Numerical consistency between python and java, transpose fix

src/main/java/org/broadinstitute/hellbender/engine/filters/ReadGroupBlackListReadFilter.java

@@ -39,14 +39,15 @@ public final class ReadGroupBlackListReadFilter extends ReadFilter implements Se
     // Command line parser requires a no-arg constructor
     public ReadGroupBlackListReadFilter() {};
 
-        /**
-         * Creates a filter using the lists of files with blacklisted read groups.
-         * Any entry can be a path to a file (ending with "list" or "txt" which
-         * will load blacklist from that file. This scheme works recursively
-         * (ie the file may contain names of further files etc).
-         */
+    /**
+     * Creates a filter using the lists of files with blacklisted read groups.
+     * Any entry can be a path to a file (ending with "list" or "txt" which
+     * will load blacklist from that file. This scheme works recursively
+     * (ie the file may contain names of further files etc).
+     */
     public ReadGroupBlackListReadFilter(final List<String> blackLists, final SAMFileHeader header) {
         super.setHeader(header);
+        this.blackList.addAll(blackLists);
         final Map<String, Collection<String>> filters = new TreeMap<>();
         for (String blackList : blackLists) {
             try {

src/main/java/org/broadinstitute/hellbender/tools/walkers/vqsr/CNNScoreVariants.java

@@ -10,9 +10,9 @@
 import org.broadinstitute.barclay.help.DocumentedFeature;
 import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions;
 import org.broadinstitute.hellbender.engine.*;
-import org.broadinstitute.hellbender.engine.filters.VariantFilter;
-import org.broadinstitute.hellbender.engine.filters.VariantFilterLibrary;
+import org.broadinstitute.hellbender.engine.filters.*;
 import org.broadinstitute.hellbender.exceptions.GATKException;
+import org.broadinstitute.hellbender.utils.haplotype.HaplotypeBAMWriter;
 import org.broadinstitute.hellbender.utils.io.Resource;
 import org.broadinstitute.hellbender.utils.io.IOUtils;
 import org.broadinstitute.hellbender.utils.python.StreamingPythonScriptExecutor;
@@ -170,7 +170,7 @@ public class CNNScoreVariants extends VariantWalker {
 
     private int curBatchSize = 0;
     private int windowEnd = windowSize / 2;
-    private int windowStart = (windowSize / 2) - 1;
+    private int windowStart = windowSize / 2;
     private boolean waitforBatchCompletion = false;
     private File scoreFile;
 
@@ -190,7 +190,6 @@ protected String[] customCommandLineValidation() {
                 return new String[]{"No default architecture for tensor type:" + tensorType.name()};
             }
         }
-
         return null;
     }
 
@@ -208,6 +207,17 @@ protected VariantFilter makeVariantFilter(){
         }
     }
 
+    @Override
+    public List<ReadFilter> getDefaultReadFilters() {
+        List<ReadFilter> readFilters = new ArrayList<>();
+        readFilters.addAll(super.getDefaultReadFilters());
+        List<String> filterList = new ArrayList<>();
+        filterList.add("ID:" + HaplotypeBAMWriter.DEFAULT_HAPLOTYPE_READ_GROUP_ID);
+        filterList.add("ID:" + HaplotypeBAMWriter.DEFAULT_GATK3_HAPLOTYPE_READ_GROUP_ID);
+        readFilters.add(new ReadGroupBlackListReadFilter(filterList, null));
+        return readFilters;
+    }
+
     @Override
     public void onTraversalStart() {
         scoreKey = getScoreKeyAndCheckModelAndReadsHarmony();
@@ -319,7 +329,7 @@ private void transferReadsToPythonViaFifo(final VariantContext variant, final Re
         }
         Iterator<GATKRead> readIt = readsContext.iterator();
         if (!readIt.hasNext()) {
-            logger.warn("No reads at contig:" + variant.getContig() + "site:" + String.valueOf(variant.getStart()));
+            logger.warn("No reads at contig:" + variant.getContig() + " site:" + String.valueOf(variant.getStart()));
         }
         while (readIt.hasNext()) {
             sb.append(GATKReadToString(readIt.next()));

src/main/java/org/broadinstitute/hellbender/utils/haplotype/HaplotypeBAMWriter.java

@@ -25,7 +25,9 @@ public abstract class HaplotypeBAMWriter implements AutoCloseable {
      */
     private long uniqueNameCounter = 1;
 
