Esvee: optionally specify 'esvee_prep_dir' for inputs for assembly an…

…d caller
hartwigmedical · Dec 9, 2024 · c90e65a · c90e65a
1 parent 46666c5
commit c90e65a
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Showing 5 changed files with 34 additions and 27 deletions.
diff --git a/esvee/src/main/java/com/hartwig/hmftools/esvee/assembly/AssemblyApplication.java b/esvee/src/main/java/com/hartwig/hmftools/esvee/assembly/AssemblyApplication.java
@@ -20,6 +20,7 @@
 import static com.hartwig.hmftools.esvee.assembly.output.WriteType.JUNC_ASSEMBLY;
 import static com.hartwig.hmftools.esvee.assembly.output.WriteType.ASSEMBLY_BAM;
 import static com.hartwig.hmftools.esvee.assembly.output.WriteType.ASSEMBLY_READ;
+import static com.hartwig.hmftools.esvee.common.FileCommon.formFragmentLengthDistFilename;
 import static com.hartwig.hmftools.esvee.prep.PrepConstants.DISCORDANT_GROUP_MIN_FRAGMENTS;
 import static com.hartwig.hmftools.esvee.prep.PrepConstants.DISCORDANT_GROUP_MIN_FRAGMENTS_SHORT;
 import static com.hartwig.hmftools.esvee.prep.PrepConstants.MIN_HOTSPOT_JUNCTION_SUPPORT;
@@ -226,13 +227,15 @@ private boolean loadJunctionFiles()
 
     private void loadFragmentLengthBounds()
     {
-        if(!Files.exists(Paths.get(mConfig.FragmentLengthFile)))
+        String fragmentLengthFile = formFragmentLengthDistFilename(mConfig.PrepDir, mConfig.sampleId());
+
+        if(!Files.exists(Paths.get(fragmentLengthFile)))
         {
-            SV_LOGGER.error("missing fragment length file: {}", mConfig.FragmentLengthFile);
+            SV_LOGGER.error("missing fragment length file: {}", fragmentLengthFile);
             System.exit(1);
         }
 
-        FragmentLengthBounds fragmentLengthBounds = FragmentSizeDistribution.loadFragmentLengthBounds(mConfig.FragmentLengthFile);
+        FragmentLengthBounds fragmentLengthBounds = FragmentSizeDistribution.loadFragmentLengthBounds(fragmentLengthFile);
 
         if(fragmentLengthBounds.isValid())
         {

diff --git a/esvee/src/main/java/com/hartwig/hmftools/esvee/assembly/AssemblyConfig.java b/esvee/src/main/java/com/hartwig/hmftools/esvee/assembly/AssemblyConfig.java
@@ -33,14 +33,13 @@
 import static com.hartwig.hmftools.esvee.assembly.AssemblyConstants.DEFAULT_DISC_RATE_INCREMENT;
 import static com.hartwig.hmftools.esvee.assembly.alignment.BwaAligner.loadAlignerLibrary;
 import static com.hartwig.hmftools.esvee.assembly.output.WriteType.fromConfig;
-import static com.hartwig.hmftools.esvee.common.FileCommon.FRAG_LENGTHS_FILE;
-import static com.hartwig.hmftools.esvee.common.FileCommon.FRAG_LENGTHS_FILE_DESC;
 import static com.hartwig.hmftools.esvee.common.FileCommon.JUNCTION_FILE;
 import static com.hartwig.hmftools.esvee.common.FileCommon.JUNCTION_FILE_DESC;
+import static com.hartwig.hmftools.esvee.common.FileCommon.PREP_DIR;
+import static com.hartwig.hmftools.esvee.common.FileCommon.PREP_DIR_DESC;
 import static com.hartwig.hmftools.esvee.common.FileCommon.REF_GENOME_IMAGE_EXTENSION;
 import static com.hartwig.hmftools.esvee.assembly.output.WriteType.ASSEMBLY_READ;
 import static com.hartwig.hmftools.esvee.common.FileCommon.formEsveeInputFilename;
-import static com.hartwig.hmftools.esvee.common.FileCommon.formFragmentLengthDistFilename;
 import static com.hartwig.hmftools.esvee.common.FileCommon.formPrepInputFilename;
 import static com.hartwig.hmftools.esvee.prep.PrepConstants.PREP_JUNCTION_FILE_ID;
 
@@ -79,7 +78,7 @@ public class AssemblyConfig
     public final List<String> ReferenceBams;
 
     public final List<String> JunctionFiles;
-    public final String FragmentLengthFile;
+    public final String PrepDir;
 
     public final RefGenomeVersion RefGenVersion;
     public final RefGenomeCoordinates RefGenomeCoords;
@@ -172,6 +171,8 @@ public AssemblyConfig(final ConfigBuilder configBuilder)
         OutputDir = parseOutputDir(configBuilder);
         OutputId = configBuilder.getValue(OUTPUT_ID);
 
