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Now `align` print library-level citation notice and warnings (#305)

This fixes #285
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dbolotin committed Dec 16, 2017
1 parent d1d6fb2 commit c40e05958100d399143782f88d28b42a37468e08
Showing with 16 additions and 1 deletion.
  1. +1 −0 CHANGELOG_CURRENT
  2. +1 −1 repseqio
  3. +14 −0 src/main/java/com/milaboratory/mixcr/cli/ActionAlign.java
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@@ -1,2 +1,3 @@
Now export fields like `-nMutationsRelative` supports alignment-attached gene features (e.g. this allows to export all mutations of V gene inside CDR3 region: `-nMutationsRelative VCDR3Part VRegionWithP`)
Now `align` action prints library-level warnings and citation notice
minor: `--noMerge` option renamed to `--no-merge` in assemble action
@@ -133,6 +133,20 @@ public void go(ActionHelper helper) throws Exception {
System.out.println("Reference library: " + library.getLibraryId());
// Printing library level warnings, if specified for the library
if (!library.getWarnings().isEmpty()) {
System.out.println("Library warnings:");
for (String l : library.getWarnings())
System.out.println(l);
}
// Printing citation notice, if specified for the library
if (!library.getCitations().isEmpty()) {
System.out.println("Please cite:");
for (String l : library.getCitations())
System.out.println(l);
}
for (VDJCGene gene : library.getGenes(actionParameters.getChains())) {
if (gene.getGeneType() == GeneType.Variable) {
totalV++;

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