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ChangeLog
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commit 54af4fb2cb1134de1685cdb3dfbee177829ca300
Author: ctSkennerton <[email protected]>
Date: Wed Apr 17 10:27:15 2013 +1000
Fixed bug in cap3 assembly wrapper
The path to the input file wasn't getting passed through properly
causing cap3 to both fail and produce a number of hidden files.
This fix properly passes the input file to cap3.
commit 4b5487710626d638d4197842699bb3e53a99d9d8
Author: ctSkennerton <[email protected]>
Date: Wed Apr 17 09:54:40 2013 +1000
Fixed velvet wrapper bug
If the -o option was not set on the command line the velvet wrapper
would fail. Now added a default setting of the current working
directory so that it does not fail
commit 08a904e784038e69f365d5e0747253c34008024a
Author: ctSkennerton <[email protected]>
Date: Wed Apr 17 09:41:41 2013 +1000
Fixed bug with crass-assembler
A throwback from the previous interface was that the first
argument to the program was getting shifted off and not being
processed by getopts, which was causing all sorts of problems
commit c7ac0b37f686dfbe31b32e3a3a0def1424e5a1a5
Merge: f065f54 970477f
Author: ctSkennerton <[email protected]>
Date: Mon Dec 24 15:20:05 2012 +1000
Merge branch 'master' of github.com:ctSkennerton/crass
commit 970477fc366bc47927f5a05876c65d92047aee06
Author: ctSkennerton <[email protected]>
Date: Wed Oct 3 22:18:51 2012 +1000
forgot to update the version number in the manual
commit b6e4a270b9d637776f84c0b80f22456afe8ff600
Author: ctSkennerton <[email protected]>
Date: Wed Oct 3 19:24:26 2012 +1000
Updated the version number to 0.3.1 in configure.ac
commit 8ac2e65aa1b7b23cb08040d5df96ffe21b2b1d6d
Author: ctSkennerton <[email protected]>
Date: Wed Oct 3 19:08:32 2012 +1000
Fixed a bug in ReadHolder::dropPartials()
The logic for dropping an end partial repeat was incorrect such
that it was removing direct repeats that were close to but not
hanging over the edge of the read. This had flow on effects in
libcrispr#longReadFinder() where the last spacer in the read was
getting removed when it should not have been
commit 287e194e25c656d21a3acf2f77a39e984a92d69b
Author: ctSkennerton <[email protected]>
Date: Tue Oct 2 16:00:30 2012 +1000
changed the default for the high DR size to 47 (was 45)
commit d30e5308bd26dea7d42affa88c0ebb5fc8ed6f9b
Author: ctSkennerton <[email protected]>
Date: Tue Oct 2 15:49:43 2012 +1000
Fixed the function call to NodeManager::dumpReads()
During the merging of branches the call to NodeManager::dumpReads()
became out of sync with the method definition. This change removes
one of the parameters in WorkHorse::dumpReads() to get the two
functions back in sync
commit 8b44ba32f85b3d0c170cfd29478b6345a8903d39
Author: ctSkennerton <[email protected]>
Date: Tue Oct 2 15:30:43 2012 +1000
Removed an errant print statement
commit e687f4af5a508a10a91415261265e3d4df158095
Author: ctSkennerton <[email protected]>
Date: Tue Oct 2 15:26:29 2012 +1000
Fixed a bug in libcrispr#longReadFinder()
The if statement controlling the number of repeats in a read had
a strictly greater than comparison rather than the intended inclusive
operator. This meant that by default the number of repeats in a read
had to be 4 not 3 which was intended
commit e1028e5dce206027d58aff801eb6bf6f6ceaca60
Merge: 0847fb3 d7e32c1
Author: ctSkennerton <[email protected]>
Date: Sun Sep 30 22:28:30 2012 +1000
Merge branch 'dr_aligner'
Conflicts:
doc/manual.tex
src/crass/Makefile.am
src/crass/WorkHorse.cpp
commit d7e32c124a4cdb41a1455bd44c6a8803b930efd4
Author: ctSkennerton <[email protected]>
Date: Sun Sep 30 22:14:35 2012 +1000
Updated to version 0.3.0
This version implements a number of changes, both 'under-the-hood'
and visible to the user. First, Crass now has both short and long form
for each of it's options. Second, the assembly wrapper
is now a separate executable. The details of the new interface
are available in the PDF manual and in a new man page: crass-assember.1.
