UI issues

.travis.yml

@@ -1,3 +1,4 @@
+
 language: java
 
 sudo: false
@@ -8,12 +9,12 @@ git:
 before_install:
   - sed -i 's/git@github.com:/https:\/\/github.com\//' .gitmodules
   - git submodule update --init --recursive
+  - cd milib && mvn clean install -DskipTests -B && cd ..
   - rm -rf ./repseqio/.cache
   - mv .cache ./repseqio/.cache
-  - cd repseqio/milib && mvn clean install -DskipTests -B && cd ..
-  - mvn clean install -DskipTests -B && cd ..
+  - cd repseqio && mvn clean install -DskipTests -B && cd ..
   - mv ./repseqio/.cache .cache
-  - ./ensure-test-data.sh
+
 
 script:
   - mvn test -B && ./itests.sh test
@@ -29,4 +30,3 @@ cache:
   directories:
   - $HOME/.m2
   - .cache
-  - src/test/resources/sequences/big

itests.sh

@@ -93,9 +93,9 @@ function go_assemble {
 if [[ $create_standard_results == true ]]; then
   for s in sample_IGH test;
   do
-    mixcr align -r ${s}_paired.vdjca.report ${s}_R1.fastq ${s}_R2.fastq ${s}_paired.vdjca
+    mixcr align -s hs -r ${s}_paired.vdjca.report ${s}_R1.fastq ${s}_R2.fastq ${s}_paired.vdjca
     go_assemble ${s}_paired
-    mixcr align -r ${s}_single.vdjca.report ${s}_R1.fastq ${s}_single.vdjca
+    mixcr align -s hs -r ${s}_single.vdjca.report ${s}_R1.fastq ${s}_single.vdjca
     go_assemble ${s}_single
   done
 fi
@@ -104,6 +104,6 @@ fi
 
 if [[ $run_tests == true ]]; then
   echo "Running test case 1"
-  mixcr align -OvParameters.geneFeatureToAlign=VGeneWithP test_R1.fastq test_R2.fastq case1.vdjca
+  mixcr align -s hs -OvParameters.geneFeatureToAlign=VGeneWithP test_R1.fastq test_R2.fastq case1.vdjca
   mixcr assemble case1.vdjca case1.clns
 fi

pom.xml

@@ -52,14 +52,25 @@
             <groupId>io.repseq</groupId>
             <artifactId>repseqio</artifactId>
             <version>1.3-SNAPSHOT</version>
+            <exclusions>
+                <exclusion>
+                    <groupId>com.milaboratory</groupId>
+                    <artifactId>milib</artifactId>
+                </exclusion>
+            </exclusions>
+        </dependency>
+
+        <dependency>
+            <groupId>com.milaboratory</groupId>
+            <artifactId>milib</artifactId>
+            <version>${milib.version}</version>
         </dependency>
 
         <dependency>
             <groupId>com.milaboratory</groupId>
             <artifactId>milib</artifactId>
             <version>${milib.version}</version>
             <type>test-jar</type>
-            <scope>test</scope>
         </dependency>
 
         <dependency>

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

@@ -40,10 +40,7 @@
 import com.beust.jcommander.ParameterException;
 import com.beust.jcommander.Parameters;
 import com.beust.jcommander.validators.PositiveInteger;
-import com.milaboratory.cli.Action;
-import com.milaboratory.cli.ActionHelper;
-import com.milaboratory.cli.ActionParametersWithOutput;
-import com.milaboratory.cli.ProcessException;
+import com.milaboratory.cli.*;
 import com.milaboratory.core.PairedEndReadsLayout;
 import com.milaboratory.core.Target;
 import com.milaboratory.core.io.sequence.SequenceRead;
@@ -94,30 +91,15 @@ public ActionAlign() {
     @Override
     @SuppressWarnings("unchecked")
     public void go(ActionHelper helper) throws Exception {
-        // FIXME remove in 2.2
-        if (actionParameters.printNonFunctionalWarnings())
-            System.out.println("WARNING: -wf / --non-functional-warnings option is deprecated, will be removed in 2.2 " +
-                    "release. Use --verbose instead.");
-
         // Saving initial timestamp
         long beginTimestamp = System.currentTimeMillis();
 
