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these were developed separately and still need to be linked into analyze_seqs to be available in CHIIMP
only gc() when chunked; handle empty input correctly
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This substantially restructures the primer handling to support imperfect primer matches, IUPAC ambiguity codes in primer sequences, and several possible sequence-modifying actions for matched primers for forward/reverse/both ("none" to do nothing, "keep" to trim sequences to the primers but keep the primers as-is, "replace" to trim sequences and replace the matched primer region with the sequence from
locus_attrs, or "remove" to trim sequences to exclude the primer region). Fixes #37 and fixes #40.The sequence modification based on matched primer should obviate the need for adapter-trimming, if enabled. The defaults here keep the previous behavior (no read modification, zero mismatches allowed, not using reverse primers for matching).