+        PrepDir = configBuilder.hasValue(PREP_DIR) ? configBuilder.getValue(PREP_DIR) : OutputDir;
+
         JunctionFiles = Lists.newArrayList();
 
         if(configBuilder.hasValue(JUNCTION_FILE))
@@ -181,15 +182,12 @@ public AssemblyConfig(final ConfigBuilder configBuilder)
         else
         {
             // since Prep now reads multiple BAMs, only the tumor-labelled junctions file needs to be loaded
-            String junctionFile = formPrepInputFilename(OutputDir, TumorIds.get(0), PREP_JUNCTION_FILE_ID, OutputId);
+            String junctionFile = formPrepInputFilename(PrepDir, TumorIds.get(0), PREP_JUNCTION_FILE_ID, OutputId);
 
             if(Files.exists(Paths.get(junctionFile)))
                 JunctionFiles.add(junctionFile);
         }
 
-        FragmentLengthFile = configBuilder.getValue(
-                FRAG_LENGTHS_FILE, formFragmentLengthDistFilename(OutputDir, TumorIds.get(0)));
-
         BamToolPath = configBuilder.getValue(BAMTOOL_PATH);
 
         RefGenVersion = RefGenomeVersion.from(configBuilder);
@@ -311,7 +309,7 @@ public static void registerConfig(final ConfigBuilder configBuilder)
         configBuilder.addConfigItem(REFERENCE_BAM, false, REFERENCE_BAMS_DESC);
 
         configBuilder.addPaths(JUNCTION_FILE, false, JUNCTION_FILE_DESC);
-        configBuilder.addPaths(FRAG_LENGTHS_FILE, false, FRAG_LENGTHS_FILE_DESC);
+        configBuilder.addPaths(PREP_DIR, false, PREP_DIR_DESC);
 
         addRefGenomeConfig(configBuilder, true);
         configBuilder.addPath(REF_GENOME_IMAGE, false, REFERENCE_BAM_DESC);
@@ -373,7 +371,7 @@ public AssemblyConfig()
         ReferenceBams = Collections.emptyList();
 
         JunctionFiles = Collections.emptyList();
-        FragmentLengthFile = "";
+        PrepDir = null;
 
         RefGenVersion = V38;
         RefGenomeCoords = null;

diff --git a/esvee/src/main/java/com/hartwig/hmftools/esvee/caller/CallerApplication.java b/esvee/src/main/java/com/hartwig/hmftools/esvee/caller/CallerApplication.java
@@ -16,13 +16,11 @@
 import static com.hartwig.hmftools.esvee.caller.LineChecker.adjustLineSites;
 import static com.hartwig.hmftools.esvee.caller.VariantFilters.logFilterTypeCounts;
 import static com.hartwig.hmftools.esvee.common.FileCommon.APP_NAME;
-import static com.hartwig.hmftools.esvee.common.FileCommon.FRAG_LENGTHS_FILE;
 import static com.hartwig.hmftools.esvee.common.FileCommon.formFragmentLengthDistFilename;
 import static com.hartwig.hmftools.esvee.prep.types.DiscordantStats.formDiscordantStatsFilename;
 import static com.hartwig.hmftools.esvee.prep.types.DiscordantStats.loadDiscordantStats;
 
 import com.hartwig.hmftools.common.utils.config.ConfigBuilder;
-import com.hartwig.hmftools.common.utils.file.FileWriterUtils;
 import com.hartwig.hmftools.common.utils.version.VersionInfo;
 import com.hartwig.hmftools.common.variant.GenotypeIds;
 import com.hartwig.hmftools.common.variant.VcfFileReader;
@@ -66,14 +64,10 @@ public CallerApplication(final ConfigBuilder configBuilder)
         mPonCache = new PonCache(configBuilder);
         mHotspotCache = new HotspotCache(configBuilder);
 
-        String inputDir = FileWriterUtils.pathFromFile(mConfig.VcfFile);
-
-        String fragLengthFilename = configBuilder.getValue(
-                FRAG_LENGTHS_FILE, formFragmentLengthDistFilename(inputDir, mConfig.fileSampleId()));
-
+        String fragLengthFilename = formFragmentLengthDistFilename(mConfig.PrepDir, mConfig.fileSampleId());
         FragmentLengthBounds fragmentLengthBounds = FragmentSizeDistribution.loadFragmentLengthBounds(fragLengthFilename);
 
-        String discStatsFilename = formDiscordantStatsFilename(inputDir, mConfig.fileSampleId());
+        String discStatsFilename = formDiscordantStatsFilename(mConfig.PrepDir, mConfig.fileSampleId());
         DiscordantStats discordantStats = loadDiscordantStats(discStatsFilename);
 
