Added GetSampleName as stopgap until we have named parameters
#3538
Conversation
…tool Fixing the program group for GetSampleName M2 WDL formatting changes Making this tool experimental. Making sure that failures happen appropriately in the WDL for CollectSequencingArtifactMetrics
Codecov Report
@@ Coverage Diff @@
## master #3538 +/- ##
===============================================
+ Coverage 80.086% 80.088% +0.002%
- Complexity 17766 17773 +7
===============================================
Files 1188 1189 +1
Lines 64416 64432 +16
Branches 10007 10010 +3
===============================================
+ Hits 51588 51602 +14
Misses 8842 8842
- Partials 3986 3988 +2
|
|
@davidbenjamin Just added an additional automated test thanks to @sooheelee , but please ignore commit message. |
| programGroup = QCProgramGroup.class | ||
| ) | ||
| @BetaFeature | ||
| final public class GetSampleName extends GATKTool{ |
There was a problem hiding this comment.
Why not make this a CommandLineProgram? BTW, if the answer is that emulating getHeaderForReads would be too cumbersome, I accept it with no further argument.
There was a problem hiding this comment.
@davidbenjamin That would be my answer. I'd be rewriting that code.
| } | ||
|
|
||
| @Override | ||
| public boolean requiresReads() {return true;} |
There was a problem hiding this comment.
Even trivial methods should be formatted on different lines. e.g.
public boolean requiresReads() {
return true;
}
There was a problem hiding this comment.
@pshapiro4broad Note that I just let intelliJ write that...
| throw new UserException.BadInput("The given input bam has no header or no read groups. Cannot determine a sample name."); | ||
| } | ||
|
|
||
| final List<String> sampleNames = getHeaderForReads().getReadGroups().stream().map(s -> s.getSample()).distinct().collect(Collectors.toList()); |
There was a problem hiding this comment.
This could be simplified slightly if you collect as Set instead of List, which will let you avoid distinct(). Also I would prefer SAMReadGroupRecord::getSample over s -> s.getSample() for readability even though the lambda form is fewer characters.
| throw new UserException.BadInput("The given bam input has no sample names."); | ||
| } | ||
|
|
||
| try (final FileWriter fileWriter = new FileWriter(outputSampleNameFile, false)) { |
There was a problem hiding this comment.
Using Files is more concise, e.g.
try {
Files.write(outputSampleNameFile.toPath(), sampleNames.get(0).getBytes());
} catch (final IOException e) {
...
Changing outputSampleNameFile to be declared as Path would make this shorter as well.
There was a problem hiding this comment.
@pshapiro4broad Thanks, but get me before I merge!
GetSampleName, which will get the sample name from a bam file header.