[go: nahoru, domu]
Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Index with seeds #128

Closed
wants to merge 58 commits into from
Closed

Index with seeds #128

wants to merge 58 commits into from

Conversation

ctb
Copy link
Member
@ctb ctb commented Aug 27, 2013

This is an open pull request to discuss meznah's proposed changes.

ctb and others added 30 commits March 26, 2013 09:59
@ctb
upgraded count-density script
31eb3ae
@ctb
updated count-density-by-position to use screed.open
71bdd5d
@ctb
added flush outfp
5ace1b4
@meznah
main memory based index - vector implementation
31265d9
@meznah
fix reading the queries
1259a69
@meznah
fix the output format
876b988
@meznah
add query set for 25k
7e8556c
@meznah
add query sets
3885395
@meznah
remove the matrix and use ary of ptr to vectors
f595900
@meznah
remove the 2D array and use array of ptr
40c797d
@ctb
Update @meznah bleeding-edge branch from latest ged/bleeding-edge.
4ad7687
@ctb
merged @meznah indexClassify make rules into regular Makefile
e166871
@ctb
remove lib/test-data from @meznah branch
0fdb963
@ctb
added a simple test for the outline index
10d2522
@ctb
fixed up the first test a bit more
f149761
@ctb
made simple index & retrieve code work from Python; passed initial test
3cb9b5b
@ctb
fixed sizeof bug in @meznah indexClassify code
2aa8fd7
@ctb
finished implementing basic Python API for @meznah indexClassify code…
f3dc8df 
…; + tests
@ctb
added find_all_tags_to_taglist function; added test
193fd41
@ctb
added indexClassify code to setup.py.in template
81eaca8
@ctb
reformatted indexClassify files using astyle -A10
13c3ff4
@ctb
renamed indexClassify to outline_index
4962aed
@ctb
Merge branch 'bleeding-edge' of github.com:ged-lab/khmer into mbe
57ae595
@ctb
added some simple sandbox scripts for outline index work
a12a3c4
@ctb
added tag-density set flag to load-graph script
d24e293
@ctb
added various generated files
bd41b24
@ctb
Merge branch 'hashbits_read_parser' into mbe
7e26b54
@ctb
Merge remote-tracking branch 'ged/bleeding-edge'
b0afcaf
@ctb
Merge count-density-by-position cleanup code.
6da225d
@ctb
Merge branch 'mbe' of github.com:ctb/khmer into mbe
feb2cbe
meznah and others added 26 commits June 7, 2013 08:39
@meznah
add time funciton
c6abe84
@meznah
convert the reads to uppercase
277247c
@meznah
modified index test
690a5d2
@meznah
remove TODO and modifies Makefie in lib
20563f1
@meznah
add plot scripts
acd5a84
@ctb @meznah
updated examples code to point out that it works with bleeding-edge c…
497f068 
…urrently
@meznah
Revoke Cython support.
60e91c6
@meznah
Move dynamically-generated portion of Python setup script into a sepa…
1b367ec 
…rate file.
@meznah
Remove some Cython-support hacks from Python modules.
bd9169e
@meznah
Fix all compilation warnings in the 'khmer' implementation proper.
49f8713 
Change 'maxErrorRegion' in Jason's aligner to be an unsigned int.
@meznah
Commence writing of architecture and design document.
0e3358b
@meznah
Ignore common names for 'virtualenv' directories which may be cohabit…
e98ba58 
…ing with the sources.
@meznah
Add overview of khmer arhitecture. Add details on khmer configuration.
2f0f430
@meznah
Add notes on trace loggers and performance metrics.
9133420
@meznah
Add discussion of thread identity maps, cache managers, and cache man…
029f96d 
…ager segments.
@meznah
Add discussion of reads, read pairs, and read parsers.
0294d09
@meznah
Discuss Bloom filters and Python wrapper.
f2a7a63
@fishjord @meznah
Changed the make file to export CXX, CXXFLAGS, and LIBS fixes dib-lab#65
05cfb66
@fishjord @meznah
Added a check in ktable_get to see if the user passed a pylong. fixes d…
de9e0bc 
…ib-lab#66
@meznah
Add doxygen support
127d7e8
@meznah
sampling
4639763
@meznah
ignore test-data
e2a50be
@meznah
index with seeds implemntation
c5b3192
@meznah
add small query files
6a313dc
@meznah
add save,loada and print seeds + add stat fn + add consume_fasta_tag
092518d 
where d any positive number
@meznah
allow density for all values, use sets and maps and remove vectors,
a05e9df 
fix query format to be as inout format
@ctb
Copy link
Member Author
ctb commented Aug 27, 2013

@meznah, could you please merge in the latest changes to bleeding-edge as soon as possible? Thanks.

@meznah
Copy link
meznah commented Sep 9, 2013

Redoing with pull request against ged-lab's master branch.

@meznah meznah closed this Sep 9, 2013
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers
No reviews
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.

None yet
3 participants
@ctb @meznah @fishjord