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Commits on May 1, 2014

• r744: int overflow given MB query

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• r742: further control the max bandwidth

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Commits on Apr 24, 2014

• r727: extend seeds with SW

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Commits on Apr 23, 2014

• improved ksw_extend2()

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Commits on Apr 4, 2014

• dev-460: disallow a cigar 20M2D2I30M in extension

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Commits on Mar 28, 2014

• dev-449: unequal ins/del in global() and extend()

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• dev-448: different ins/del penalties

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Commits on Dec 30, 2013

• r427: fixed bugs in backtrack

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Commits on May 2, 2013

• Reduce dependency on utils.h - new malloc wrapping scheme.

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Commits on Apr 22, 2013

• Merge branch 'master' into master_fixes

  

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Commits on Apr 19, 2013

• r380: er... another compiling error

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• r379: fixed compiling error

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• r378: bugfix - wrong CIGAR

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Commits on Apr 11, 2013

• Merge branch 'master' into master_fixes. Merged up to master r375.

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Commits on Apr 10, 2013

• r374: fix - clipping penalty not always working

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Commits on Mar 8, 2013

• Merge branch 'master' into master_fixes

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Commits on Mar 5, 2013

• bwa-sw: ditch stdaln

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• Merge branch 'master' into master_fixes

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• r323: added Z-dropoff, a variant of blast's X-drop

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Commits on Mar 4, 2013

• code backup; more changes coming later

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Commits on Mar 1, 2013

• Merge branch 'master' into master_fixes

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• Merge branch 'master' into master_fixes

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Commits on Feb 28, 2013

• r306: introduce clipping penalty

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Commits on Feb 27, 2013

• r301: left-align indels

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Commits on Feb 21, 2013

• clean bill from valgrind

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Commits on Feb 12, 2013

• bugfix: bug in the new ksw.c

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• updated to the latest ksw; NOT TESTED YET!!!

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Commits on Feb 8, 2013

• Don't use narrow band.

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Commits on Feb 5, 2013

• fixed a silly bug in ksw_extend()

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• calling ksw_global(); ksw_extend() is buggy!

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• added comments

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• explicitly use bit to keep bt matrix

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• implemented NW backtrack

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• towards reimplementing banded NW alignment

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Commits on Feb 4, 2013

• fixed a couple of leaks; buggy atm

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