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Fixing UI issues

This fixes #342
This fixes #292
This fixes #280
This fixes #279
This fixes #208
This fixes #203
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dbolotin authored and PoslavskySV committed Jun 28, 2018
1 parent 8076984 commit b0bded8fe619935e7c634d8360a889267959a464
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@@ -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
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@@ -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 [[ $run_tests == true ]]; then
echo "Running test case 1"
mixcr align -OvParameters.geneFeatureToAlign=VGeneWithP test_R1.fastq test_R2.fastq case1.vdjca
mixcr align -s hs -OvParameters.geneFeatureToAlign=VGeneWithP test_R1.fastq test_R2.fastq case1.vdjca
mixcr assemble case1.vdjca case1.clns
fi
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13 pom.xml
@@ -52,14 +52,25 @@
<groupId>io.repseq</groupId>
<artifactId>repseqio</artifactId>
<version>1.3-SNAPSHOT</version>
<exclusions>
<exclusion>
<groupId>com.milaboratory</groupId>
<artifactId>milib</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>com.milaboratory</groupId>
<artifactId>milib</artifactId>
<version>${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>
@@ -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 AlignParameters params() {
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 AlignParameters params() {
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 AlignParameters params() {
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 AlignParameters params() {
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() {
@@ -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 ActionParameters params() {
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"})
@@ -40,11 +40,6 @@
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);
}

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