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Commits on Oct 1, 2020

• Merge pull request #47 from terencewtli/master

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  terencewtli

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  ca68143

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• Merge branch 'master' into master

  terencewtli

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Commits on Sep 29, 2020

• edited pop_size to be its own module. changed max_extrap, and now step size is based on the initial distinct reads. removed break statement from vector_median_and_ci

  terencewtli

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Commits on Sep 23, 2020

• Setting some initial values for the pop_size

  andrewdavidsmith

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• Adding the pop_size module

  andrewdavidsmith

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Commits on Sep 22, 2020

• added convergence criteria for lc_extrap/pop_size: converge when difference between iterations < 1.0

  terencewtli

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Commits on Sep 3, 2020

• Removing the silent rules from configure.ac so bug reports will be more informative

  andrewdavidsmith

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Commits on Aug 22, 2020

• merged pop_size module with lc_extrap. flag is passed into lc_extrap to indicate the module type, and corresponding default msg/output is modified

  terencewtli

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Commits on Aug 21, 2020

• added main body for pop_size module. removed unneeded includes and using std statements. replaced functions that used std:: in main

  terencewtli

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Commits on Aug 20, 2020

• added docs directory to Makefile.am

  terencewtli

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• Adding more test data, this time the Shakespeare data, and in both histogram and counts values formats

  andrewdavidsmith

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• Just trying to keep line wraps consistent

  andrewdavidsmith

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• Added checks for carriage returns in hist or vals input which indicates dos or mac format files, which usually cause a crash

  andrewdavidsmith

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Commits on Aug 9, 2020

• Update README.md

  terencewtli

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• Update README.md

  terencewtli

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• updated manual: removed note on requiring GSL

  terencewtli

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• updated version number

  terencewtli

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• changed binning rng to be dependent on the seed from preseq

  terencewtli

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Commits on Aug 8, 2020

• updated autotools for new version + inclusion of data dir

  terencewtli

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• replaced histogram format file

  terencewtli

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Commits on Aug 7, 2020

• removed bam2mr.cpp - can no longer compile after changes to smithlab_cpp

  terencewtli

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Commits on Aug 6, 2020

• changed the mr file to a different data file

  terencewtli

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• fixed bug in to-mr.cpp - setting mapper to general by default

  terencewtli

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• added data directory consisting of hist, bam, and mr formats. added link to more data for testing

  terencewtli

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Commits on Aug 4, 2020

• made small adjustments to some function formatting

  terencewtli

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• removed code that set seed to random if not specified by user

  terencewtli

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Commits on Aug 3, 2020

• replaced gsl functions for LU decomposition/determinant. removed GSL headers, guards, and compilation flags in Makefile. removed GSL configuration support in autotools files

  terencewtli

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Commits on Aug 1, 2020

• switched to relative paths for submodules

  terencewtli

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Commits on Jul 31, 2020

• Wrapped some long lines

  andrewdavidsmith

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Commits on Jul 30, 2020

• Update README.md

  terencewtli

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• fixed Makefile.am to properly set HAVE_GSL

  terencewtli

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• put guards around GSL code in moment_sequence.cpp. Makefile in src directory can now compile with GSL support

  terencewtli

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• major code changes: removed gsl in preseq.cpp except for bound_pop. updated configure.ac to enable gsl for bound_pop.

  terencewtli

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Commits on Jul 27, 2020

• Cleaning up some code

  andrewdavidsmith

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Commits on Jul 26, 2020

• fixed methpipe typo

  terencewtli

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