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Commits on Jul 8, 2019

• Fix error positioning the file when searching for EOL and the buffer is exhausted.

  brianwalenz

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  94bfaac

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Commits on Jul 5, 2019

• Add homopoly-compression support; add 2-bit ACGT and 3-bases-in-8-bit ACGTN encodings.

  brianwalenz

  committed
  3c35b83

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• Add support for IFF files; remove memory-mapped file support; fix error with seek() where the buffer would always be reloaded.

  brianwalenz

  committed
  9f10c4a

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• Add interface between stuffedBits abd readBuffer/writeBuffer.

  brianwalenz

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  2b06be7

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• Add increaseArrayPair().

  brianwalenz

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  2b836b4

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Commits on Jun 28, 2019

• Comment removal of fofn files since those are sentinels and removing them too early breaks ovlstore cleanup

  skoren

  committed
  b00a9c2

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• Add import of paf format, fix paf dump which was missing () for proper operation order, add identity to paf dump

  skoren

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  360a37d

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Commits on Jun 27, 2019

• Don't return a value before the first valid data point.

  brianwalenz

  committed
  7733c8c

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• Output reverse oriented reads too.

  brianwalenz

  committed
  650fdc2

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• Correctly decide if 'simulate' mode has a genome supplied.

  brianwalenz

  committed
  f40aed4

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• Fix numerous problems detecting the state of precompute computation and overlap store construction when using object storage.

  brianwalenz

  committed
  3c80cef

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• Don't destroy our config object before we're done using it.

  brianwalenz

  committed
  672fa5d

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Commits on Jun 10, 2019

• Remove unused bits of C++11. Issue 1383.

  brianwalenz

  committed
  093a51f

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• Remove (ancient) utilities for working with Illumina reads.

  brianwalenz

  committed
  890f679

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• Add README for soon-to-be deleted code for working with Illumina reads.

  brianwalenz

  committed
  7e7af45

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Commits on Jun 7, 2019

• Allow read trimming to run in batches.

  brianwalenz

  committed
  aa8c2ec

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• Add verbose flag.

  brianwalenz

  committed
  7998301

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• Move onSuccess from end of output to end of main. Issue marbl#1382.

  brianwalenz

  committed
  dd7ab3c

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Commits on Jun 5, 2019

• Fix severe performance degradation when reading overlaps for a read.

  brianwalenz

  committed
  fadb4eb

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Commits on Jun 4, 2019

• Add option purgeOverlaps. Remove saveOverlaps=stores.

  brianwalenz

  committed
  e48d0d8

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Commits on Jun 3, 2019

• Add method to delete the on-disk data for an ovFile.

  brianwalenz

  committed
  abefe70

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• Rearrange comments.

  brianwalenz

  committed
  d309ad6

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• Add option to delete inputs when done.

  brianwalenz

  committed
  53344e9

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Commits on May 31, 2019

• Extend AS_UTL_unlink() to take prefix.suffix file names.

  brianwalenz

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  1260723

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• Use 'new' 'select/ncpus' format for requesting resources in PBSpro.

  brianwalenz

  committed
  a685c38

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• Remove read kmer databases when we're done with them.

  brianwalenz

  committed
  ec37af0

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• Respect hapMemory add -memeory option for splitHaplotypes.

  brianwalenz

  committed
  9eec1f6

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• Limit the size of the lookup table to realistic sizes, for when memory is unlimited.

  brianwalenz

  committed
  eab14af

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• Cleanup the meryl database when done using it if saveMerCounts=false.

  brianwalenz

  committed
  d225e3f

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Commits on May 30, 2019

• Detect if we need to restrict filenames to POSIX 'fully portable filenames'.

  brianwalenz

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  c8152a7

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Commits on May 21, 2019

• Fix option checking for simulate and sample modes.

  brianwalenz

  committed
  7e7f912

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• Fix template construction issue, where partially aligned reads are not realigned to find the full alignment, and result in a false tandem repeat in the template. Possibly rarely occurs in 'real' da…

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  brianwalenz

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  f7af8aa

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• Add support for PacBio HiFi, needs to be tuned and refined still.

  brianwalenz

  committed
  04fe55d

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• Don't use constructor args after object is created.

  brianwalenz

  committed
  8867f0a

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• Reimplement readBuffer::seek() to avoid a disk access if possible.

  brianwalenz

  committed
  5f21a4e

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