Merge branch 'hotfix/v1.7.3'

CHANGELOG

@@ -1,4 +1,17 @@
 
+MiXCR 1.7.3 (17 May 2016)
+========================
+
+-- Fixed: wrong boundaries of CDR1-CDR3 in Rat IGH/IGK references imported from IMGT
+-- Fixed: bug leading to incorrect parsing of input/output file paths with spaces
+-- Fixed: bug leading to incorrect parsing of input/output file paths with spaces
+-- Automatic adjustment of featureToAlign in assemble action; fixes `NPE` in some use-cases of RNA 
+   data analysis with IMGT reference
+-- Added support for FreeBSD in mixcr script
+-- minor: Human-readable error messages for illegal analysis options with IMGT reference
+-- minor: Added human-readable error message for unknown species
+
+
 MiXCR 1.7.2 ( 5 May 2016)
 ========================
 

doc/export.rst

@@ -587,7 +587,7 @@ In any way, first one need to specify additonal option ``--index`` for the :ref:
 
     mixcr assemble --index index_file alignments.vdjca output.clns
 
-This will tell MiXCR to store mapping in the file ``index_file``. Now one can use ``index_file`` in order to access this information. For example using ``-cloneId`` option for ``exportAlignments`` command:
+This will tell MiXCR to store mapping in the file ``index_file`` (actually two files will be created: ``index_file`` and ``index_file.p`` both of which are used to store the index; in further options one should specify only ``index_file`` without ``.p`` extension and MiXCR will automatically read both required files). Now one can use ``index_file`` in order to access this information. For example using ``-cloneId`` option for ``exportAlignments`` command:
 
 ::
 
@@ -663,7 +663,7 @@ Finally, one can export reads aggregated by each clone into separate ``.fastq``
 
     mixcr align -g -l IGH input.fastq alignments.vdjca.gz
 
-With this option MiXCR will store original reads in the ``.vdjca`` file. Then one can export reads corresponding for particular clone with ``exportReads`` command. For example, export all reads that were assembled into the first clone (clone with cloneId = 1):
+With this option MiXCR will store original reads in the ``.vdjca`` file. Then one can export reads corresponding for particular clone with ``exportReads`` command. For example, export all reads that were assembled into the first clone (clone with cloneId = 0):
 
 ::
 

importFromIMGT.sh

@@ -97,6 +97,11 @@ do
   # Workaround for *** IMGT malformed files
   if [[ "$(echo ${species} | tr [:upper:] [:lower:])" == mus* ]] && [[ "$locus" == TR[AD] ]]; then
     comm="$comm -p imgt_a1"
+    echo "Special paramenters for Mouse TRA/D genes activated."
+  fi
+  if [[ "$(echo ${species} | tr [:upper:] [:lower:])" == rat* ]] && [[ "$locus" == IG[HK] ]]; then
+    comm="$comm -p imgt_a2"
+    echo "Special paramenters for Rat IGH/K genes activated."
   fi
 
   # Output file info on the last iteration

mixcr

@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
 java="java"
 
@@ -52,6 +52,13 @@ case $os in
         maxMb=$(($rFreeMb-$delta))
         dir="$(dirname "$(readlink -f "$0")")"
     ;;
+    FreeBSD)
+        freeBlocks=$(vmstat -s | grep -E 'free$' | awk '{ print $1 }')
+        inactiveBlocks=$(vmstat -s | grep inactive | awk '{ print $1 }')
+        freeMb=$(( ($freeBlocks+$inactiveBlocks)*4096/1048576 ))
+        maxMb=$(($freeMb-$delta))
+        dir=$(dirname "$(readlinkUniversal "$0")")    
+    ;;
     *)
        echo "Unknown OS."
        exit 1
@@ -87,7 +94,7 @@ do
 
             ;;
         *)
-            mixcrArgs+=(${key})
+            mixcrArgs+=("${key}")
             ;;
     esac
 done

pom.xml

@@ -32,7 +32,7 @@
 
     <groupId>com.milaboratory</groupId>
     <artifactId>mixcr</artifactId>
-    <version>1.7.2</version>
+    <version>1.7.3</version>
     <packaging>jar</packaging>
     <name>MiXCR</name>
 

src/main/java/com/milaboratory/mixcr/assembler/CloneFactoryParameters.java

@@ -103,6 +103,22 @@ public GeneFeature getFeatureToAlign(GeneType geneType) {
             return params.getFeatureToAlign();
     }
 
