Adding option to take input from stdin - #124
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…mplaints about mismatching types in std::div
…buffer from stdin
…mes, checking multiple reads, and ensuring they give integer values for tile ids
…at the first 16k bytes of each buffer load; this probably should be done differently
…stdin, with user-specified format as either fastq or sam, and with user-specified colon position for tile id within read names
…he code to work with the fastq records can be more similar to other file formats. Tests show memory mapping does help with speed, but with enough files analyzed at the same time, memory mapping is slower. These changes will make it easier to remove the memory mapping later.
… can be identified, following FastQC, mostly as a precaution in case the user mis-specifies the tile id position within reads when data is read from stdin
…ng tests for stdin
…overrep cutoff so that on very small data and stdin the overrep wont trigger at 1 observation
…m stdin because of changes to output for dups and overrep
…including handling tiles
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