         // Getting aligner parameters
         VDJCAlignerParameters alignerParameters = actionParameters.getAlignerParameters();
 
         // FIXME remove in 2.3
-        if (actionParameters.getSaveOriginalReads()) {
-            System.out.println("WARNING: -g / --save-reads option is deprecated, will be removed in 2.3 " +
-                    "release. Use -OsaveOriginalReads=true.");
-            alignerParameters.setSaveOriginalReads(true);
-        }
-
-        // FIXME remove in 2.3
-        if (actionParameters.getSaveReadDescription()) {
-            System.out.println("WARNING: -a / --save-description option is deprecated, will be removed in 2.3 " +
-                    "release. Use -OsaveOriginalReads=true.");
+        if (actionParameters.getSaveOriginalReads() || actionParameters.getSaveReadDescription())
             alignerParameters.setSaveOriginalReads(true);
-        }
 
         if (!actionParameters.overrides.isEmpty()) {
             // Perform parameters overriding
@@ -126,12 +108,6 @@ public void go(ActionHelper helper) throws Exception {
                 throw new ProcessException("Failed to override some parameter.");
         }
 
-        // FIXME remove in 2.2
-        if (actionParameters.allowDifferentVJLoci != null && actionParameters.allowDifferentVJLoci) {
-            System.out.println("Warning: usage of --diff-loci is deprecated. Use -OallowChimeras=true instead.");
-            alignerParameters.setAllowChimeras(true);
-        }
-
         // Creating aligner
         VDJCAligner aligner = VDJCAligner.createAligner(alignerParameters,
                 actionParameters.isInputPaired(), !actionParameters.getNoMerge());
@@ -341,11 +317,6 @@ public static class AlignParameters extends ActionParametersWithOutput {
                 names = {"-b", "--library"})
         public String library = "default";
 
-        // TODO remove in 2.2 release
-        @Parameter(description = "Print warnings for non-functional V/D/J/C genes",
-                names = {"-wf", "--non-functional-warnings"})
-        public Boolean nonFunctionalWarnings = null;
-
         @Parameter(description = "Verbose warning messages.",
                 names = {"--verbose"})
         public Boolean verbose = null;
@@ -367,14 +338,17 @@ public static class AlignParameters extends ActionParametersWithOutput {
         public String jsonReport = null;
 
         @Parameter(description = "Species (organism), as specified in library file or taxon id. " +
-                "Possible values: hs, HomoSapiens, musmusculus, mmu, hsa, 9606, 10090 etc..",
-                names = {"-s", "--species"})
+                "Possible values: hs, HomoSapiens, musmusculus, mmu, hsa, 9606, 10090 etc.",
+                names = {"-s", "--species"},
+                required = true)
         public String species = "hs";
 
+        @Deprecated
+        @DeprecatedParameter(value = "Use --chains only for exportAlignments and exportClones", version = "2.2")
         @Parameter(description = "Specifies immunological chain gene(s) for alignment. If many, separate by comma ','. " +
                 "Available chains: IGH, IGL, IGK, TRA, TRB, TRG, TRD, etc...",
                 names = {"-c", "--chains"})
-        public String chains = "ALL";
+        public String chains = "ALL"; //FIXME remove in 2.3
 
         @Parameter(description = "Processing threads",
                 names = {"-t", "--threads"}, validateWith = PositiveInteger.class)
@@ -389,20 +363,21 @@ public static class AlignParameters extends ActionParametersWithOutput {
         public Boolean noMerge;
 
         @Deprecated
+        @DeprecatedParameter("Use -OsaveOriginalReads=true.")
         @Parameter(description = "Copy read(s) description line from .fastq or .fasta to .vdjca file (can then be " +
                 "exported with -descrR1 and -descrR2 options in exportAlignments action).",
                 names = {"-a", "--save-description"})
-        public Boolean saveReadDescription;
+        public Boolean saveReadDescription; //FIXME remove in 2.3
 