+    public CloneFactoryParameters setFeatureToAlign(GeneType geneType, GeneFeature feature) {
+        if (geneType == GeneType.Diversity)
+            if (dParameters == null)
+                throw new IllegalArgumentException("No D parameters.");
+            else
+                dParameters.setGeneFeatureToAlign(feature);
+        else {
+            VJCClonalAlignerParameters params = getVJCParameters(geneType);
+            if (params == null)
+                throw new IllegalArgumentException("No parameters for " + geneType + ".");
+            else
+                params.setFeatureToAlign(feature);
+        }
+        return this;
+    }
+
     public CloneFactoryParameters setVJCParameters(GeneType geneType, VJCClonalAlignerParameters parameters) {
         if (parameters == null)
             vdcParameters.remove(geneType);

src/main/java/com/milaboratory/mixcr/cli/ActionAlign.java

@@ -74,8 +74,10 @@ public void go(ActionHelper helper) throws Exception {
 
         if (!actionParameters.overrides.isEmpty()) {
             alignerParameters = JsonOverrider.override(alignerParameters, VDJCAlignerParameters.class, actionParameters.overrides);
-            if (alignerParameters == null)
+            if (alignerParameters == null) {
                 System.err.println("Failed to override some parameter.");
+                return;
+            }
         }
 
         VDJCAligner aligner = VDJCAligner.createAligner(alignerParameters,
@@ -87,19 +89,57 @@ public void go(ActionHelper helper) throws Exception {
             return;
         }
 
+        // Checking species
+        int speciesId = ll.getSpeciesTaxonId(actionParameters.species);
+
+        if (speciesId == -1)
+            speciesId = Species.fromString(actionParameters.species);
+
+        if (speciesId == -1) {
+            System.err.println("Can't find species with id: " + actionParameters.species);
+            return;
+        }
+
+        boolean warnings = false;
+
         for (Locus locus : actionParameters.getLoci()) {
-            LocusContainer lc = ll.getLocus(actionParameters.species, locus);
+            LocusContainer lc = ll.getLocus(speciesId, locus);
             if (lc == null) {
-                if (params().printWarnings())
+                if (params().printWarnings()) {
                     System.err.println("WARNING: No records for " + locus);
+                    warnings = true;
+                }
                 continue;
             }
-            for (Allele allele : lc.getAllAlleles())
-                if (alignerParameters.containsRequiredFeature(allele) &&
-                        (allele.isFunctional() || !actionParameters.isFunctionalOnly()))
-                    aligner.addAllele(allele);
-                else if (params().printWarnings() && allele.isFunctional())
-                    System.err.println("WARNING: Functional allele excluded " + allele.getName());
+            for (Allele allele : lc.getAllAlleles()) {
+                if (actionParameters.isFunctionalOnly() && !allele.isFunctional())
+                    continue;
+                if (!alignerParameters.containsRequiredFeature(allele)) {
+                    if (params().printWarnings()) {
+                        System.err.println("WARNING: Allele " + allele.getName() +
+                                " doesn't contain full " + GeneFeature.encode(alignerParameters
+                                .getFeatureToAlign(allele.getGeneType())) + " (excluded)");
+                        warnings = true;
+                    }
+                    continue;
+                }
+                aligner.addAllele(allele);
+            }
+        }
+
+        if (warnings)
+            System.err.println("To turn off warnings use '-nw' option.");
+
+        if(aligner.getVAllelesToAlign().isEmpty()){
+            System.err.println("No V alleles to align. Aborting execution. See warnings for more info " +
+                    "(turn warnings by adding -w option).");
+            return;
+        }
+
+        if(aligner.getVAllelesToAlign().isEmpty()){
+            System.err.println("No J alleles to align. Aborting execution. See warnings for more info " +
+                    "(turn warnings by adding -w option).");
+            return;
         }
 
         AlignerReport report = actionParameters.report == null ? null : new AlignerReport();
@@ -194,6 +234,10 @@ public static class AlignParameters extends ActionParametersWithOutput {
                 names = {"-w", "--warnings"})
         public Boolean warnings = null;
 
