Optional "runmode" (-m) flags now offer several different major VaSeBuilder run modes:
F (Full): Outputs an acceptor-donor hybrid set of fastqs. Default.
D (Donor only): Outputs a pair of combined donor fastq files, without any acceptor reads.
P (Per-variant): Outputs only donor fastq files, with a separate pair of fastq files per variant.
X (No fastqs): Does not output any fastq files.
C (Continue from contexts): Allows user to supply a pre-made VaSeBuilder variant context file (such as from a runmode X run) and continue building the desired fastq using the variants in the file. Does not output any new variant context files. Must be combined with one of the other flags (e.g. FC, DC, PC). Setting C by itself defaults to FC. Note that trying to run in mode XC will work, but will essentially do nothing.
Other changes:
Cleaned up some code.
Changed duplicate read checking method when writing non-P-mode fastq files to prevent exponentially longer and longer runtimes.
Optional "runmode" (-m) flags now offer several different major VaSeBuilder run modes:
F (Full): Outputs an acceptor-donor hybrid set of fastqs. Default.
D (Donor only): Outputs a pair of combined donor fastq files, without any acceptor reads.
P (Per-variant): Outputs only donor fastq files, with a separate pair of fastq files per variant.
X (No fastqs): Does not output any fastq files.
C (Continue from contexts): Allows user to supply a pre-made VaSeBuilder variant context file (such as from a runmode X run) and continue building the desired fastq using the variants in the file. Does not output any new variant context files. Must be combined with one of the other flags (e.g. FC, DC, PC). Setting C by itself defaults to FC. Note that trying to run in mode XC will work, but will essentially do nothing.
Other changes: