Bug fixes for ctx_reads; Memory calculations fixed for all commands

Fix memory issues with all commands:
- all commands now include sizeof(BinaryKmer)*8

seq_reader.c:
- compare read names without truncating them

ctx_reads.c:
1. add single-ended output file, even with PE input
2. add output lock
3. fixed bug using nthreads instead of MAX_IO_THREADS dropped some files
4. fixed bad assert on is_pe (can have SE reads with PE interleaved file)
5. fixed seg fault on incrementing read_counter
6. fix bug exiting on success instead of error (!err_occurred)
7. create directories for output path
8. default to FASTQ output
9. count number of SE + PE reads