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Final corrections for two previous PRs.

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dbolotin committed Sep 28, 2018
1 parent afab7a6 commit 661e28c3b1f097decce85bad027c2ed3ecbdcce0
@@ -59,8 +59,8 @@
public final class ClnAWriter implements PipelineConfigurationWriter,
AutoCloseable,
CanReportProgressAndStage {
static final String MAGIC_V2 = "MiXCR.CLNA.V02";
static final String MAGIC = MAGIC_V2;
static final String MAGIC_V3 = "MiXCR.CLNA.V03";
static final String MAGIC = MAGIC_V3;
static final int MAGIC_LENGTH = MAGIC.length();
/**
@@ -48,8 +48,8 @@
public final class VDJCAlignmentsWriter implements VDJCAlignmentsWriterI {
public static final int DEFAULT_ENCODER_THREADS = 3;
static final String MAGIC_V12 = "MiXCR.VDJC.V12";
static final String MAGIC = MAGIC_V12;
static final String MAGIC_V13 = "MiXCR.VDJC.V13";
static final String MAGIC = MAGIC_V13;
static final int MAGIC_LENGTH = 14;
static final byte[] MAGIC_BYTES = MAGIC.getBytes(StandardCharsets.US_ASCII);
@@ -154,15 +154,11 @@ public static FullSeqAssembleResult assembleContigs(final AssembleResult assembl
OutputPort<Clone[]> parallelProcessor = new ParallelProcessor<>(cloneAlignmentsPort, cloneAlignments -> {
try {
FullSeqAssembler fullSeqAssembler = new FullSeqAssembler(cloneFactory, align.parameters.fullSeqAssemblerParameters, cloneAlignments.clone, align.parameters.alignerParameters);
FullSeqAssembler.RawVariantsData rawVariantsData = fullSeqAssembler.calculateRawData(() -> {
try {
return cloneAlignments.alignments();
} catch (IOException e) {
throw new RuntimeException(e);
}
});
FullSeqAssembler fullSeqAssembler = new FullSeqAssembler(cloneFactory,
align.parameters.fullSeqAssemblerParameters, cloneAlignments.clone,
align.parameters.alignerParameters);
FullSeqAssembler.RawVariantsData rawVariantsData =
fullSeqAssembler.calculateRawData(cloneAlignments::alignments);
return fullSeqAssembler.callVariants(rawVariantsData);
} catch (Throwable re) {

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