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epi2me-labs / modbam2bed

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Supplying -m argument multiple times only seems to output the data from last option provided #25

Closed mp15 closed 1 year ago

mp15 commented 2 years ago

Version: a51fc3549a413eb1bff14085944f7e0b31a507b9 I tried:

modbam2bed/modbam2bed -e -m 5mC -m 5hmC --cpg --chg -t 10 -p clive /lustre/scratch117/core/sciops_repository/references/Homo_sapiens/GRCh38_full_analysis_set_plus_decoy_hla/all/fasta/Homo_sapiens.GRCh38_full_analysis_set_plus_decoy_hla.fa PAM63114/bonito_calls.bam PAM63167/bonito_calls.bam PAM63974/bonito_calls.bam

This successfully completed but only output the 5hmC data not the 5mC data. One would expect either both output (in an interleaved fashion retaining sort order) or an error message saying that this combination is unsupported.

cjw85 commented 2 years ago

This is an oversight, the program should error and warn that only one modified base can be processed at a time.

cjw85 commented 1 year ago

modbam2bed is now deprecated. This won't be fixed.