The other changes that will be noticable to the user is the flow of
crass has changed so that the initial patterns are found, then clustered,
then the second search is run.
There have been other changes 'under-the-hood' which means that you
may find Crass finding more reads or even new DR types for the
same datasets!!
commit 0060ac5aac3f78b053ec157e23d0ab0436314c90
Merge: d5908be 1cb5559
Author: ctSkennerton <[email protected]>
Date: Sun Sep 30 19:07:20 2012 +1000
Merge branch 'master' of github.com:ctSkennerton/crass
commit d5908be7a0745cfccb02be69e997600bc41fa0ab
Merge: a739e21 ebacf7e
Author: ctSkennerton <[email protected]>
Date: Sun Sep 30 19:05:50 2012 +1000
Merge branch 'dr_aligner'
commit ebacf7e82068146e074fddf9865c25ef003fd6e4
Author: ctSkennerton <[email protected]>
Date: Sun Sep 30 19:05:04 2012 +1000
Refactored out the assembly wrapper into a separate executable
commit deb9b4de8bcfeaa20b90a35ac2b0dfa048087e6f
Author: ctSkennerton <[email protected]>
Date: Sun Sep 30 17:15:54 2012 +1000
Ironed out the bugs in the new algorithm for aligning DR clusters together
commit 0df9198404f3d726a06fdc38cc3cea69cf79ae92
Author: ctSkennerton <[email protected]>
Date: Sun Sep 30 16:45:03 2012 +1000
Chaged some logging statements and memory allocation
Readholder objects used to be constructed exlusively on the heap
requiring alot of 'new' and 'delete' statements. In the new version
a readholder is made on the stack and only if it passes all of the
tests will the memory be copyied onto a new readholder. Also the
logging statments have been updated in libcrispr so that Crass
will no longer print out many lines of text for the progress through
the search algothims, instead only a single line is used for both
the singltonfinder and the initial finder
commit 86ed2dbfc560a131208b5481cc9557b801abf5ca
Author: ctSkennerton <[email protected]>
Date: Fri Sep 28 23:01:18 2012 +1000
Updated the method call to Aligner::calculateDRZone()
Removed the two arguments to the function as they were changed into
member variables of the class, and could therefore be called
directly.
commit 6cb704e6f56c65e37bd900adc755e99d5c3b12d7
Author: ctSkennerton <[email protected]>
Date: Fri Sep 28 22:58:33 2012 +1000
Updated help and documentation
Changed the user options so that all options have both a long
and short form. Updated the manual file to reflect these changes.
Updated the latex manual to add in extra options and change the
order in which the options are described in the manual so that they
are alphabetical, the same ordering as in the man file.
commit 6f941244337318ad13bb03288adc8928e32c4c6d
Author: ctSkennerton <[email protected]>
Date: Fri Sep 28 21:58:56 2012 +1000
Completed the refactor of the DR alignments into a separate class... let the debugging begin!
commit 4fff330739b3afedb9b17f8fd17e7610d14112b0
Author: ctSkennerton <[email protected]>
Date: Sat Sep 22 15:17:21 2012 +1000
begin changing the way the DR boundaries are called
commit bfecf8ec3bf84647fc44f34216bad9f13dfdc08b
Author: ctSkennerton <[email protected]>
Date: Thu Sep 20 23:17:02 2012 +1000
Refactoring out Code into Aligner Class
commit 3192e6ef59729bf2ba7da98d042d3a5c0caaa696
Author: ctSkennerton <[email protected]>
Date: Sat Sep 15 19:33:37 2012 +1000
The new alignment algorithm runs through the whole way.
