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Dynamic mst #16

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@dsli208 dsli208 commented Sep 5, 2018

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fataltes and others added 30 commits June 6, 2018 05:24
@fataltes
First big commit for chronomatic comp. stats.
25e3926
let CMake take CXXFLAGS on the command line
587d13d
@fataltes
Added mci to cmake file
dfb1aa1
fixed it
e2f561a
@fataltes
resolved a few bugs
b758c34
@fataltes
included kmer.h
dc466a8
@fataltes
fixed the bugs in the bfs algorithm and logic of operators
87cb8e0
@fataltes
reformating
a69a7f4
@fataltes
resolved merge conflict
f25687f
@fataltes
correct version (not scalable yet)
9a11b78
@fataltes
Added the distance calculator
fc37687
@fataltes
walkEqcls provides different statistics/capabilities/tests that requi…
28a0aab 
…re traversing eq. cls. table
@fataltes
required headers for walkEqcls
480e32b
@fataltes
added the new target walkEqcls
8956213
@fataltes
Adding two tests: ssbt on columns & unique delta bvs
4789ad1
@fataltes
updated and added a couple more tests and features
e152304
@fataltes
added num_samples as an argument to validate_uniqueness subcommand fo…
f71d2b2 
…r walkEqcls
@fataltes
1) Ignore self-loops in neighbor calculations
b767b58 
2) Consider neighbors of distance 0
@fataltes
Code to get list of edges between equivalence classes using kmers in …
1339d5f 
…dbg (no threshold)
@fataltes
Merging monochromaticStats and current develop into this new branch s…
6f115f4 
…o that we have everything together.
@fataltes
Needed some cleaning first.
509a2b7 
1) Used clipp for input arguments
2) Added two commands, one for just outputting some information about the CCs and the other for actually building the MSF datastructure
3) Added MSF as a target to cmake file
@fataltes
Add the ability to build parent bv
c6b1008
@fataltes
Start using boost for MST
7654c73
@fataltes
A simple MST boost test!
ab09c65 
(also removed realParent from MSF)
@fataltes
A very important commit containing the whole algorithm to find the ro…
a8f325e 
…ot of the mst (including the dummy node) + outputting stats about it.
@fataltes
output edge weight
d207152
@fataltes
output edge weight
1268e5c
@fataltes
Added number of set bits as weights of 0-end edges while building the…
0b05660 
… graph (before building MST)
@fataltes
Storing all the required data structures to retrieve color classes.
345b977
@fataltes
separating different delta calculations based on if a node is connect…
76047be 
…ed to the zero node or not.
fataltes and others added 30 commits August 21, 2018 18:56
@fataltes
Adding the initial skeleton for colorEncoding dynamically.
b48477e
@fataltes
Adding hammingDistance implementation
320fae7
@fataltes
Adding buildColor implementation
d4632a9
@fataltes
Adding maxWeightsTillLCA implementation
2c68c42
@fataltes
Calling colorEncoder from inside add_kmer in coloreddbg
4e6b7a4
@fataltes
Adding the very important method for taking care of dangling pointers
0e18b13
@fataltes
Add serialization to the colorEncoder
e04d34f
@fataltes
still not fully working
45e7b2e
@fataltes
fixed a bug. went to the next (cut in a loop for breaking a loop)
e1ff70c
@fataltes
fixed the loop. got into another
95045e0
@fataltes
works (except for serialization) :happy:
80aeff9
@fataltes
works!! :dance:
7febf96
@prashantpandey
Adding auto resize.
5138bd0
@prashantpandey
Fixing a minor corner condition in find_samples code.
e96e251
@prashantpandey
Fixing a minor bug in the itertor in coloreddbg.h
542ea3c
@fataltes
This works correctly ;p
fcd68c2
@fataltes
cleaning the code
8f3a64e
@fataltes
resizing parentbv
66dcea9
@fataltes
haven't had bitvector.cc from the beginning
328577e
@fataltes
and also haven't had build_eq_graph.cc from the beginning
c8e6dd3
@fataltes
the file ended up in the wrong place
30458d9
@fataltes
adding the cache log, removing find() in addEdge.
a6b6d98
@fataltes
Adding a new stats about how mst weight grows by adding new kmers
7429cb0
@prashantpandey
Removing cutoffs and adding non-filtered squeakr files warning.
dd3ce40
@prashantpandey
minor gqf file fix porting.
33fc709
@prashantpandey
Changing open flag in qf_usefile.
a2e11e8
@prashantpandey
Adding cqf logging code back.
8b413e1
@prashantpandey
Changed logging interval in construction phase.
30d6ece
@fataltes
mmapping CQF
fcd8834
@fataltes
Merge remote-tracking branch 'remotes/origin/simplification_and_clean…
da7466a 
…up' into dynamicMST

# Conflicts:
#	include/bitvector.h
#	include/coloreddbg.h
#	include/cqf.h
#	include/cqf/gqf.h
#	src/CMakeLists.txt
#	src/coloreddbg.cc
#	src/gqf/gqf.c
#	src/validatemantis.cc
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3 participants
@dsli208 @fataltes @prashantpandey