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Commits on Feb 16, 2019

• If gird job submission fails, wait 10 seconds and try again. Issue marbl#1154.

  brianwalenz

  committed
  d11fd03

Commits on Feb 15, 2019

• Don't allow bam inputs. Issue marbl#1231.

  brianwalenz

  committed
  130a20d

• Explicitly check that the SGE PE is appropriate; allocation_rule=$pe_slots and job_is_first_task=true. Issue marbl#1028.

  brianwalenz

  committed
  a29bb50

• Merge pull request marbl#1244 from mptrsen/master

  Show description for c117a38
  brianwalenz

  authored
  c117a38

Commits on Feb 14, 2019

• Extend histogran and lookup to 64-bit values.

  brianwalenz

  committed
  9f31726

• Fix syntax error and add support for wtdbg2 output (gzipped by default)

  

  Malte Petersen

  committed
  9a808a6

Commits on Feb 12, 2019

• Allow setting a persistent value in the input.

  brianwalenz

  committed
  bfbf88e

• Implement a histogram that supports kmers that occur more than 32 million times. Issue marbl#1182.

  brianwalenz

  committed
  dc859c7

• Increase ovsMemory by 2 GB prior to job submission to prevent paging when physical memory is an exact multiple of job size.

  brianwalenz

  committed
  c538153

• Use sqCache to reduce I/O load.

  brianwalenz

  committed
  6e1888d

• Increase memory for falconsense by 2 GB. Needed to cache reads.

  brianwalenz

  committed
  c829440

• Add, but don't use, sqCache.

  brianwalenz

  committed
  d1722ad

• In sqReadData_encode2bit(), allocate chunk memory only if the inout pointer is NULL.

  brianwalenz

  committed
  67dd703

• Add toString(sqRead_version).

  brianwalenz

  committed
  dbf63ed

Commits on Feb 8, 2019

• Move edlib to utility/.

  brianwalenz

  committed
  b241431

• Remove never-used (or finished) method for computing corrected reads using the overlap error adjustment framework.

  brianwalenz

  committed
  7aaff9b

• Disable reporting of bits used to store alignment.

  brianwalenz

  committed
  f66b90b

• Remove unused test of stack trace reporting.

  brianwalenz

  committed
  bffe3ac

Commits on Jan 31, 2019

• Don't try to find coordinates for reads that aren't used in generating the consensus. Issue marbl#1225, maybe.

  brianwalenz

  committed
  490b517

Commits on Jan 29, 2019

• Add stddevTest to BUILDTESTS.

  brianwalenz

  committed
  6509201

• Fix, maybe, crash in ovlStoreStats. Issue marbl#1223.

  brianwalenz

  committed
  b78b376

Commits on Jan 24, 2019

• Don't save raw mhap output when saveOverlaps=stores.

  brianwalenz

  committed
  23dbfe4

• Be thread safe when printing kmers.

  brianwalenz

  committed
  4fb5e5f

• Merge pull request marbl#1219 from godotgildor/master

  Show description for b071055
  brianwalenz

  authored
  b071055

Commits on Jan 19, 2019

• Merge pull request marbl#4 from godotgildor/dx_retry_upload_ua

  Show description for edc513a
  godotgildor

  authored
  edc513a

• Patching retry upload code

  Show description for 34521d9
  

  Brett T. Hannigan

  committed
  34521d9

Commits on Jan 17, 2019

• Comments on secret options. Shhh!

  brianwalenz

  committed
  9e6834c

• Store read-to-tig alignments in tgStore, fix (but not fully) multialignment output.

  brianwalenz

  committed
  a6871e4

• Set the recomputed min/max positions in the tgTig output, too.

  brianwalenz

  committed
  dc94228

• Fix memory leak: not releasing read bases/quals.

  brianwalenz

  committed
  634b051

• Add an untested copy constructor for stuffedBits.

  brianwalenz

  committed
  598ff79

Commits on Jan 11, 2019

• Add gridEngineResourceOption; replaces gridEngineMemoryOption and gridEngineThreadsOption.

  brianwalenz

  committed
  27ebc98

Commits on Jan 10, 2019

• Allow matches to N (and n) ambiguity bases. Based on Martinsos/edlib@92f6a3f.

  brianwalenz

  committed
  3a3c336

Commits on Jan 9, 2019

• Add limited support for mutating sequences.

  brianwalenz

  committed
  dfacdcb

Commits on Jan 3, 2019

• Update copyright block (and remove a stray whitespace).

  brianwalenz

  committed
  93e66aa

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