Removed the exceptions in WorkHorse::getOffsetAgainstMaster() to
properly handle cases where the forward and reverse scores are
the same or when neither score is high enough
commit 1cb5559e81a66f52b72c7ffc4e1beabd7b00530a
Author: Connor T. Skennerton <[email protected]>
Date: Wed Sep 12 22:26:11 2012 +1000
Update README.md
Changed a couple of links, the CRT one was wrong and libcrispr's
was out of date. Also added a mention to klib in the contributed
code section.
commit 468a0dbebe266be7579aa24af8290f84d78203f0
Author: ctSkennerton <[email protected]>
Date: Tue Sep 11 00:37:38 2012 +1000
New implementation of aligning reads based on the DR is complete. Now need to test for edge cases
commit 0847fb350419523c6b0a6e66bc1d30898dc4c95b
Author: ctSkennerton <[email protected]>
Date: Sun Sep 9 01:13:32 2012 +1000
updated the manual
commit 7a00ba39ac70ba94611f8a1fc518e2fc21b2b709
Merge: a281b2b a739e21
Author: ctSkennerton <[email protected]>
Date: Sun Sep 9 00:12:54 2012 +1000
Merge branch 'master' of github.com:ctSkennerton/crass
commit 95a5bbd67203917affe5454b39627a0b12f64882
Merge: 227c0e2 d21891c
Author: ctSkennerton <[email protected]>
Date: Sat Sep 8 18:35:40 2012 +1000
Merge branch 'dr_aligner' of github.com:ctSkennerton/crass into dr_aligner
commit d21891c761ddaddca32ad5169dbaeb4465d7b996
Author: ctSkennerton <[email protected]>
Date: Sat Sep 8 18:34:36 2012 +1000
add in the ksw source files
commit 227c0e2ba88b79a49dedcd3a1f1c4e99586d82fb
Author: ctSkennerton <[email protected]>
Date: Sat Sep 8 01:52:46 2012 +1000
changed 'NULL' to '\0' in SeqUtils#reverseComplement() to fix a compiler error found in gcc4.5.4
commit 52f0ce32d51936b5b4b0d62433fe3aa17021cdc1
Author: ctSkennerton <[email protected]>
Date: Sat Sep 8 01:58:27 2012 +1000
changed some logic in LoggerSimp::Inst() to remove compiler errors in gcc4.6.3
commit 23028edf549e86ec4aa94f73c1091b2b0b89237f
Author: ctSkennerton <[email protected]>
Date: Sat Sep 8 15:46:18 2012 +1000
Changing the underlying algorithm used to place DRs into the coverage array for determining the consensus DR
commit a739e21283bf04734a47dd746b0df74ba299abed
Author: Connor T. Skennerton <[email protected]>
Date: Sat Sep 8 02:05:39 2012 +1000
Update README to include new compiler versions
commit 533d2f44674b6e127fde5e784bce0e2605194961
Author: ctSkennerton <[email protected]>
Date: Sat Sep 8 01:58:27 2012 +1000
changed some logic in LoggerSimp::Inst() to remove compiler errors in gcc4.6.3
commit 0c4220e554c2c29f133106b1292bf6ddf5cebd83
Author: ctSkennerton <[email protected]>
Date: Sat Sep 8 01:52:46 2012 +1000
changed 'NULL' to '\0' in SeqUtils#reverseComplement() to fix a compiler error found in gcc4.5.4
commit 0d1f2e69f183adaa1649596266ee648305070b64
Author: ctSkennerton <[email protected]>
Date: Sat Sep 8 01:49:00 2012 +1000
remove reference to gcc4.5 in README, has not been tested in this environment
commit 3e71ac487182cd13abb8f94a467d65dced0bd1a2
Author: ctSkennerton <[email protected]>
Date: Thu Aug 30 20:26:59 2012 +1000
keeping on tracking down this bug
commit b66636a0ade4f745ef10380fb3b9155ccbff0a3e
Author: ctSkennerton <[email protected]>
Date: Wed Aug 29 06:55:29 2012 +1000
tracking down a but in WorkHorse::populateCoverageArray
commit a281b2b7e350eae300b903517e8f7e50096382f2