-    private static final String DEFAULT_HAPLOTYPE_READ_GROUP_ID = "ArtificialHaplotypeRG";
+    public static final String DEFAULT_HAPLOTYPE_READ_GROUP_ID = "ArtificialHaplotypeRG";
+    // For read filters that need backwards compatibility with the GATK3 artificial haplotype
+    public static final String DEFAULT_GATK3_HAPLOTYPE_READ_GROUP_ID = "ArtificialHaplotype";
     private static final int bestHaplotypeMQ = 60;
     private static final int otherMQ = 0;
 

src/main/python/org/broadinstitute/hellbender/vqsr_cnn/vqsr_cnn/inference.py

@@ -43,14 +43,14 @@ def score_and_write_batch(args, model, file_out, fifo, batch_size, python_batch_
     variant_data = []
     read_batch = []
 
-    for i in range(batch_size):
+    for _ in range(batch_size):
         fifo_line = fifo.readline()
         fifo_data = fifo_line.split(defines.SEPARATOR_CHAR)
 
         variant_data.append(fifo_data[0] + '\t' + fifo_data[1] + '\t' + fifo_data[2] + '\t' + fifo_data[3])
         reference_batch.append(reference_string_to_tensor(fifo_data[4]))
         annotation_batch.append(annotation_string_to_tensor(args, fifo_data[5]))
-        variant_types.append(fifo_data[6])
+        variant_types.append(fifo_data[6].strip())
 
         fidx = 7 # 7 Because above we parsed: contig pos ref alt reference_string annotation variant_type
         if args.tensor_name in defines.TENSOR_MAPS_2D and len(fifo_data) > fidx:
@@ -69,7 +69,7 @@ def score_and_write_batch(args, model, file_out, fifo, batch_size, python_batch_
             _, ref_start, _ = get_variant_window(args, var)
             insert_dict = get_inserts(args, read_tuples, var)
             tensor = read_tuples_to_read_tensor(args, read_tuples, ref_start, insert_dict)
-            reference_sequence_into_tensor(args, fifo_data[4], tensor)
+            reference_sequence_into_tensor(args, fifo_data[4], tensor, insert_dict)
             if os.path.exists(tensor_dir):
                 _write_tensor_to_hd5(args, tensor, annotation_batch[-1], fifo_data[0], fifo_data[1], fifo_data[6])
             read_batch.append(tensor)
@@ -201,8 +201,8 @@ def cigar_string_to_tuples(cigar):
 
 def get_variant_window(args, variant):
     index_offset = (args.window_size//2)
-    reference_start = variant.pos-(index_offset+1)
-    reference_end = variant.pos+index_offset
+    reference_start = variant.pos-index_offset
+    reference_end = variant.pos + index_offset + (args.window_size%2)
     return index_offset, reference_start, reference_end
 
 
@@ -245,6 +245,7 @@ def read_tuples_to_read_tensor(args, read_tuples, ref_start, insert_dict):
 
             if i == args.window_size:
                 break
+
             if b == defines.SKIP_CHAR:
                 continue
             elif flag_start == -1:
@@ -290,8 +291,6 @@ def read_tuples_to_read_tensor(args, read_tuples, ref_start, insert_dict):
             else:
                 tensor[channel_map['mapping_quality'], j, flag_start:flag_end] = mq
 
-
-
     return tensor
 
 
@@ -335,9 +334,15 @@ def sequence_and_qualities_from_read(args, read, ref_start, insert_dict):
     return rseq, rqual
 
 
-def reference_sequence_into_tensor(args, reference_seq, tensor):
+def reference_sequence_into_tensor(args, reference_seq, tensor, insert_dict):
     ref_offset = len(set(args.input_symbols.values()))
 
+    for i in sorted(insert_dict.keys(), key=int, reverse=True):
+        if i < 0:
+            reference_seq = defines.INDEL_CHAR*insert_dict[i] + reference_seq
+        else:
+            reference_seq = reference_seq[:i] + defines.INDEL_CHAR*insert_dict[i] + reference_seq[i:]
+
     for i,b in enumerate(reference_seq):
         if i == args.window_size:
             break

src/main/resources/org/broadinstitute/hellbender/tools/walkers/vqsr/training.py

@@ -607,11 +607,11 @@ def reference_sequence_into_tensor(args, reference_seq, tensor):
             else:
                 tensor[ref_offset+args.input_symbols[b], :, i] = 1.0
         elif b in vqsr_cnn.AMBIGUITY_CODES:
-            ambiguous_vector = np.transpose(np.tile(vqsr_cnn.AMBIGUITY_CODES[b], (args.read_limit, 1)))
+            ambiguous_vector = np.tile(vqsr_cnn.AMBIGUITY_CODES[b], (args.read_limit, 1))
             if K.image_data_format() == 'channels_last':
                 tensor[:, i, ref_offset:ref_offset+4] = ambiguous_vector
             else:
-                tensor[ref_offset:ref_offset+4, :, i] = ambiguous_vector
+                tensor[ref_offset:ref_offset+4, :, i] = np.transpose(ambiguous_vector)
 
 
 def flag_to_array(flag):