+        @Parameter(description = "Don't print warnings",
+                names = {"-nw", "--no-warnings"})
+        public Boolean noWarnings = null;
+
         @Parameter(description = "Parameters",
                 names = {"-p", "--parameters"})
         public String alignerParametersName = "default";
@@ -270,7 +314,12 @@ public String getInputForReport() {
         }
 
         public boolean printWarnings() {
-            return warnings != null && warnings;
+            if (warnings != null && noWarnings != null)
+                throw new ParameterException("Simultaneous use of -w and -nw.");
+            if (warnings == null)
+                return !"mi".equals(ll) && noWarnings == null;
+            else
+                return warnings;
         }
 
         public Set<Locus> getLoci() {

src/main/java/com/milaboratory/mixcr/cli/ActionAssemble.java

@@ -43,7 +43,10 @@
 import com.milaboratory.mixcr.basictypes.CloneSetIO;
 import com.milaboratory.mixcr.basictypes.VDJCAlignmentsReader;
 import com.milaboratory.mixcr.reference.Allele;
+import com.milaboratory.mixcr.reference.GeneFeature;
+import com.milaboratory.mixcr.reference.GeneType;
 import com.milaboratory.mixcr.reference.LociLibraryManager;
+import com.milaboratory.mixcr.vdjaligners.VDJCAlignerParameters;
 import com.milaboratory.primitivio.PipeWriter;
 import com.milaboratory.util.SmartProgressReporter;
 import org.mapdb.DB;
@@ -65,9 +68,12 @@ public class ActionAssemble implements Action {
 
     @Override
     public void go(ActionHelper helper) throws Exception {
-        List<Allele> alleles;
+        final List<Allele> alleles;
+        final VDJCAlignerParameters alignerParameters;
         try (VDJCAlignmentsReader reader = new VDJCAlignmentsReader(actionParameters.getInputFileName(), LociLibraryManager.getDefault())) {
             alleles = reader.getUsedAlleles();
+            // Saving aligner parameters to correct assembler parameters
+            alignerParameters = reader.getParameters();
         }
 
         AlignmentsProvider alignmentsProvider = AlignmentsProvider.Util.createProvider(
@@ -83,6 +89,16 @@ public void go(ActionHelper helper) throws Exception {
                 System.err.println("Failed to override some parameter.");
         }
 
+        // Adjusting features to align for correct processing
+        for (GeneType geneType : GeneType.values()) {
+            GeneFeature featureAssemble = assemblerParameters.getCloneFactoryParameters().getFeatureToAlign(geneType);
+            GeneFeature featureAlignment = alignerParameters.getFeatureToAlign(geneType);
+            if (featureAssemble == null || featureAlignment == null)
+                continue;
+            GeneFeature intersection = GeneFeature.intersection(featureAlignment, featureAssemble);
+            assemblerParameters.getCloneFactoryParameters().setFeatureToAlign(geneType, intersection);
+        }
+
         try (CloneAssembler assembler = new CloneAssembler(assemblerParameters, false, alleles)) {
 
             CloneAssemblerReport report = actionParameters.report == null ? null : new CloneAssemblerReport();

src/main/java/com/milaboratory/mixcr/reference/GeneFeature.java

@@ -658,9 +658,9 @@ public static String encode(GeneFeature feature) {
         return encode(feature, true);
     }
 
-    static String encode(GeneFeature feature, boolean copact) {
+    static String encode(GeneFeature feature, boolean compact) {
         ensureInitialized();
-        if (copact) {
+        if (compact) {
             String s = nameByFeature.get(feature);
             if (s != null)
                 return s;
@@ -670,7 +670,7 @@ static String encode(GeneFeature feature, boolean copact) {
         out:
         for (int i = 0; i < encodes.length; ++i) {
             ReferenceRange region = feature.regions[i];
-            if (copact) {
+            if (compact) {
                 String base = null;
                 for (GeneFeature a : available)
                     if (match(region, a)) {

src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAligner.java

@@ -100,19 +100,19 @@ public Allele getAllele(GeneType type, int index) {
         return allelesToAlign.get(type).get(index);
     }
 
-    protected List<Allele> getVAllelesToAlign() {
+    public List<Allele> getVAllelesToAlign() {
         return allelesToAlign.get(GeneType.Variable);
     }
 
-    protected List<Allele> getDAllelesToAlign() {
+    public List<Allele> getDAllelesToAlign() {
         return allelesToAlign.get(GeneType.Diversity);
     }
 
-    protected List<Allele> getJAllelesToAlign() {
+    public List<Allele> getJAllelesToAlign() {
         return allelesToAlign.get(GeneType.Joining);
     }
 
-    protected List<Allele> getCAllelesToAlign() {
+    public List<Allele> getCAllelesToAlign() {
         return allelesToAlign.get(GeneType.Constant);
     }