Aslo report pindel insertions

Author: bbimber

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/MergeLoFreqVcfHandler.java

@@ -340,23 +340,27 @@ public void processFilesRemote(List<SequenceOutputFile> inputFiles, JobContext c
                                     continue;
                                 }
 
-                                int length = Integer.parseInt(line[3]) - Integer.parseInt(line[2]) - 1;  //NOTE: pindel reports one base upstream+downstream as part of the indel
-                                writer.writeNext(new String[]{ctx.getSequenceSupport().getCachedReadset(so.getReadset()).getName(), String.valueOf(so.getRowid()), String.valueOf(so.getReadset()), "Pindel", line[1], line[2], line[3], String.valueOf(length), "", line[0], line[4], "", line[5], line[6]});
-
+                                int end1 = Integer.parseInt(line[3]) - 1;  //pindel reports the end as one bp downstream of the event, so drop 1 bp even though we're keeping 1-based
+                                int length = end1 - Integer.parseInt(line[2]);  //NOTE: pindel reports one base upstream+downstream as part of the indel
                                 if ("D".equalsIgnoreCase(line[0]))
                                 {
-                                        ReferenceSequence rs = getReferenceSequence(ctx, genomeIds.iterator().next(), line[1]);
-                                        int start0 = Integer.parseInt(line[2]) - 1;
-                                        char alt = (char)rs.getBases()[start0];
+                                    ReferenceSequence rs = getReferenceSequence(ctx, genomeIds.iterator().next(), line[1]);
+                                    int start0 = Integer.parseInt(line[2]) - 1; //for consistency with VCFs, retain the first REF base, as pindel reports
+                                    char alt = (char)rs.getBases()[start0];
 
-                                        int end1 = Integer.parseInt(line[3]) - 1;  //pindel reports the end as one bp downstream of the event, so drop 1 bp even though we're keeping 1-based
-                                        String ref = new String(Arrays.copyOfRange(rs.getBases(), start0, end1), StringUtilsLabKey.DEFAULT_CHARSET);
-                                        if (ref.length() != length + 1)
-                                        {
-                                            throw new PipelineJobException("Improper pindel parsing: " + so.getRowid() + "/" + line[2] + "/" + line[3] + "/" + ref + "/" + alt);
-                                        }
+                                    String ref = new String(Arrays.copyOfRange(rs.getBases(), start0, end1), StringUtilsLabKey.DEFAULT_CHARSET);
+                                    if (ref.length() != length + 1)
+                                    {
+                                        throw new PipelineJobException("Improper pindel parsing: " + so.getRowid() + "/" + line[2] + "/" + line[3] + "/" + ref + "/" + alt);
+                                    }
 
-                                        uniqueIndels.add(line[1] + "<>" + line[2] + "<>" + ref + "<>" + alt);
+                                    uniqueIndels.add(line[1] + "<>" + line[2] + "<>" + ref + "<>" + alt);
+
+                                    writer.writeNext(new String[]{ctx.getSequenceSupport().getCachedReadset(so.getReadset()).getName(), String.valueOf(so.getRowid()), String.valueOf(so.getReadset()), "Pindel", line[1], line[2], String.valueOf(end1), String.valueOf(length), ref, String.valueOf(alt), line[4], "", line[5], line[6]});
+                                }
+                                else
+                                {
+                                    writer.writeNext(new String[]{ctx.getSequenceSupport().getCachedReadset(so.getReadset()).getName(), String.valueOf(so.getRowid()), String.valueOf(so.getReadset()), "Pindel", line[1], line[2], String.valueOf(end1), String.valueOf(length), "", line[0], line[4], "", line[5], line[6]});
                                 }
                             }
                         }

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/PindelAnalysis.java

@@ -229,6 +229,8 @@ public static File runPindel(AnalysisOutputImpl output, PipelineContext ctx, Rea
         {
             writer.writeNext(new String[]{"Type", "Contig", "Start", "End", "Depth", "ReadSupport", "Fraction"});
             parsePindelOutput(ctx, writer, new File(outPrefix.getPath() + "_D"), minFraction, minDepth, gatkDepth);
+            parsePindelOutput(ctx, writer, new File(outPrefix.getPath() + "_SI"), minFraction, minDepth, gatkDepth);
+            parsePindelOutput(ctx, writer, new File(outPrefix.getPath() + "_LI"), minFraction, minDepth, gatkDepth);
             parsePindelOutput(ctx, writer, new File(outPrefix.getPath() + "_INV"), minFraction, minDepth, gatkDepth);
         }
         catch (IOException e)
@@ -241,6 +243,11 @@ public static File runPindel(AnalysisOutputImpl output, PipelineContext ctx, Rea
 
     private static void parsePindelOutput(PipelineContext ctx, CSVWriter writer, File pindelFile, double minFraction, int minDepth, File gatkDepthFile) throws IOException
     {
+        if (!pindelFile.exists())
+        {
+            return;
+        }
+
         try (BufferedReader reader = Readers.getReader(pindelFile))
         {
             String line;