umi collapse fails with fastq input

[gfialk]

umicollapse is failing whan using fastq input. The command I'm running is:
umicollapse fastq -i in.fastq.gz -o out.fastq.gz
and I'm getting the following error:
Exception in thread "main" java.lang.ClassCastException: class umicollapse.util.FASTQRead cannot be cast to class umicollapse.util.SAMRead (umicollapse.util.FASTQRead and umicollapse.util.SAMRead are in unnamed module of loader 'app')
at umicollapse.merge.MapQualMerge.merge(MapQualMerge.java:9)
at umicollapse.main.DeduplicateFASTQ.deduplicateAndMerge(DeduplicateFASTQ.java:53)
at umicollapse.main.Main.main(Main.java:166)

[Daniel-Liu-c0deb0t]

That's because FASTQ reads do not have a mapping quality, so the default mapping quality merging scheme cannot be used. Try adding --merge avgqual to the command-line arguments.

[Daniel-Liu-c0deb0t]

A better warning (or a different default setting) probably should be provided, so this needs to be worked on.

[gfialk]

Hi Daniel. Thanks so much for your quick and helpfull response. I was wandering if there was any way of getting the deduplication statistics when I collapse a fastq file with UMICollapse? (something similar to the --output-stats of umi-tools) Best, Gavriel ‫בתאריך יום ג׳, 24 במרץ 2020 ב-2:49 מאת ‪Daniel Liu‬‏ <‪ notifications@github.com‬‏>:‬

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A better warning (or a different default setting) probably should be provided, so this is an open issue. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#1 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AGFYN4MH4HEZFNYNEYTJCNTRI77TFANCNFSM4LSHIE2Q> .

[Daniel-Liu-c0deb0t]

Currently, there is no way to do so. Of course, this should not be too hard to implement as a optional flag, like UMI-tools. However, I chose to not implement it because efficiency must be sacrificed in order to collect extra statistics.

[Daniel-Liu-c0deb0t]

When deduplicating FASTQ files, merging using average quality scores is now the default, so this issue is resolved.

[gfialk]

Great! Thanks for the update

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On 17 Oct 2020, at 9:00, Daniel Liu ***@***.***> wrote: When deduplicating FASTQ files, merging using average quality scores is now the default, so this issue is resolved. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#1 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AGFYN4MO23A5DN2ZEOSXGKTSLEXJBANCNFSM4LSHIE2Q>.