Author: ctSkennerton <[email protected]>
Date: Wed Aug 29 06:28:12 2012 +1000
remove unnecessary variable from NodeManager::dumpReads
commit 147ef84a17238e2191675a6a884794e055886f0d
Author: ctSkennerton <[email protected]>
Date: Sun Jun 10 15:29:41 2012 +1000
Added in another test dataset
commit 98b6d9c81e4e98573959a78f01c4fb68e73cfa8c
Author: ctSkennerton <[email protected]>
Date: Tue Aug 28 23:19:35 2012 +1000
Fixed bug in Makefile that was causing SearchChecker to not be compiled silently
commit ec53431b3cf944eb1c6525afc1abb82a1cae2cc7
Author: ctSkennerton <[email protected]>
Date: Tue Aug 28 23:21:23 2012 +1000
refactored WorkHorse::printXML and WorkHorse::printSpacerGraphs into a single function: WorkHorse::outputResults
commit 91400cd1d12a34f32c84c6714c2f630618209f42
Author: ctSkennerton <[email protected]>
Date: Tue Aug 28 23:19:35 2012 +1000
Fixed bug in Makefile that was causing SearchChecker to not be compiled silently
commit 4c1c3a3f36983506ce3e735ab5b937f1673fe815
Author: ctSkennerton <[email protected]>
Date: Tue Aug 28 23:18:53 2012 +1000
minor code cleanup in libcrispr#findSingletonsMultiVector
commit 4e3a9ddc96213baa08afe0be2f6c41990905ab00
Merge: b218991 c2dbfce
Author: ctSkennerton <[email protected]>
Date: Tue Aug 28 16:17:02 2012 +1000
Merge branch 'master' into nr_repeats
commit 67115c44e63d6ac68daabcf60e5fef46b39879ce
Author: Connor T. Skennerton <[email protected]>
Date: Mon Aug 27 06:58:52 2012 +1000
Update TODO.md
commit db1ac30288574357a600f85251998385261bc777
Author: Connor T. Skennerton <[email protected]>
Date: Mon Aug 27 06:57:38 2012 +1000
Update TODO.md
commit c2dbfcec461bc5ffd547a06080dd8627f1d1d1c0
Author: ctSkennerton <[email protected]>
Date: Mon Aug 27 06:41:45 2012 +1000
updated the manual with the relevant changes for version 0.2.17
commit f065f54db6b665795be919609a16ad8400b3192f
Merge: a3107b9 6c729cf
Author: ctSkennerton <[email protected]>
Date: Mon Aug 27 06:03:15 2012 +1000
Merge branch 'master' of github.com:ctSkennerton/crass
commit 6c729cf3994b790409aad481f6d828440f942ad6
Author: ctSkennerton <[email protected]>
Date: Mon Aug 27 05:55:53 2012 +1000
Updated config files for v0.2.17
commit 65eba6408936915d145c438bde7c58dc66839e60
Author: ctSkennerton <[email protected]>
Date: Mon Aug 27 05:29:49 2012 +1000
removed old readme file and updated the libcrispr m4 macro to work with the new version
commit 49ec04d6ad08b4b378910cffccd0ca39119c59ca
Author: ctSkennerton <[email protected]>
Date: Fri Aug 24 06:51:06 2012 +1000
typo in readme
commit 891e169bd6fc0f9b8db6f821e047ad9c3575e640
Author: ctSkennerton <[email protected]>
Date: Fri Aug 24 06:49:31 2012 +1000
a few minor updates to the readme
commit f312c690a86045d7923111347e3e425567c99e92
Author: ctSkennerton <[email protected]>
Date: Fri Aug 24 06:24:26 2012 +1000
changed readme to markdown
commit 72be231583deea365cfe437a1325946f1ca757fd
Author: ctSkennerton <[email protected]>
Date: Fri Aug 24 06:04:12 2012 +1000
changed the naming scheme for lib crisp headers
commit f9552635c6092baa2cfb743cfbdaec6896b1d9cb
Author: ctSkennerton <[email protected]>
Date: Fri Aug 24 05:32:26 2012 +1000
small update to the manual
commit a3107b9aadfb40d3e64463cf59a88734e852c4d0
Merge: 51e449e d8afdbf
