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bfast Log


Commit Date  
[ed42c1] (HEADmaster) by Nils Homer Nils Homer

* max reached may be improperly set

2011-12-16 06:36:57 Tree
[3afad2] by Nils Homer Nils Homer

* do not open with "ab" on a regular file, only on a gz tmp file

2011-12-16 06:14:03 Tree
[0c97a5] by Nils Homer Nils Homer

Merge branch 'master' of ssh://bfast.git.sourceforge.net/gitroot/bfast/bfast

2011-12-08 20:38:49 Tree
[0144a0] by Nils Homer Nils Homer

* positioning printed twice in program parameters in postprocess

2011-12-08 20:37:20 Tree
[22e1e7] by Nils Homer Nils Homer

* moving master to 0.7.0b

2011-10-29 19:30:10 Tree
[993bb4] (bfast.0.7.0a) by Nils Homer Nils Homer

* moving master to 0.7.0a

2011-10-29 19:29:53 Tree
[1ebb03] by Nils Homer Nils Homer

* -k not accepted

2011-10-25 01:52:49 Tree
[42e0bc] by Nils Homer Nils Homer

* adding an option -k to not reverse compliment the second end

2011-10-25 01:45:55 Tree
[53cc32] by Nils Homer Nils Homer

* updating manual for the -P option

2011-10-25 01:35:49 Tree
[584d39] by Nils Homer Nils Homer

* fixing some pairing command line issues

2011-10-25 01:33:47 Tree
[9f96fc] by Nils Homer Nils Homer

* no pairing is now the default

2011-10-17 21:37:39 Tree
[f679b8] by Nils Homer Nils Homer

* fixing a typo

2011-10-17 04:54:06 Tree
[fd5f94] by Nils Homer Nils Homer

* -Y was inverted

2011-10-17 04:49:30 Tree
[9881ac] by Nils Homer Nils Homer

* adding a no pairing option
* -Y was not parsed in postprocess

2011-10-17 04:44:38 Tree
[141457] by Nils Homer Nils Homer

* drastically changing paired end / mate pair processing
** removing paired end / mate pair rescue
** user must now specify the input type (paired end or mate pair)

2011-10-17 04:36:28 Tree
[192313] by Nils Homer Nils Homer

Merge branch 'master' of ssh://bfast.git.sourceforge.net/gitroot/bfast/bfast

2011-10-16 18:11:34 Tree
[b42e75] by Nils Homer Nils Homer

* pipe output uncompressed BAM to samtools sort

2011-10-16 18:10:35 Tree
[74efb1] by Nils Homer Nils Homer

* cleanUsedIntermediateFiles should be optional

2011-09-15 01:05:16 Tree
[7d1f09] by Nils Homer Nils Homer

* new options to convert color qualities to base qualities

2011-09-03 18:34:59 Tree
[920726] by Nils Homer Nils Homer

Merge branch 'master' of ssh://bfast.git.sourceforge.net/gitroot/bfast/bfast

2011-08-09 15:01:00 Tree
[edc441] by Nils Homer Nils Homer

* tracking the repetitiveness of key hits t factor into the mapping quality

2011-08-09 15:00:13 Tree
[c32284] by Nils Homer Nils Homer

* better error message for parsing the RG in the postprocess -r

2011-08-09 14:55:26 Tree
[6f2ed4] by Nils Homer Nils Homer

* updating the manual to include the -F parameter in bfast match

2011-08-09 03:44:03 Tree
[2a9679] by Nils Homer Nils Homer

* adding an option to ignore reads that have too many key hits (-F);
* decrease this value/fraction to increase specificity at the cost of sensitivity
* maxNumMatches was not always being annotated as such in bfast match
* implementing lock-less threading
* bfast localalign was not enforcing maxNumMatches (-M)

2011-08-09 03:40:30 Tree
[7eb9a1] by Nils Homer Nils Homer

* better buffering during merge step of the index creation

2011-08-09 03:13:13 Tree
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