignmentTrack extends AbstractTrack {
         double w = frame.getEnd() - origin;
 
         // Get some buffer (+/- 1/2 screen)
-        String mafChr = chrMappings == null ? chr : chrMappings.get(chr);
+        String mafChr = chrMappings != null && chrMappings.containsKey(chr) ? chrMappings.get(chr) : chr;
         int start = (int) Math.max(0, origin - w);
         int end = (int) (origin + 2 * w);
 
@@ -224,7 +224,7 @@ public class MultipleAlignmentTrack extends AbstractTrack {
 
         double locScale = context.getScale();
 
-        if (locScale > 1) {
+        if (locScale > 10) {
             Rectangle r = new Rectangle(rect);
             if (visibleNameRect != null) {
                 r.y = visibleNameRect.y;
@@ -243,7 +243,7 @@ public class MultipleAlignmentTrack extends AbstractTrack {
         int end = (int) frame.getEnd();
 
         List<MultipleAlignmentBlock> alignments = null;
-        if (loadedAlignments != null && loadedAlignments.contains(chr, start, end)) {
+        if (loadedAlignments != null && loadedAlignments.overlaps(chr, start, end)) {
             alignments = loadedAlignments.getAlignments();
             if (alignments != null) {
                 for (MultipleAlignmentBlock ma : alignments) {
@@ -391,6 +391,9 @@ public class MultipleAlignmentTrack extends AbstractTrack {
         boolean contains(String chr, int start, int end) {
             return this.start <= start && this.end >= end && this.chr.equals(chr);
         }
+        boolean overlaps(String chr, int start, int end) {
+            return this.start <= end && this.end >= start && this.chr.equals(chr);
+        }
 
         public List<MultipleAlignmentBlock> getAlignments() {
             return alignments;

src/main/java/org/broad/igv/prefs/Constants.java

@@ -284,7 +284,8 @@ final public class Constants {
             SAM_QUICK_CONSENSUS_MODE,
             SAM_ALLELE_THRESHOLD,
             SAM_FLAG_LARGE_INDELS,
-            SAM_LARGE_INDELS_THRESHOLD
+            SAM_LARGE_INDELS_THRESHOLD,
+            SAM_SHOW_INSERTION_MARKERS
     );
 
 }

src/main/java/org/broad/igv/renderer/SequenceRenderer.java

@@ -77,7 +77,7 @@ public class SequenceRenderer {
         Color a = ColorUtilities.stringToColor(prefs.get(COLOR_A), new Color(0, 150, 0));
         Color c = ColorUtilities.stringToColor(prefs.get(COLOR_C), Color.blue);
         Color t = ColorUtilities.stringToColor(prefs.get(COLOR_T), Color.red);
-        Color g = ColorUtilities.stringToColor(prefs.get(COLOR_G), Color.gray);
+        Color g = ColorUtilities.stringToColor(prefs.get(COLOR_G), new Color(209,113,5));
         Color n = ColorUtilities.stringToColor(prefs.get(COLOR_N), Color.gray);
 
         nucleotideColors.put('A', a);

src/main/java/org/broad/igv/sam/AlignmentPacker.java

@@ -459,14 +459,14 @@ public class AlignmentPacker {
                 }
             case MOVIE: // group PacBio reads by movie
                 readNameParts = al.getReadName().split("/");
-                if (readNameParts.length != 3) {
+                if (readNameParts.length < 3) {
                     return "";
                 }
                 movieName = readNameParts[0];
                 return movieName;
             case ZMW: // group PacBio reads by ZMW
                 readNameParts = al.getReadName().split("/");
-                if (readNameParts.length != 3) {
+                if (readNameParts.length < 3) {
                     return "";
                 }
                 movieName = readNameParts[0];