-        //TODO delete -v in 2.2
         @Parameter(description = "Write alignment results for all input reads (even if alignment has failed).",
-                names = {"-v", "--write-all"})
+                names = {"--write-all"})
         public Boolean writeAllResults;
 
         @Deprecated
+        @DeprecatedParameter("Use -OsaveOriginalReads=true")
         @Parameter(description = "Copy original reads (sequences + qualities + descriptions) to .vdjca file.",
                 names = {"-g", "--save-reads"})
-        public Boolean saveOriginalReads;
+        public Boolean saveOriginalReads; //FIXME remove in 2.3
 
         @Parameter(description = "Write not aligned reads (R1).",
                 names = {"--not-aligned-R1"})
@@ -412,11 +387,6 @@ public static class AlignParameters extends ActionParametersWithOutput {
                 names = {"--not-aligned-R2"})
         public String failedReadsR2 = null;
 
-        @Parameter(description = "Allow alignments with different chains of V and J hits.",
-                names = {"-i", "--diff-loci"}, hidden = true)
-        public Boolean allowDifferentVJLoci = null;
-
-
         public String getSpecies() {
             return species;
         }
@@ -450,15 +420,8 @@ public Boolean getSaveOriginalReads() {
             return saveOriginalReads != null && saveOriginalReads;
         }
 
-        @Deprecated
-        public boolean printNonFunctionalWarnings() {
-            return nonFunctionalWarnings != null && nonFunctionalWarnings;
-        }
-
         public boolean verbose() {
-            return (verbose != null && verbose) ||
-                    // FIXME remove in 2.2
-                    (nonFunctionalWarnings != null && nonFunctionalWarnings);
+            return verbose != null && verbose;
         }
 
         public boolean printWarnings() {

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

@@ -36,10 +36,6 @@ public ActionAssemblePartialAlignments() {
 
     @Override
     public void go(ActionHelper helper) throws Exception {
-        if (parameters.writePartial != null)
-            System.err.println("'-p' option is deprecated and will be removed in 2.2. " +
-                    "Use '-d' option to drop not-overlapped partial reads.");
-
         // Saving initial timestamp
         long beginTimestamp = System.currentTimeMillis();
         PartialAlignmentsAssemblerParameters assemblerParameters = PartialAlignmentsAssemblerParameters.getDefault();
@@ -126,10 +122,6 @@ public static class AssemblePartialAlignmentsParameters extends ActionParameters
                 names = {"-o", "--overlapped-only"})
         public Boolean overlappedOnly;
 
-        @Parameter(description = "[Deprecated, enabled by default] Write partial sequences (for recurrent overlapping).",
-                names = {"-p", "--write-partial"})
-        public Boolean writePartial;
-
         @Parameter(description = "Drop partial sequences which were not assembled. Can be used to reduce output file " +
                 "size if no additional rounds of 'assemblePartial' are required.",
                 names = {"-d", "--drop-partial"})

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

@@ -40,11 +40,6 @@ public class ActionExportParameters<T extends VDJCObject> extends ActionParamete
             names = {"-c", "--chains"})
     public String chains = "ALL";
 
-    @Deprecated
-    @Parameter(description = "Limit export to specific chain (e.g. TRA or IGH) (fractions will be recalculated)",
-            names = {"-l", "--loci"}, hidden = true)
-    public String chains_legacy = null;
-
     @Parameter(description = "Specify preset of export fields (possible values: 'full', 'min'; 'full' by default)",
             names = {"-p", "--preset"})
     public String preset;
@@ -98,12 +93,6 @@ public String getInputFile() {
     }
 
     public Chains getChains() {
-        if (chains_legacy != null) {
-            if (!chains.equals("ALL"))
-                throw new ParameterException("Use -c without -l parameter.");
-            System.out.println("WARNING: using of -l (--loci) option is deprecated; use -c (--chains) instead.");
-            return Chains.parse(chains_legacy);
-        }
         return Chains.parse(chains);
     }