Integrity check (#444)

This fixes #397

doc/analyze.rst

@@ -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.
 

itests.sh

@@ -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