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Integrity check (#444)

This fixes #397
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dbolotin committed Oct 24, 2018
1 parent fc517e6 commit f2d661a71aaed5bfb994ef871fc77a19e8a2e6fd
Showing with 355 additions and 232 deletions.
  1. +3 −3 doc/analyze.rst
  2. +6 −0 itests.sh
  3. +126 −127 mixcr_completion
  4. +1 −1 src/main/java/com/milaboratory/mixcr/basictypes/AlignmentsIO.java
  5. +3 −3 src/main/java/com/milaboratory/mixcr/basictypes/ClnAReader.java
  6. +4 −1 src/main/java/com/milaboratory/mixcr/basictypes/ClnAWriter.java
  7. +5 −2 src/main/java/com/milaboratory/mixcr/basictypes/ClnsWriter.java
  8. +2 −1 src/main/java/com/milaboratory/mixcr/basictypes/CloneSetIO.java
  9. +92 −17 src/main/java/com/milaboratory/mixcr/basictypes/IOUtil.java
  10. +13 −4 src/main/java/com/milaboratory/mixcr/basictypes/PipelineConfigurationReader.java
  11. +5 −1 src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsWriter.java
  12. +6 −5 src/main/java/com/milaboratory/mixcr/cli/ACommand.java
  13. +11 −5 src/main/java/com/milaboratory/mixcr/cli/ACommandWithOutput.java
  14. +30 −22 src/main/java/com/milaboratory/mixcr/cli/{ACommandWithResume.java → ACommandWithSmartOverwrite.java}
  15. +15 −2 ...xcr/cli/{ACommandWithResumeWithSingleInput.java → ACommandWithSmartOverwriteWithSingleInput.java}
  16. +1 −1 src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java
  17. +11 −17 src/main/java/com/milaboratory/mixcr/cli/CommandAnalyze.java
  18. +1 −1 src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java
  19. +1 −1 src/main/java/com/milaboratory/mixcr/cli/CommandAssembleContigs.java
  20. +1 −1 src/main/java/com/milaboratory/mixcr/cli/CommandAssemblePartialAlignments.java
  21. +3 −1 src/main/java/com/milaboratory/mixcr/cli/CommandExport.java
  22. +2 −4 src/main/java/com/milaboratory/mixcr/cli/CommandExtend.java
  23. +1 −1 src/main/java/com/milaboratory/mixcr/cli/CommandFilterAlignments.java
  24. +8 −5 src/main/java/com/milaboratory/mixcr/cli/CommandInfo.java
  25. +1 −1 src/main/java/com/milaboratory/mixcr/cli/CommandMergeAlignments.java
  26. +2 −4 src/main/java/com/milaboratory/mixcr/cli/CommandSlice.java
  27. +1 −1 src/main/java/com/milaboratory/mixcr/cli/CommandSortAlignments.java
@@ -295,18 +295,18 @@ As in the case of ``analyze amplicon``, required option ``--starting-material``
Resuming execution / re-analyzing
---------------------------------

MiXCR allows to continue aborted execution or re-analyze existing data with updated parameters, without complete re-processing of each of pipeline steps. This is possible with ``--resume`` option. For example, suppose the analysis was performed with the default options:
MiXCR allows to continue aborted execution or re-analyze existing data with updated parameters, without complete re-processing of each of pipeline steps. This is possible with ``--overwrite-if-required`` option. For example, suppose the analysis was performed with the default options:

::
mixcr analyze shotgun --species hs --starting-material rna data_R1.fastq data_R2.fastq analysis_name


Now to re-analyze the data with updated options for :ref:`assemble <ref-assemble>`, one can pass ``--resume`` option in order to avoid unnecessary invocation of ``align``, ``assemblePartial`` and ``extend``:
Now to re-analyze the data with updated options for :ref:`assemble <ref-assemble>`, one can pass ``--overwrite-if-required`` option in order to avoid unnecessary invocation of ``align``, ``assemblePartial`` and ``extend``:

::

mixcr analyze shotgun --force --resume --species hs --starting-material rna --assemble "-ObadQualityThreshold=0" data_R1.fastq data_R2.fastq analysis_name
mixcr analyze shotgun --overwrite-if-required --species hs --starting-material rna --assemble "-ObadQualityThreshold=0" data_R1.fastq data_R2.fastq analysis_name

This way, the previous results of :ref:`align <ref-align>`, :ref:`assemblePartial <ref-assemblePartial>` and :ref:`extend <ref-extend>` will be used, while :ref:`assembly step <ref-assemble>` will be re-executed.

@@ -106,4 +106,10 @@ if [[ $run_tests == true ]]; then
echo "Running test case 1"
mixcr align -s hs -OvParameters.geneFeatureToAlign=VGeneWithP test_R1.fastq test_R2.fastq case1.vdjca
mixcr assemble case1.vdjca case1.clns

echo "Running test case 2"
mixcr analyze shotgun -f --species hs --contig-assembly --impute-germline-on-export --starting-material rna test_R1.fastq test_R2.fastq case2

echo "Running test case 3"
mixcr analyze amplicon --receptor-type tra --impute-germline-on-export -s hs --starting-material rna --contig-assembly --5-end v-primers --3-end j-primers --adapters no-adapters test_R1.fastq test_R2.fastq case3
fi
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