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Optionally --ignoreStrand/-i can be specified to ignore the strand information and treat forward/reverse the same.
Optionally --ignoreStrand/-i can be specified to ignore the strand information and treat forward/reverse the same.
trimBam will modify the sequences to 'N', and the quality string to '!'
trimBam will modify the sequences to 'N', and the quality string to '!' unless the optional parameter --clip/-c is specified. If --clip/-c is specified, the ends will be soft clipped instead of modified.
When soft clipping (--clip/-c):
* output is not sorted (start positions may change after soft clipping)
* soft clips already in the read are maintained or added to
** if 3 bases were clipped and 2 are specified to be clipped, no change is made to that end
** if 3 bases were clipped and 5 are specified to be clipped, 2 additional bases are clipped from that end
* if the entire read would be soft clipped, no clipping is done, and instead the read is marked as unmapped
= Parameters =
= Parameters =
