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Commits on Aug 1, 2018

• Update java options to reduce GC time and threads (issue marbl#993) and memory

  skoren

  committed
  8a5f64a

• update call to seq store creation

  skoren

  committed
  9ac225d

• Fix bug which was truncating some large contigs

  skoren

  committed
  9341a0c

Commits on Jul 30, 2018

• Don't initialize arrays that get initialized later.

  brianwalenz

  committed
  6e94b72

• Don't initialize non-static class members.

  brianwalenz

  committed
  3fedc07

• Fix a couple of integer overflows when there are LOTS of skip kmers.

  brianwalenz

  committed
  27adf7a

• Implement 'Plan B'.

  brianwalenz

  committed
  14cfa33

• For seqStore inputs, allow counting in N batches using segment=x/N.

  brianwalenz

  committed
  aa32158

• Add debug operation 'compare' to report which kmers differ between two databases.

  brianwalenz

  committed
  cef52c2

• Fix error message when kmer size isn't set.

  brianwalenz

  committed
  2e2adb0

• Enable thread support for constructing the exact lookup table.

  brianwalenz

  committed
  be9a3fc

• Remove description of --hashstrings (doesn't exist anymore) and remove --maxreadlen (not useful anymore).

  brianwalenz

  committed
  e065081

• Add an option to dump reverse-complement reads.

  brianwalenz

  committed
  b44e180

• If a block is loaded that has no kmers, load another block before returning the kmer.

  brianwalenz

  committed
  c7b3928

Commits on Jul 27, 2018

• Add '/' to decodeRange(), for specifying a piece out of set.

  brianwalenz

  committed
  51eb416

Commits on Jul 26, 2018

• Merge pull request marbl#1019 from rick-heig/patch-1

  Show description for e6d1892
  skoren

  authored
  e6d1892

• Typo in FAQ

  Show description for 26ce70d
  rick-heig

  authored
  26ce70d

Commits on Jul 23, 2018

• Fix/finish exact kmer lookups; add basic analysis of kmers in reads.

  brianwalenz

  committed
  33df82d

• Add support for directly reading sequence from a seqStore.

  brianwalenz

  committed
  fca1102

• Replace AS_UTL_fileExists() with pathExists(), fileExists() and directoryExists().

  brianwalenz

  committed
  d539a54

• Report version of compiler that isn't acceptable.

  brianwalenz

  committed
  1dbf1a2

• Change how MacOS decides which compiler to use; remove Clang support and the OpenMP stubs it needed.

  brianwalenz

  committed
  d6204ff

• Use CXX for testing if stack trace is supported.

  brianwalenz

  committed
  d5fce1e

• Report the compiler actually being used, not the one set when 'make' was called.

  brianwalenz

  committed
  f5c0dff

Commits on Jul 21, 2018

• Put 'stack trace' in the 'system' library.

  brianwalenz

  committed
  74274f5

• Guard against multiple inclusion.

  brianwalenz

  committed
  c2a8dff

• Fold reverse-complementing into 'sequence' library.

  brianwalenz

  committed
  1674b22

• Import the freshly re-implemented 'meryl' (and 'sequence').

  brianwalenz

  committed
  231896d

• Convert tabs to spaces.

  brianwalenz

  committed
  da012a3

• Collect all system/hardware related functions into system.H.

  brianwalenz

  committed
  9375de2

• Collect all string processing classes/functions into strings.H.

  brianwalenz

  committed
  8076733

• Collect all file handling classes into files.H.

  brianwalenz

  committed
  d41e9b2

• Remover dependency on libkmer's kMer object.

  brianwalenz

  committed
  a876555

• Move implementation of readBuffer and writeBuffer out of class definition.

  brianwalenz

  committed
  690bccb

• Move various bits used only by meryl et alia from utility/ to meryl-san/.

  brianwalenz

  committed
  e1ed8a5

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