chapmanb/bcbb — pull request #67 by roryk (2013-01-28 07:36:35+00:00)
Title: 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.