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# Summary Milestone Status Owner Created Updated Priority
238 bowtie 0.12.7 colorspace unmapped but mapped None open 2012-09-05 2012-09-05 5  
236 Bowtie 2 - un-conc flag reduces performance None pending 2012-08-22 2012-12-16 5  
233 incorrect sam flags with one unmapped mate in beta7 None open 2012-08-20 2012-08-20 5  
232 --reorder None pending 2012-08-17 2012-12-16 5  
231 YS tag missing if specify --no-discordant None pending 2012-08-17 2012-12-16 5  
229 bt2_inspect.cpp, line 218. None pending Ben Langmead 2012-08-13 2012-12-18 5  
222 BT2 assert aligner_bt.cpp:1070: Assertion `bs_[curid].isSol None pending 2012-07-17 2012-12-16 5  
218 SAM file not playing nice mpileup None pending 2012-07-13 2012-08-08 5  
204 bowtie2 XS:i tag lost when --no-discordant specified None pending 2012-05-16 2012-12-16 5  
192 bowtie2 quality scores same for every read with paired-ends None pending 2012-04-13 2012-06-25 5  
186 regarding pre-buit indexes None pending 2012-03-17 2012-06-25 5  
181 empty reads offset pairs None open 2012-02-24 2012-02-24 5  
149 Uridines in FASTA file and command line None open 2011-10-13 2011-10-13 5  
147 locating index doesn't behave as specified in manual None open 2011-08-24 2011-08-24 5  
146 Failed on running myrna human example None open 2011-08-08 2011-08-08 5  
131 Infinite cycle None open 2011-05-19 2011-05-19 5  
127 Processing error None open 2011-03-29 2011-12-14 5  
126 crossbow / CrossbowIface.pm bug? None open 2011-03-21 2011-03-21 5  
125 crossbow manifest file format None open 2011-03-21 2011-03-21 5  
124 Bowtie 12.7 crashes periodically on Windows when using -p>1 None open 2011-03-04 2011-03-04 5  
123 Tophat: Incorrect file listed as missing None open 2011-02-24 2011-02-24 5  
116 Missing sequences and errors in sequence lengths None open 2010-12-16 2010-12-16 5  
114 Crossbow output directory None open 2010-11-30 2010-11-30 5  
108 --best gives not the best None open 2010-11-02 2010-11-19 5  
106 crossbow-1.1.0 Soapsnp.pl line 368 None open 2010-10-22 2013-11-09 5  
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