Code

Partition sweep#164

Code

Closed

camillescott wants to merge 105 commits intodib-lab:masterdib-lab/khmer:masterfrom camillescott:partition_sweepcamillescott/khmer:partition_sweepCopy head branch name to clipboard

Commits

Commits on Jul 25, 2013

• Merge github.com:ged-lab/khmer into bleeding-edge

  camillescott

  committed
  8844c12

  Copy full SHA for 8844c12

• Merge branch 'bleeding-edge' of github.com:ged-lab/khmer into bleeding-edge

  camillescott

  committed
  e32703b

  Copy full SHA for e32703b

• added threading params to filter-abund.py

  camillescott

  committed
  2ee322c

  Copy full SHA for 2ee322c

Commits on Aug 2, 2013

• Merge branch 'graceful-fail2' into bleeding-edge

  Show description for a7d6343
  camillescott

  committed
  a7d6343

  Copy full SHA for a7d6343

• Merge branch 'bleeding-edge' of github.com:ged-lab/khmer into bleeding-edge

  Show description for 4378a7b
  camillescott

  committed
  4378a7b

  Copy full SHA for 4378a7b

Commits on Aug 8, 2013

• Merge pull request #1 from ged-lab/bleeding-edge

  Show description for d9fda8f
  camillescott

  committed
  d9fda8f

  Copy full SHA for d9fda8f

Commits on Aug 28, 2013

• Merge branch 'bleeding-edge' of github.com:ged-lab/khmer into bleeding-edge

  camillescott

  committed
  d3bb3d2

  Copy full SHA for d3bb3d2

Commits on Sep 2, 2013

• Merge branch 'bleeding-edge' of github.com:cswelcher/khmer into bleeding-edge

  camillescott

  committed
  32fa1c6

  Copy full SHA for 32fa1c6

• moved graph traversal functionality up to Hashtable base class from Hashbits

  ctb

  committed
  afe46ec

  Copy full SHA for afe46ec

• removed unused/mostly untested traversal and graph complexity code

  ctb

  committed
  f73d3fa

  Copy full SHA for f73d3fa

• initial code for graph partitioning based on abundance

  ctb

  committed
  370ca2f

  Copy full SHA for 370ca2f

Commits on Sep 4, 2013

• fixed bug in count_partitions; fixed associated tests; abundance partitioning works

  ctb

  committed
  2004ede

  Copy full SHA for 2004ede

• Merge branch 'master' of github.com:ged-lab/khmer into graph_partitioning_on_abundance

  Show description for 4aa1fdd
  ctb

  committed
  4aa1fdd

  Copy full SHA for 4aa1fdd

• added some comments to abundance partitioning tests

  ctb

  committed
  68c5ced

  Copy full SHA for 68c5ced

• added compare_partitions function

  ctb

  committed
  d6eb05c

  Copy full SHA for d6eb05c

• added another test for partition comparison

  ctb

  committed
  031984a

  Copy full SHA for 031984a

• Added typedefs to hashtable.hh

  camillescott

  committed
  c9467fb

  Copy full SHA for c9467fb

• Added function prototype for consume and tag with colors

  camillescott

  committed
  05edfb8

  Copy full SHA for 05edfb8

• added subset_partition_size_distribution function to counting hashes

  ctb

  committed
  f65a1b2

  Copy full SHA for f65a1b2

• added code for SubsetPartition objects in Python

  ctb

  committed
  43d330e

  Copy full SHA for 43d330e

Commits on Sep 5, 2013

• shifted counting hash subset functions onto the new subset object

  ctb

  committed
  ddc8711

  Copy full SHA for ddc8711

• added partition_sizes function to retrieve partition IDs & sizes

  ctb

  committed
  8c7763a

  Copy full SHA for 8c7763a

• added partition_sizes test

  ctb

  committed
  306a294

  Copy full SHA for 306a294

• replaced now-missing function hash_subset_count_partitions for hashbits

  ctb

  committed
  ccffe06

  Copy full SHA for ccffe06

• added partition coverage calculations

  ctb

  committed
  34031ff

  Copy full SHA for 34031ff

• added some simple tests for partition average coverages

  ctb

  committed
  9592b55

  Copy full SHA for 9592b55

• added code to insert colors into colormap

  camillescott

  committed
  0e92a8d

  Copy full SHA for 0e92a8d

Commits on Sep 6, 2013

• added consume_fasta functions

  camillescott

  committed
  1465c74

  Copy full SHA for 1465c74

• merged in refactor from ged-lab/graph_partitioning_on_abundance

  camillescott

  committed
  e19e139

  Copy full SHA for e19e139

• promoted new code to hashtable to be in line with refactor

  camillescott

  committed
  b33c71a

  Copy full SHA for b33c71a

• added _cmap_contains back in after being nuked by merge

  camillescott

  committed
  c097fb5

  Copy full SHA for c097fb5

• fixed for proper pointers/refs, added reverse color map

  camillescott

  committed
  90e8306

  Copy full SHA for 90e8306

• added sweep function, getters for colors and tags, started color reconciliation

