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Commits on Sep 5, 2020

• If a sqRead_unset read is requested, use sqRead_defaultVersion instead.

  brianwalenz

  committed
  8da1b99

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• Unset the 'normal' flag before converting sqRead_which to a string.

  brianwalenz

  committed
  3c90152

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• Change sqReadDataWriter_importData() so that it doesn't write to the imported metadata; move set*Bases() from .H to .C.

  brianwalenz

  committed
  dff1b12

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• Filter based on homopoly compressed length (if enabled); compute the length of a read when sequence is added to the read, instead of when the read is added to the store.

  brianwalenz

  committed
  258941d

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• Move sqReadDataWriter() default initializers to class definition.

  brianwalenz

  committed
  1241bb7

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• Don't assert basesLen > 0; but it must be NUL terminated.

  brianwalenz

  committed
  ac1cddd

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• Minor; add missing (and not stricly necessary) 'break' to switch cases that simply return.

  brianwalenz

  committed
  7cc2c71

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• Add comments about sqRead_defaultVersion; add include(), exclude(), is() and isNot() functions.

  brianwalenz

  committed
  c79bd30

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Commits on Aug 24, 2020

• Asssert that read sequences end with a NUL.

  brianwalenz

  committed
  74c6ed8

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• Move sqRead initialization to class definition.

  brianwalenz

  committed
  c4248c4

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Commits on Aug 12, 2020

• Only report the default sqStore read type in the various Dump binaries.

  brianwalenz

  committed
  288a006

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Commits on Aug 7, 2020

• Fix sqStore and tgStore structs to be trivially copyable; read stashing (utgcns, falconsense) changed a lot.

  brianwalenz

  committed
  6d4f967

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Commits on Mar 27, 2020

• Simplify license text included in source files.

  brianwalenz

  committed
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Commits on Feb 25, 2020

• Adjust header files to compile with submodules.

  brianwalenz

  committed
  47b5074

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Commits on Feb 24, 2020

• Remove stray whitespace.

  brianwalenz

  committed
  ef22127

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Commits on Feb 13, 2020

• When ignoring reads, ignore in all copies of the metadata. Issue marbl#1619.

  brianwalenz

  committed
  d9130cc

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Commits on Oct 8, 2019

• Add sqReadSeq_setAllClear(), needed in 4f0b206.

  brianwalenz

  committed
  f3b5f72

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Commits on Sep 10, 2019

• Add sqRead_normal to get a default compressed store back to uncompressed state.

  brianwalenz

  committed
  707bd0a

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Commits on Aug 8, 2019

• Set clear ranges in both normal and compressed sequences.

  brianwalenz

  committed
  da08666

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• Remove library features; all were unused. Greatly simplify sqStoreCreate; stop checking quality; Use utility/sequence to read input files.

  brianwalenz

  committed
  5746014

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Commits on Jul 5, 2019

• Implement version 8 of seqStore. Working, but not complete and not well tested.

  brianwalenz

  committed
  40763d8

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Commits on Mar 25, 2019

• Allow blobs in a partitioned store to be larger than 4 GB. Fixes assert(blob[0] == 'B').

  brianwalenz

  committed
  06f1d32

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Commits on Feb 12, 2019

• Add, but don't use, sqCache.

  brianwalenz

  committed
  d1722ad

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• Add toString(sqRead_version).

  brianwalenz

  committed
  dbf63ed

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Commits on Jan 3, 2019

• Update derived-from text in copyright blurb.

  brianwalenz

  committed
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Commits on Oct 17, 2018

• Add some comments about where sqReadData::_read is set.

  brianwalenz

  committed
  2de3695

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Commits on May 4, 2018

• Increase blob file size limit to 1GB.

  brianwalenz

  committed
  f7b9b62

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• Bump sqStore version number, again, to effectively unlimit the number of blobs, segments and partitions.

  brianwalenz

  committed
  5654d27

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Commits on Apr 18, 2018

• Rename gatekeeper/gkpStore to sequence store/seqStore. Existing assemblies should be upgradable by just renaming *.gkpStore to *.seqStore.

  brianwalenz

  committed
  01d1823

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