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Commits on Aug 10, 2015

• Update license and history.

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  4bdd019

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• Obsolete.

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• Remove now obsolete directory.

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• Move old licensing/ files to root.

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• Change how coverage cutoffs are computed. Instead of using input read coverage times genome

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• Change the local correction coverage from 10x to 2x.

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Commits on Aug 8, 2015

• Move erateEstimate plot/test scripts to the proper place.

  brianwalenz

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• Remove old mate-based utilities.

  brianwalenz

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Commits on Aug 7, 2015

• Partial implementation of tgStoreLoad, cleanup of tgStoreDump.

  brianwalenz

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• Allow reading input tigs from the store, an ascii layout, or a binary multialignment.

  brianwalenz

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• Improve command line error reporting.

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• Cleanup bogart implementation.

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Commits on Aug 5, 2015

• Increase the allowed edit space from errorRate * READLEN to READLEN.

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• Disable DP_Compare and Local_Overlap_AS_forCNS during exploratory alignments.

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• Fix bash bug ("33>file" vs "33 > file"), improve logging of unitigs in store.

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• Compute the amount of the read covered by overlaps using the portion of the

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• Cleanup debug logging.

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• Changes to debug logging durring bubble popping.

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Commits on Aug 3, 2015

• Report unitig sizes if the tigStore exists.

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Commits on Jul 30, 2015

• Remove most of the previous try and try harder attempts at aligning the read.

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• Allow reads with no placement. They'll have position (0,0), and a warning is generated.

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• Set exit code based on failures.

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• Disable display of alignments during realign*().

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Commits on Jul 29, 2015

• Change best.edges and best.contains from showing %error to fraction error.

  brianwalenz

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• Detect when AS_global.H parameters are different from those in the store, and fail.

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• Set local max coverage for correction to 10x estimated coverage.

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• Don't set local max coverage if it isn't defined.

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  c52f799

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• Fix reporting of loaded and skipped bases/reads.

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• Convert overlap counters to 64 bit.

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Commits on Jul 28, 2015

• Make display() work on either the best saved value or an intermediate value.

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• Remove cleanup of initial gap in delta value; now done in consensus.

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• Trivial, remove comment.

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• Fix log-space scaling failure; failed on very deep unitigs.

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• Skip positive traces (gaps in the read) at the start of the align.

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• Re-enable showing the intermediate multialigns (via -V), other minor logging changes.

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