  camillescott

  committed
  ce1d027

  Copy full SHA for ce1d027

Commits on Sep 9, 2013

• color sweep added

  camillescott

  committed
  24f7380

  Copy full SHA for 24f7380

• added parse function to python glue

  camillescott

  committed
  a961a21

  Copy full SHA for a961a21

• added a spin lock for tag_colors (not strictly necessary, but ctb likes explicit things i hear)

  camillescott

  committed
  1c07a01

  Copy full SHA for 1c07a01

• adding sweep glue

  camillescott

  committed
  e0f7dca

  Copy full SHA for e0f7dca

• woot compiles and segfaults i win

  camillescott

  committed
  a64264d

  Copy full SHA for a64264d

Commits on Sep 10, 2013

• consuming, coloring, and sweeping functions successfully integrated with python glue, appear to be outputting correct colors

  camillescott

  committed
  db935a1

  Copy full SHA for db935a1

• silly testing python script added (need to add nose tests)

  camillescott

  committed
  e6ba546

  Copy full SHA for e6ba546

Commits on Sep 13, 2013

• added function to tag fasta by partition id

  camillescott

  committed
  0e350c0

  Copy full SHA for 0e350c0

Commits on Sep 16, 2013

• a few comments on @cswelcher code

  ctb

  committed
  2b1b6b2

  Copy full SHA for 2b1b6b2

Commits on Sep 17, 2013

• Merge pull request #2 from ctb/partition_sweep

  Show description for bfc0896
  camillescott

  committed
  bfc0896

  Copy full SHA for bfc0896

Commits on Sep 18, 2013

• exposing more stuff for python glue

  camillescott

  committed
  67c1b45

  Copy full SHA for 67c1b45

• Merge branch 'partition_sweep' of github.com:cswelcher/khmer into partition_sweep

  camillescott

  committed
  b7c5e97

  Copy full SHA for b7c5e97

Commits on Sep 19, 2013

• added more glue functions

  camillescott

  committed
  d948a6e

  Copy full SHA for d948a6e

Commits on Sep 24, 2013

• finished tag export to python land and fixed tag parsing to ull int. added direct get_tag_colors to python land

  camillescott

  committed
  ba9cab4

  Copy full SHA for ba9cab4

• mucking about with get_all_tags function, temporarily broken...

  camillescott

  committed
  90f9dba

  Copy full SHA for 90f9dba

Commits on Sep 25, 2013

• fixed issues with get_all_tags

  camillescott

  committed
  5689442

  Copy full SHA for 5689442

• fixed in-call increment re ctb comment

  camillescott

  committed
  18ebd4a

  Copy full SHA for 18ebd4a

• added n_colors python function

  camillescott

  committed
  22333f2

  Copy full SHA for 22333f2

• added test_consume_fasta_and_tag_with_colors, test passes

  camillescott

  committed
  b51df47

  Copy full SHA for b51df47

• fixed consume_partitioned_fasta_and_tag_with_colors to properly check for color existence and use color pointers

  camillescott

  committed
  d131776

  Copy full SHA for d131776

• added delete of temp colorptrmap

  camillescott

  committed
  afd1792

  Copy full SHA for afd1792

Commits on Sep 26, 2013

• added khmer colormap changes

  camillescott

  committed
  0f10ae5

  Copy full SHA for 0f10ae5

• added dealloc func

  camillescott

  committed
  6043518

  Copy full SHA for 6043518

• Merge branch 'partition_sweep' of github.com:cswelcher/khmer into partition_sweep

  camillescott

  committed
  96a572d

  Copy full SHA for 96a572d

• changed delete of tmp colorptrmap to clear

  camillescott

  committed
  eb94496

  Copy full SHA for eb94496

• updated color_tst, remove soon

  camillescott

  committed
  3684974

  Copy full SHA for 3684974

• Merge branch 'partition_sweep' of github.com:cswelcher/khmer into partition_sweep

  camillescott

  committed
  0b07d7f

  Copy full SHA for 0b07d7f

• added bunch more tests, TODO fix n_colors

  camillescott

  committed
  bc767df

  Copy full SHA for bc767df

• added a sweep-reads script to scripts, TODO add tests

  camillescott

  committed
  d29061c

  Copy full SHA for d29061c

Commits on Sep 27, 2013

• added test for correctness of color tagging and traversal

  camillescott

  committed
  feb0f39

  Copy full SHA for feb0f39

• started traversal optimization

  camillescott

  committed
  01f233d

  Copy full SHA for 01f233d

Commits on Sep 30, 2013

• fixed color allocation error; added persistent color to color pointer map and associated allocation funtion run checks for all newly allocated colors

  camillescott

  committed
  1b97d8c

  Copy full SHA for 1b97d8c

• changed back deref on color sweep after bugfixing, switched python exposed consume_sequence_and_tag_with_colors to use new color allocation function

