CollectIlluminaLaneMetrics does not handle read structures with molecular indexes

[nh13]

The read structure 75T8B75T works but 8M67B75T does not. The error I get is:

Exception in thread "main" picard.PicardException: Don't have both phasing and prephasing values for tile
    at picard.illumina.parser.TileMetricsUtil.getTilePhasingValues(TileMetricsUtil.java:116)
    at picard.illumina.parser.TileMetricsUtil.parseTileMetrics(TileMetricsUtil.java:95)
    at picard.illumina.CollectIlluminaLaneMetrics$IlluminaLaneMetricsCollector.readLaneTiles(CollectIlluminaLaneMetrics.java:110)
    at picard.illumina.CollectIlluminaLaneMetrics$IlluminaLaneMetricsCollector.collectLaneMetrics(CollectIlluminaLaneMetrics.java:123)
    at picard.illumina.CollectIlluminaLaneMetrics.doWork(CollectIlluminaLaneMetrics.java:91)
    at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:208)
    at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:95)
    at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:105)

[nh13]

@yfarjoun assigning this to you since I want to ask if you have seen this in your production environment, given you demultiplex and collect metrics using Picard.

[nh13]

This also doesn't work with skips: 1S74T8B75T

[yfarjoun]

We are aware that it doesn't work with molecular barcodes, but we do not have the priority to fix it...

Would you like to contribute a fix?

Y

On Thu, Nov 17, 2016 at 1:44 PM, Nils Homer notifications@github.com wrote:

This also doesn't work with skips: 1S74T8B75T

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[nh13]

An obvious hack is to convert the skip and molecular barcode segments to a template segment (hint: that's my current workaround). I may contribute a fix if it becomes a major issue going forward for me (it's not). It's good to have this documented as a bug so that if other folks have the same problem they know they aren't the only ones.

[vdauwera]

@nh13 @yfarjoun Should this have been closed when #697 went in?

[yfarjoun]

not quite. this workaround doesn't resolve the underlying fundamental problem...

On Wed, Jan 18, 2017 at 6:03 PM, Geraldine Van der Auwera < notifications@github.com> wrote:

@nh13 https://github.com/nh13 @yfarjoun https://github.com/yfarjoun Should this have been closed when #697 https://github.com/broadinstitute/picard/pull/697 went in?

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[nh13]

it doesn't handle skips and barcodes when present in both the index and in-line in the reads