Author: ctSkennerton <[email protected]>
Date: Sat Jul 7 22:58:25 2012 +1000
Merge branch 'master' of github.com:ctSkennerton/crass
commit d8afdbfbc6a7199c874dc1fb10d95823c568b4b0
Author: ctSkennerton <[email protected]>
Date: Fri Jun 29 22:08:19 2012 +1000
Updated the manual a bit
commit 3c3de0a123064fed71d093c2ad6d8ec3e964ca42
Author: Connor T. Skennerton <[email protected]>
Date: Sat Jun 16 13:57:36 2012 +1000
Changed the default cutoff length for long reads in libcrispr#decideWhichSeach() to accomodate Illumina 150bp reads
commit 51e449e0d0a0117b3f68cab729da2ebbcc1cefe3
Author: ctSkennerton <[email protected]>
Date: Sun Jun 10 15:29:41 2012 +1000
Added in another test dataset
commit b218991d67e9a83fe7a5a95ea252dde762646577
Author: ctSkennerton <[email protected]>
Date: Mon Jun 11 18:24:59 2012 +1000
Fixed a bug in WorkHorse::createNonRedundantSet() that was causing the NR repeats to be incorrect
commit c783640961f920f6b7cfe9c3603a13d4336d8117
Author: ctSkennerton <[email protected]>
Date: Mon Jun 11 02:45:03 2012 +1000
Added in a new test file
commit a31b9242df99606007726ea6b17ef2cdc1a8b40a
Author: ctSkennerton <[email protected]>
Date: Mon Jun 11 02:42:38 2012 +1000
Fixed a bug in libcrispr#findSingletonsMultiVector() that was causing DR boundaries to be called incorrectly
commit c0d0fa8757b6af6d2d652bcbab1bd57521179522
Author: ctSkennerton <[email protected]>
Date: Mon Jun 11 02:41:46 2012 +1000
Changed the return value of WuManber::Search() to be a struct
commit 95fe5d642da4d4021c04dac7e4c5e11b6f370a55
Merge: 5997bd6 acff928
Author: ctSkennerton <[email protected]>
Date: Sun Jun 10 15:29:59 2012 +1000
Merge branch 'master' into nr_repeats
commit 5997bd67601c8087915714ed4cf852494b90b470
Author: ctSkennerton <[email protected]>
Date: Sun Jun 10 15:29:41 2012 +1000
Added in another test dataset
commit acff928c6c30a837a1ed4dcd170e14750c92df5d
Author: ctSkennerton <[email protected]>
Date: Sat Jun 9 20:34:25 2012 +1000
Added in a couple of test files
commit 9fc798ce44c812a03014a98bbe83e3282eef723d
Author: ctSkennerton <[email protected]>
Date: Sat Jun 9 20:25:06 2012 +1000
Fixed a bug in WorkHorse::calculateDRConsensus() that was causing low coverage groups to have the DRs called incorrectly
commit 2f75f832b7fe16d98b558cb50b4bd4e80add3013
Author: ctSkennerton <[email protected]>
Date: Sat Jun 9 20:21:30 2012 +1000
Changed CRASS_DEF_KMER_MAX_ABUNDANCE_CUTOFF to 0.23 to better reflect real-world DR statistics
commit dd11ce4f96e7e7f62bdc19f9c2e9af4f91be612d
Merge: 0e48318 d2a369f
Author: ctSkennerton <[email protected]>
Date: Thu Jun 7 15:41:26 2012 +1000
Merge branch 'clean_fix_2'
commit d2a369fd36a990b61cc923e9d312135ada39c382
Author: ctSkennerton <[email protected]>
Date: Thu Jun 7 15:39:59 2012 +1000
Fixed a bug in CrisprNode::getDiscountedCoverage() that was causing the wrong node to be removed
commit 0e48318d93d572e70266caf511e5c5c6df8f2dd8
Merge: 4e44bfc fec1f39
Author: ctSkennerton <[email protected]>
Date: Thu Jun 7 15:39:19 2012 +1000
Merge branch 'clean_fix_2'
commit fec1f39487d70a892b82709a3c24a95020775eb5
Author: ctSkennerton <[email protected]>
Date: Mon Jun 4 16:30:59 2012 +1000
moved code across from libcrispr into crass
commit b5bfe1d54714b1a3ef778e90f2279e88cc9bc6fd
Author: ctSkennerton <[email protected]>