         SV_LOGGER.info("fragment length dist: {}", fragmentLengthBounds);

diff --git a/esvee/src/main/java/com/hartwig/hmftools/esvee/caller/CallerConfig.java b/esvee/src/main/java/com/hartwig/hmftools/esvee/caller/CallerConfig.java
@@ -15,10 +15,10 @@
 import static com.hartwig.hmftools.common.utils.file.FileWriterUtils.parseOutputDir;
 import static com.hartwig.hmftools.esvee.assembly.AssemblyConfig.SV_LOGGER;
 import static com.hartwig.hmftools.esvee.common.FileCommon.DEPTH_VCF_SUFFIX;
-import static com.hartwig.hmftools.esvee.common.FileCommon.FRAG_LENGTHS_FILE;
-import static com.hartwig.hmftools.esvee.common.FileCommon.FRAG_LENGTHS_FILE_DESC;
 import static com.hartwig.hmftools.esvee.common.FileCommon.INPUT_VCF;
 import static com.hartwig.hmftools.esvee.common.FileCommon.INPUT_VCF_DESC;
+import static com.hartwig.hmftools.esvee.common.FileCommon.PREP_DIR;
+import static com.hartwig.hmftools.esvee.common.FileCommon.PREP_DIR_DESC;
 import static com.hartwig.hmftools.esvee.common.FileCommon.formEsveeInputFilename;
 
 import java.nio.file.Files;
@@ -36,7 +36,9 @@ public class CallerConfig
     public final String SampleId;
     public final String ReferenceId;
     public final RefGenomeVersion RefGenVersion;
+
     public final String VcfFile;
+    public final String PrepDir;
 
     public final String OutputDir;
     public final String OutputId;
@@ -63,6 +65,8 @@ public CallerConfig(final ConfigBuilder configBuilder)
             VcfFile = formEsveeInputFilename(OutputDir, fileSampleId, DEPTH_VCF_SUFFIX, OutputId);
         }
 
+        PrepDir = configBuilder.hasValue(PREP_DIR) ? configBuilder.getValue(PREP_DIR) : OutputDir;
+
         RefGenVersion = RefGenomeVersion.from(configBuilder);
 
         SpecificChromosomes = loadSpecificChromsomes(configBuilder);
@@ -110,7 +114,7 @@ public static void registerConfig(final ConfigBuilder configBuilder)
         configBuilder.addConfigItem(SAMPLE, SAMPLE_DESC);
         configBuilder.addConfigItem(REFERENCE, REFERENCE_DESC);
         configBuilder.addPath(INPUT_VCF, false, INPUT_VCF_DESC);
-        configBuilder.addPaths(FRAG_LENGTHS_FILE, false, FRAG_LENGTHS_FILE_DESC);
+        configBuilder.addPaths(PREP_DIR, false, PREP_DIR_DESC);
         configBuilder.addInteger(MANUAL_REF_DEPTH, "Manually set ref depth for testing", 0);
 
         addOutputOptions(configBuilder);

diff --git a/esvee/src/main/java/com/hartwig/hmftools/esvee/common/FileCommon.java b/esvee/src/main/java/com/hartwig/hmftools/esvee/common/FileCommon.java
@@ -26,16 +26,24 @@ public final class FileCommon
     public static final String ESVEE_FILE_ID = "esvee";
     public static final String PREP_FILE_ID = "esvee.prep";
 
+    public static final String PREP_DIR = "esvee_prep_dir";
+    public static final String PREP_DIR_DESC = "Esvee prep input directory";
+
+    /*
+    public static final String ASSEMBLY_DIR = "esvee_assembly_dir";
+    public static final String ASSEMBLY_DIR_DESC = "Esvee assembly input directory";
+
+    public static final String REF_DEPTH_DIR = "esvee_ref_depth_dir";
+    public static final String REF_DEPTH_DIR_DESC = "Esvee ref depth input directory";
+    */
+
     public static final String RAW_VCF_SUFFIX = "raw" + VCF_ZIP_EXTENSION;
     public static final String DEPTH_VCF_SUFFIX = "ref_depth" + VCF_ZIP_EXTENSION;
 
     // common config
     public static final String JUNCTION_FILE = "junction_file";
     public static final String JUNCTION_FILE_DESC = "Esvee Prep junction file, default is to match by sample name";
 
-    public static final String FRAG_LENGTHS_FILE = "frag_length_file";
-    public static final String FRAG_LENGTHS_FILE_DESC = "Esvee Prep fragment length distribution file, default is to match by sample name";
-
     public static final String FILE_NAME_DELIM = ".";
 
     public static final String REF_GENOME_IMAGE_EXTENSION = ".img";