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# Summary Milestone Status Owner Created Updated Priority
350 Confuses quality score with read name when quality starts with @ v0.9.0 open 2016-09-07 2016-09-07 5  
349 Indexing a reference genome error v0.9.0 open 2016-04-14 2016-04-14 5  
348 New format index files of bowtie2 v.2.2.8 v0.9.0 open 2016-03-18 2016-03-18 5  
347 bowtie 2.2.7 will not run on OSX 10.10.5 (macports) v0.9.0 open 2016-02-19 2016-02-23 5  
346 Colorspace Error v0.9.0 open 2016-02-07 2016-02-07 5  
344 local mode alignments with N's in the reference v0.9.0 open 2016-01-07 2016-01-07 5  
343 bowtie 1.1.2 - wrong alignment position when --best option used with large (ebwtl) index v0.9.0 open 2015-12-07 2015-12-07 5  
341 bowtie fails to find perfect match (paired-end) v0.9.0 open 2015-08-14 2015-08-14 1  
336 bad_alloc Bowtie 2.2.5 v0.9.0 open 2015-06-05 2015-08-10 1  
340 bowtie2 generates wrong length in SAM/BAM header v0.9.0 open 2015-08-06 2015-08-06 5  
337 Bowtie2 Mapping Inconsistency v0.9.0 open 2015-06-29 2015-07-11 5  
338 Bowtie not finding reverse complementary match v0.9.0 open 2015-06-29 2015-07-09 5  
332 paired-end bowtie with --all --try-hard doesn't report all possibilities v0.9.0 open 2015-04-03 2015-04-03 2  
330 Incorrect mapping positions/TLEN field Bowtie2 (2.2.4) v0.9.0 open 2015-02-25 2015-02-25 5  
317 invalid reads in unmapped fastq (missing @ symbol) v0.9.0 open 2014-07-22 2015-02-24 5  
326 Bowtie 1.1.1 hangs when run on indexes built on databases >15GB v0.9.0 open 2015-01-06 2015-02-17 5  
328 Incorrect TLEN sign for reverse complement paired reads? v0.9.0 open 2015-02-11 2015-02-17 5  
106 crossbow-1.1.0 Soapsnp.pl line 368 None open 2010-10-22 2015-02-03 5  
304 Uniqueness miscomputed by Ns in Bowtie 1.0.0 v0.9.0 open Ben Langmead 2014-03-19 2015-01-16 5  
298 -a option reports different read matches for two identical repeats in reference v0.9.0 open 2013-12-26 2015-01-08 5  
323 Mapping rate anomaly for fragments slightly greater than maxins v0.9.0 open 2014-11-21 2014-11-24 5  
320 unexpected bowtie2 unpaired alignment behavior v0.9.0 open 2014-08-19 2014-08-19 5  
303 XS field is the same for best and non-best scoring alignments of a same read v0.9.0 open 2014-03-12 2014-08-19 5  
319 Bowtie2 -a option MAPQ scores not 0 or 255; also, question about split references v0.9.0 open 2014-08-07 2014-08-07 5  
318 -u/--qupto arg must be at least 1 v0.9.0 open 2014-07-30 2014-07-31 5  
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