Date: Sun Jun 3 01:43:05 2012 +1000
Fixed a bug in WorkHorse::addMetadataToDOM where the spacer graph file was not getting outputted
commit 0429055fe7a2ee99deb6393c5f087cc9a482c3d0
Author: ctSkennerton <[email protected]>
Date: Sat Jun 2 00:55:03 2012 +1000
small code clean up
commit 722653a4585511a4124725ccfc20855cfaffdc13
Author: ctSkennerton <[email protected]>
Date: Sat Jun 2 00:54:28 2012 +1000
Added in some typedefs
commit ff08384049ee353bf2f44e7fe87feb2289fdbe7c
Merge: 4519f1e d4abf01
Author: ctSkennerton <[email protected]>
Date: Sat Jun 2 00:33:10 2012 +1000
Merge branch 'master' into nr_repeats
Conflicts:
src/crass/WorkHorse.cpp
src/crass/WorkHorse.h
src/crass/libcrispr.cpp
src/crass/libcrispr.h
commit 4e44bfc4a5400418d29d9888b1ee3d56e236d948
Author: ctSkennerton <[email protected]>
Date: Sat May 26 11:10:51 2012 +1000
Fixed a bug where reads that began or ended in spacers were being hashly removed
commit 97cd85876797e3abe866112b9d32e35e2366cd3f
Author: ctSkennerton <[email protected]>
Date: Wed May 23 23:09:10 2012 +1000
updated version to v0.2.14
commit 88b3b3d38f2a9cf10f615606740169c517dbc353
Author: ctSkennerton <[email protected]>
Date: Wed May 23 23:07:29 2012 +1000
Fixed a bug in libcrispr#qcFoundRepeats which was causing an exception to be thrown in rare circumstanses
commit d4abf01f973da09cb7a69e3366fb23ff8f0a49b0
Author: ctSkennerton <[email protected]>
Date: Sun May 20 22:03:44 2012 +1000
Removed references to the libcrispr submodule. Should now be installed like any other library
commit e46438f1fcd5baa95e2f165ad6e5da1969084d4d
Author: ctSkennerton <[email protected]>
Date: Sun May 20 22:02:36 2012 +1000
removed debugging statments and updated the the version number to 0.2.13 in preperation for merge into master
commit c5b0bc497a248b42e5b9994c75e68349f0cc3b07
Author: ctSkennerton <[email protected]>
Date: Sat May 19 17:15:09 2012 +1000
changed the build system for libcrispr
commit df7e602c0033760d3c175c516f02143c5b6eff8f
Author: ctSkennerton <[email protected]>
Date: Sat May 19 13:12:04 2012 +1000
removed some files that were move into another repo
commit 44ec088af2cef6f730a98dca87750e271951287a
Author: ctSkennerton <[email protected]>
Date: Sat May 19 01:25:33 2012 +1000
Switched to the new build system with libcrispr as a submodule
commit 38500de3f7d74ab6af5a28f07e9d9837420e5131
Author: ctSkennerton <[email protected]>
Date: Sat May 19 01:18:54 2012 +1000
Changed a #include statement
commit 04991e4357355a7488f76cbfd49a5377138a8675
Author: ctSkennerton <[email protected]>
Date: Sat May 19 00:51:01 2012 +1000
Added StringCheck back into repo
commit 5cd8a0abc5bd3402349b9d40732f9dc764a54c66
Merge: bb48d50 cac331b
Author: ctSkennerton <[email protected]>
Date: Sat May 19 00:36:56 2012 +1000
Merge branch 'crispr_1_1' into spacer_cleaning_fix
Conflicts:
src/crass/Makefile.am
src/crass/WorkHorse.cpp
commit bb48d5032a46078fa0b2da286822f90efb51dae9
Author: ctSkennerton <[email protected]>
Date: Fri May 18 23:28:40 2012 +1000
Changed the include statements for libcrispr related files
commit c4ef62b5a44599336fa5b3e0137c0e2fd0c90835
Author: ctSkennerton <[email protected]>
Date: Fri May 18 22:38:20 2012 +1000
Fixed a bug in CrisprNode::getDiscountedCoverage() which was causing the wrong node to be removed during cleaning
