/1 and /2 suffixes in paired-end reads

Hi, Can umi-tools analyze paired-end reads with /1 and /2 suffixes instead of 1:N and 2:N ?

trying with v0.5.5 and get the error message below with umi-tools extract:

umi-tools extract 
--bc-pattern=XXXXXX 
--bc-pattern2 CCCCCCNNNN 
--stdin H619_RG_C000QSP_6_1_CC9HDACXX_S0_L001_R1_001.fastq.gz 
--stdout H619_RG_C000QSP_6_1_CC9HDACXX_S0_L001_R1_001_extracted.fastq.gz 
--read2-in H619_RG_C000QSP_6_1_CC9HDACXX_S0_L001_R2_001.fastq.gz 
--read2-out H619_RG_C000QSP_6_1_CC9HDACXX_S0_L001_R2_001_extracted.fastq.gz 
--filter-cell-barcode 
--whitelist=whitelist.txt

Read pairs do not match H3:1:CC9HDACXX:6:2209:1046:2076/1 != H3:1:CC9HDACXX:6:2209:1046:2076/2

Thanks,

[IanSudbery]

I wonder if instead of having two options we should just have one, that takes the delimiter and only uses it if one is provided. In fact I reckon that we already have a default, which is space.

On Fri, 15 Mar 2019, 4:16 pm Tom Smith, [e-mail] wrote:

Great. Let me know when you’ve run the alignment and deduplication and confirmed this all works OK. Then I’ll merge this into the master and close the issue.

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[TomSmithCGAT]

This is now resolved in the master branch with option --ignore-read-pair-suffixes and will be available in the next release shortly