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Commits on Nov 19, 2014

• r1005: insert arbitrary header lines

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Commits on Nov 18, 2014

• r998: smart pairing; allow mixture of SE/PE reads

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Commits on Nov 13, 2014

• r984: updated to the latest kseq.h

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Commits on Nov 10, 2014

• r983: bugfix - wrong mate info

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Commits on Oct 30, 2014

• r963: expose mask_level

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Commits on Oct 28, 2014

• r960: merge changes from the master branch

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Commits on Oct 22, 2014

• r943: change the default -y to 20, but ...

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  lh3

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• r942: ignore ALT hits when counting n_sub for ...

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Commits on Oct 21, 2014

• r941: set a min length for 3rd-round seeding

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• r940: fixed a bug - missing primary hit

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• r939: fixed a memory leak (issue lh3#35)

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• r933: with bwa-postalt ready, drop option -g

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Commits on Oct 20, 2014

• r930: use 3rd round seeding by default

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  lh3

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• r929: added simplified LAST-like seeding

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• r926: prepare to move -g to bwa-postalt.js

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Commits on Oct 17, 2014

• r915: fixed broken example.c

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• r912: very minor improvement

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• r911: check before attempting adding

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Commits on Oct 16, 2014

• r907: revert to -g.8 by default

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• r906: don't reduce non-ALT mapQ by default

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• r905: lower peak RAM for "shm -f"

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• r904: optionally create tmp files for shm staging

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• r903: updated revision number

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Commits on Oct 15, 2014

• shared memory

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• r898: read the index into a single memory block

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• r896: more flexible ALT reading

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Commits on Oct 14, 2014

• r895: increase the default max_XA_hits_alt to 200

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• r890: bns_intv2rid() may wrongly return -1

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Commits on Oct 2, 2014

• r880: bug in writing .ann file

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Commits on Sep 30, 2014

• r878: XA is given to the best alignment

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Commits on Sep 28, 2014

• r876: optionally ignore idxbase.alt file

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Commits on Sep 26, 2014

• r875: invalid SAM output for ALT hits

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Commits on Sep 19, 2014

• r868: use soft clip for ALT hits

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• r867: fixed a few bugs; added ALT hits to XA

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Commits on Sep 18, 2014

• These files were committed on a wrong branch

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