commit 128de46bf298bc32b6e02fdc489e303d13642667
Author: ctSkennerton <[email protected]>
Date: Fri May 18 18:06:42 2012 +1000
added in kseq.cpp into the git repo
commit de89ef06a8803b0f0b009d933830fc6b2f4b1ac2
Author: minillinim <[email protected]>
Date: Fri May 18 16:46:12 2012 +1000
fixed the memory leak by de-macroin' the kseq.h 'quaqmire'
commit 92fffa789a9bb863f254faac7ce3dc3a2a5e082c
Author: ctSkennerton <[email protected]>
Date: Fri May 18 14:01:26 2012 +1000
Debugging the graphs
commit 4c5b5fa4c0ef471ee48bd5fd3c9f901cf5b50f7c
Author: ctSkennerton <[email protected]>
Date: Thu May 17 22:00:13 2012 +1000
Fixed an error in CrisprNode::setEdgeAttachState() introduced during refactoring
commit a4fd10afb766d6bc373a76beaa07e96193835304
Author: ctSkennerton <[email protected]>
Date: Thu May 17 21:28:49 2012 +1000
minor code cleanup
commit a260d916bafafaa0f325430de0b4b771a8411020
Author: ctSkennerton <[email protected]>
Date: Thu May 17 21:28:05 2012 +1000
Refactored CrisprNode::printEdges() and CrisprNode::setAttach()
commit cac331b35827e64808a81e3cb2cf9a1c558b3f04
Merge: 4153afd f0d0302
Author: ctSkennerton <[email protected]>
Date: Thu May 17 20:23:04 2012 +1000
Merge branch 'master' of github.com:ctSkennerton/crass into crispr_1_1
Conflicts:
configure.ac
man/crisprtools.1
src/crass/NodeManager.h
src/crass/WorkHorse.h
src/crisprtools/StatTool.cpp
src/libcrispr
src/libcrispr/Exception.h
commit f0d0302902f666cc9e2ff9290f699dba364f8728
Author: minillinim <[email protected]>
Date: Thu May 17 16:57:29 2012 +1000
upped version to 0.2.12
commit ea1cc658ac3da05f1ac6494762fe8bdcde07fce3
Author: minillinim <[email protected]>
Date: Thu May 17 16:54:17 2012 +1000
Fixed a bug in bubble clear where the wrong guy was gettin' removed
commit 38c9e3a9076e56906de185da6dea59a8f8ab1551
Author: ctSkennerton <[email protected]>
Date: Sun May 13 19:18:59 2012 +1000
fixed a print statement in libcrispr#findSingletonsMultiVector()
commit f6b73406b421ebb65940f6c6815200ad58417d6e
Author: ctSkennerton <[email protected]>
Date: Sun May 13 19:17:55 2012 +1000
small code clean up
commit 37f865ec17f8c7a4c5655fad10cf9c62e1484cef
Author: ctSkennerton <[email protected]>
Date: Sun May 13 19:15:33 2012 +1000
Added in new test to WorkHorse::parseSeqFiles() that reverts the accepted DR and spacer length after the initial find if removeHomopolymers is in place. fixes #56
commit f39f55f1e8de92511df7d7ef19cbef8438e61b2d
Author: ctSkennerton <[email protected]>
Date: Sat May 12 18:31:35 2012 +1000
added in a new variable in libcrispr#shortReadSearch() and libcrispr#longReadSearch() that saves the encoded DR for libcrispr#findSingletons(). fixes #55
commit 483f40ddb74e52506ca91d69305385631047956d
Author: ctSkennerton <[email protected]>
Date: Sat May 12 17:52:37 2012 +1000
Added in a decode() call in libcrispr#shortReadSearch() so that the correct DR and read is being stored. Resolved issue #54
commit c541d373182b17e0bb7ec37787be5a1e8d88e38c
Author: minillinim <[email protected]>
Date: Fri May 11 10:24:53 2012 +1000
oops
commit 24ccbb52c7659f83bf5364c444c32cfb5877dfdb
Author: minillinim <[email protected]>
Date: Fri May 11 10:22:44 2012 +1000
Added connors lovely changes to stats flanker calculations.
