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

Far too large pull - grid/slurm support, checkpointing, extra features #73

Open
wants to merge 57 commits into
base: master
Choose a base branch
from
+4,745 −4,501
Open

Far too large pull - grid/slurm support, checkpointing, extra features #73

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
57 commits
Select commit Hold shift + click to select a range
b09b81d
This branch supports grid/slurm (and possibly other remote queueing
Feb 19, 2019
5268334
Mild reformat and warning removal
Mar 22, 2019
c121957
removed id from seq index
Mar 22, 2019
d97eada
remove rand() calls, reformatting
Mar 25, 2019
21fc258
changed min/max read id to overlap counts
Mar 25, 2019
48db467
minor cleanup
Mar 25, 2019
c0c3cd9
cleaned up packdb
Mar 26, 2019
9eca72d
added read/candidate ordering for improved throughput
Apr 1, 2019
ef131a7
refactored candidate thread loop
Apr 1, 2019
c74943c
made fasta to pac conversion restartable
Apr 1, 2019
b118c88
testing reordering reads
Apr 3, 2019
7ef87a8
added branch for number of reads vs u4_t
Apr 4, 2019
c7bee6c
added options for reordering and preprocessing
Apr 9, 2019
4a2f1d6
more prep towards reordering properly
Apr 10, 2019
c272e9d
added option for binary output to mecat2pw
Apr 10, 2019
04003aa
shifting candidate handling to new format
Apr 12, 2019
502f7b5
Merge branch 'master' of https://github.com/xiaochuanle/MECAT
Apr 13, 2019
e57eb43
added MECAT2 defaults, fixed memory reduction bugs
Apr 16, 2019
3a71f31
random cleanup: stderr -> cerr, timer cleanup
Apr 17, 2019
dfac5c6
trashed reorder attempt
Apr 17, 2019
64b0266
changed sorting ec_list to better order reads
Apr 17, 2019
dd464d0
cleaned up some comparison functions
Apr 17, 2019
8f773ad
added k/m/g suffixes to integer options
Apr 17, 2019
cf26d54
changed some fprintf to use cerr instead
Apr 18, 2019
dc89bb8
convert id_list to vector<>
Apr 18, 2019
5e38cb8
changed cns_table to vector
Apr 18, 2019
cf9127a
whoops, forgot to check for errors before commiting
Apr 18, 2019
d924f37
changed CnsAln and CnsAlns to vectors
Apr 18, 2019
d872961
removed some duplicate and obsolete code
Apr 19, 2019
83c5425
converted M5Record to use vector instead of malloc
Apr 19, 2019
3b43bc2
changed DiffRunningData from malloc to vectors
Apr 19, 2019
21349b5
added max_aln_size back in after accidentally removing it
Apr 22, 2019
625a676
finished changes from defined (large) array buffers to vectors and st…
Apr 23, 2019
5199f25
remove extra buffer read/write when getting alignments
Apr 29, 2019
56383b1
moved to copy() over memcpy, unified left/right buffers
May 1, 2019
6b1fa4f
in the middle of testing, this is a save point
May 1, 2019
1e82d14
still working on bug, but got rid of bsearch in dw.cpp
May 3, 2019
7d62c5d
fixed bugs, improved speed of alignment finding
May 3, 2019
7025c3c
increase RM from 100k to 500k
May 3, 2019
80fdb91
back to static allocation
May 4, 2019
dab77e2
perform better static sizing of GetAlignment() buffers
May 4, 2019
36cf1e7
added exit files to allow detection of failed execution of sub-tasks
May 5, 2019
bcd394e
general cleanup, moved error_rate to options
May 7, 2019
c2aa22a
cleaned up Align() a bit
May 7, 2019
da5b08c
minor pre-alloc fix
May 9, 2019
d53721f
char -> uint1, pthread mutex -> c++11
May 9, 2019
9b7c353
minor cleanup and reformatting
May 9, 2019
5d8af26
narrowed d_path buffer to reflect cutoff
May 15, 2019
6cc539c
comments, refined d_path size
May 15, 2019
6c9bd55
include cleanup, corrected Align() loop termination
May 21, 2019
b0fe741
more cleanup of header file includes
May 21, 2019
e9f3a9f
added timing to output
May 24, 2019
33c64a3
Minor cleanup, added lto, moved if out of inner Align loop
Jun 14, 2019
c96a93b
type cleanup, header file cleanup
Jun 14, 2019
9c9a0cc
vectorization of mecat2cns inner loop, some cleanup
Jun 19, 2019
c21c2fc
improved inner loop
Jun 21, 2019
8e172fa
random cleanup
Jun 24, 2019
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
6 changes: 6 additions & 0 deletions .gitignore
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -45,3 +45,9 @@ $RECYCLE.BIN/
Network Trash Folder
Temporary Items
.apdisk

# Manual backup files
*.orig

# binaries directory
Linux-amd64
Loading