This PR adds a new flag, -c true/false, which controls whether Flexiplex should report chimeric reads. With it enabled, any chimeric reads will be labelled with a _C suffix in the read identifier. By default, this is false so despite the change in identifier, by default, all pipelines should still work with no change in functionality.
For instance, when this option is enabled, if the read with identifier @BC_UMI#READID_+1of2 is chimeric, it will become @BC_UMI#READID_+1of2_C.
This PR adds a new flag,
-c true/false, which controls whether Flexiplex should report chimeric reads. With it enabled, any chimeric reads will be labelled with a_Csuffix in the read identifier. By default, this is false so despite the change in identifier, by default, all pipelines should still work with no change in functionality.For instance, when this option is enabled, if the read with identifier
@BC_UMI#READID_+1of2is chimeric, it will become@BC_UMI#READID_+1of2_C.