Fixes to Tophat/Bowtie2

1) Look for bowtie path as "bowtie" not "bowtie2" in program: when using bowtie2.
2) Fixed a dictionary getting mutated problem when adding options.
3) Bowtie2 does not seem to respect the -X parameter:

    bowtie2  -X 2000 -x test/data/bowtie2/e_coli -1 test/data/s_1_1_10k.fq -2 test/data/s_1_2_10k.fq -S wtf.sam
    SLXA-EAS1_89:1:1:672:654        99      Chromosome      3919889 42      35M     =       3920066 212     GCTACGGAATAAAACCAGGAACAACAGACCCAGCA     cccccccccccccccccccc]c``cVcZccbSYbY     AS:i:0  XN:i:0  XM:i:0  XO:i:0  XG:i:0  NM:i:0  MD:Z:35 YS:i:0  YT:Z:CP
    SLXA-EAS1_89:1:1:672:654        147     Chromosome      3920066 42      35M     =       3919889 -212    TGAAGCCATGATGCCTTTTACCCTTTGTTGTTAAT     Z````[[`[b`bb^bb[^[`bbb`Ubbb`bbbbbb     AS:i:0  XN:i:0  XM:i:0  XO:i:0  XG:i:0  NM:i:0  MD:Z:35 YS:i:0  YT:Z:CP
    SLXA-EAS1_89:1:1:968:480	65	Chromosome	6795	42	35M	=	2854300	2847540	AACACCAGATCGCTTTAGGGTTGTTCAGGCGTAAA	cccccccccccccccccccccc`cccc``c```^`	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:35	YS:i:0	YT:Z:DP
    SLXA-EAS1_89:1:1:968:480	129	Chromosome	2854300	42	35M	=	6795	-2847540	GTTGATTGTGCGCGTGCTGAAAGAAACCAACGGCG	cccccccccccccccccc]cccccccccccccccc	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:35	YS:i:0	YT:Z:DP

For the time being I changed the inner distance calculation around to use the median and remove any fragments > 3x the standard deviation but now that I write this, I realize I should just manually do -X when making the calculation.