  camillescott

  committed
  2113c23

  Copy full SHA for 2113c23

• working on new traversal code, broke off neighbor finding to its own function

  camillescott

  committed
  072adfd

  Copy full SHA for 072adfd

Commits on Oct 1, 2013

• implemented new perimeter traversal as part of sweep opimization

  camillescott

  committed
  88154dc

  Copy full SHA for 88154dc

• fixed error with new perimeter alg

  camillescott

  committed
  ab23874

  Copy full SHA for ab23874

• fixed error in traversal params

  camillescott

  committed
  74c9a88

  Copy full SHA for 74c9a88

• fixed func prototype to match prev change

  camillescott

  committed
  05cbe35

  Copy full SHA for 05cbe35

• fixed bug in color allocation during consume_fasta, fixed unexpected behavior in new traversal code and improved performance, fixed tests, added new function for exporting all colors

  camillescott

  committed
  235b746

  Copy full SHA for 235b746

• added new tests for n_colors and get_color_dict

  camillescott

  committed
  4806913

  Copy full SHA for 4806913

Commits on Oct 2, 2013

• fixed incorrect memory estimation on sweep-reads-by-partition

  camillescott

  committed
  15d7a88

  Copy full SHA for 15d7a88

• squashed bug with using a traversal range of 0

  camillescott

  committed
  b20d00a

  Copy full SHA for b20d00a

• couple debugging things added to subset

  camillescott

  committed
  add2eab

  Copy full SHA for add2eab

Commits on Oct 3, 2013

• added new test file

  camillescott

  committed
  bf5a544

  Copy full SHA for bf5a544

• final optimizations to traversal

  camillescott

  committed
  e8d06aa

  Copy full SHA for e8d06aa

• added temporary testing scripts, different sweep scripts, etc

  camillescott

  committed
  76e91d7

  Copy full SHA for 76e91d7

• addded fix for tag color correctness test not working on HPCC, still no idea why it failed

  camillescott

  committed
  23c197e

  Copy full SHA for 23c197e

• c++ land color test

  camillescott

  committed
  b2f6164

  Copy full SHA for b2f6164

• changes to test-Colors

  camillescott

  committed
  fd9728a

  Copy full SHA for fd9728a

Commits on Oct 7, 2013

• resync with hpcc

  camillescott

  committed
  4c419ed

  Copy full SHA for 4c419ed

• changes to test-colors

  camillescott

  committed
  e8466b1

  Copy full SHA for e8466b1

• fixed test-colors issue

  camillescott

  committed
  c23c26d

  Copy full SHA for c23c26d

Commits on Oct 10, 2013

• testing out buffer based spitter

  camillescott

  committed
  639099f

  Copy full SHA for 639099f

• some changes to buffered splitting

  camillescott

  committed
  aca8b2c

  Copy full SHA for aca8b2c

Commits on Oct 17, 2013

• fixed conflict with ktable test in lib Makefile

  camillescott

  committed
  b71e086

  Copy full SHA for b71e086

Commits on Oct 22, 2013

• added debugging option to make

  camillescott

  committed
  fa8d5bd

  Copy full SHA for fa8d5bd

• fixed color test build params

  camillescott

  committed
  4e30cec

  Copy full SHA for 4e30cec

• couple changes to color-Test

  camillescott

  committed
  cd86674

  Copy full SHA for cd86674

• changes to original sweep reads, now deprecated...

  camillescott

  committed
  e54b216

  Copy full SHA for e54b216

• Merge branch 'master' of github.com:cswelcher/khmer

  camillescott

  committed
  b871ad6

  Copy full SHA for b871ad6

Commits on Nov 1, 2013

• added combined sweep and file output script

  camillescott

  committed
  d13cb52

  Copy full SHA for d13cb52

Commits on Nov 4, 2013

• Merge branch 'master' of github.com:ged-lab/khmer

  camillescott

  committed
  412eec9

  Copy full SHA for 412eec9

Commits on Nov 5, 2013

• changed bad env line

  camillescott

  committed
  8120362

  Copy full SHA for 8120362

Commits on Nov 12, 2013

• important change in traversal code: removed optimization which truncated search at that breadth when a tag is found

  camillescott

  committed
  0d89921

  Copy full SHA for 0d89921

• Merge branch 'master' into partition_sweep

  camillescott

  committed
  c6035a1

  Copy full SHA for c6035a1

Commits on Nov 13, 2013

• added default parameters to buffered sweep

  camillescott

  committed
  bd2fcdb

  Copy full SHA for bd2fcdb

• added error handling to file opening and buffer flushing

  camillescott

  committed
  9278ecd

  Copy full SHA for 9278ecd

• added warning output for errors, updated description

  camillescott

  committed
  ac63a8b

  Copy full SHA for ac63a8b

• added minimum k and hashsizes to prevent inanely complex useless searches

  camillescott

  committed
  d524257

  Copy full SHA for d524257

• started tests

  camillescott

  committed
  3a7ff00

  Copy full SHA for 3a7ff00

Commits on Nov 14, 2013

• working on tests

  camillescott

  committed
  37ac9d8

  Copy full SHA for 37ac9d8

• changed something...

  camillescott

  committed
  0ccb623

  Copy full SHA for 0ccb623