Draft: Add WGS read reconstruction for ROI

src/main/java/nl/wur/bif/pantools/analysis/region_analysis/ExtractFunctionsCLI.java

@@ -2,6 +2,8 @@ package nl.wur.bif.pantools.analysis.region_analysis;
 
 import nl.wur.bif.pantools.Pantools;
 import nl.wur.bif.pantools.utils.BeanUtils;
+import nl.wur.bif.pantools.utils.FileUtils;
+import nl.wur.bif.pantools.utils.Globals;
 import nl.wur.bif.pantools.utils.GraphUtils;
 import nl.wur.bif.pantools.utils.cli.mixins.SelectGenomes;
 import nl.wur.bif.pantools.utils.cli.validation.Constraints.OutputDirectory;
@@ -75,6 +77,11 @@ public class ExtractFunctionsCLI implements Callable<Integer> {
     )
     private boolean writeRepeats;
 
+    @Option(names = {"--reads-file"},
+            description = "Tab-delimited file with library names and corresponding read files. Default: none"
+    )
+    private Path readsFile;
+
     //TODO: add --write-blast option to visualize BLASTP and BLASTN results
 
     private String[] functions;
@@ -103,14 +110,14 @@ public class ExtractFunctionsCLI implements Callable<Integer> {
             GraphUtils.validateRepeats(); // check that repeats are present
         }
 
-        // determine whether to use the fast option
-        boolean fast = !writeGfa && !writeUnitigs;
+        // always use fast option, except when writing GFA or unitigs, or using read files
+        boolean fast = !writeGfa && !writeUnitigs && readsFile == null;
         if (!fast) {
             Pantools.logger.warn("Using a slow method for extraction.");
         }
 
         final RegionExtractor regionExtractor = new RegionExtractor(outputPath);
-        regionExtractor.extractFunctions(functions, flanking, writeAnnotations, writeGfa, writeHomology, writeUnitigs, writeRepeats, fast);
+        regionExtractor.extractFunctions(functions, flanking, writeAnnotations, writeGfa, writeHomology, writeUnitigs, writeRepeats, FileUtils.parseReadsFile(readsFile), fast);
 
         return 0;
     }
@@ -126,6 +133,11 @@ public class ExtractFunctionsCLI implements Callable<Integer> {
                 throw new ParameterException(spec.commandLine(), "Functions must be GO, InterPro, Pfam or TIGRFAM");
             }
         }
+
+        // Assert that K is smaller than 64 when using reads (because of storing 2bit version of k-mers in long)
+        if (readsFile != null && Globals.K_SIZE > 63) {
+            throw new ParameterException(spec.commandLine(), "K should be smaller than 63 when using reads");
+        }
     }
 
     public Pantools getPantools() {