commit b4145d13cce671e7db83bfdb480743e61c41003d
Author: minillinim <[email protected]>
Date: Fri May 11 10:22:22 2012 +1000
resolved an issue where the number of flanking sequences was inflating the standard deviation of the spacer length, causing groups to be unwittingly destroyed
(cherry picked from commit 627642d7856c742d3c093e587293001c8f615a07)
Conflicts:
src/crass/NodeManager.h
commit 4153afd3ad2af3c51e519d5c66e767f9b0bae5bb
Author: ctSkennerton <[email protected]>
Date: Thu May 10 21:28:39 2012 +1000
Change interface so that we now search of read identifiers rather than contains
commit 2c90902299263ec0414dfe8e62a0bcda9ecb6a11
Author: ctSkennerton <[email protected]>
Date: Thu May 10 21:27:48 2012 +1000
Fixed an issue with NodeManager::dumpReads() where the memory address and not the value was being outputted
commit ed13601a786f2a8079252d68a32bceaf9ba2489f
Author: ctSkennerton <[email protected]>
Date: Thu May 10 21:23:44 2012 +1000
Forced the read output in ReadHolder::print() to be in fasta as there were problems with multiple file type getting concatenated together. This will also resolve issue #31
commit 98c547f89e389195f4fe8a9417c7d862cac27f96
Author: ctSkennerton <[email protected]>
Date: Wed May 9 23:15:10 2012 +1000
Some minor code cleanups
commit 627642d7856c742d3c093e587293001c8f615a07
Author: ctSkennerton <[email protected]>
Date: Wed May 9 23:11:29 2012 +1000
resolved an issue where the number of flanking sequences was inflating the standard deviation of the spacer length, causing groups to be unwittingly destroyed
commit ab896ac8581c87d5c34ce45ea71f5befc7136449
Author: ctSkennerton <[email protected]>
Date: Mon May 7 17:28:03 2012 +1000
updated version to 0.2.11
commit 9742fe48279a1d2b81c3755fd2e65a8f1ca7af79
Author: ctSkennerton <[email protected]>
Date: Mon May 7 17:24:39 2012 +1000
fixed a bug in ReadHolder::encode() where the output string was getting corrupted causing SeqUtils#reverseComplement() to fail. Resolves issue #51
commit 116722707154192b99374949ed7846d2acbc4d5d
Author: ctSkennerton <[email protected]>
Date: Sat May 5 00:02:58 2012 +1000
updated the make files to remove references to crisprtools
commit 49fe8eeeb0f35db507ff43ce18ab3a3f19f51724
Author: ctSkennerton <[email protected]>
Date: Sat May 5 00:00:34 2012 +1000
removed crisprtools out of the repository. It is now in its own repo
commit d8309e62e88fd889e7f7d81c440d53448e802b44
Author: ctSkennerton <[email protected]>
Date: Fri May 4 22:55:45 2012 +1000
changed libcrispr to be a submodule
commit 647c0bba7bfb1bcb359535c6d585e4f6ddc4d4ad
Author: ctSkennerton <[email protected]>
Date: Thu May 3 21:10:35 2012 +1000
massive commit to update crass to support cirpsr 1.1 format
commit 5f3360363436414dfbe0ddc1f50268defa53b547
Author: ctSkennerton <[email protected]>
Date: Wed May 2 22:08:23 2012 +1000
added in alot of exception handling for trying to track down some bugs when using --removeHomopolymers option
commit cbd13220406f826d0b8deab00ce594cafef55464
Author: ctSkennerton <[email protected]>
Date: Mon Apr 30 20:32:00 2012 +1000
Fixed a bug in NodeManager::splitIntoContigs() that was causing the
first cross node to be assigned the same contig ID as the last cap node
contig
commit 80eeb68a5364795a81263b6d89064d8d2c50baf3
Author: ctSkennerton <[email protected]>
Date: Mon Apr 30 20:29:59 2012 +1000
Properly initialized the total read count in
StatTool::calculateAgregateSTats()
commit d1b76bac28ea3bec12ab60e26dd990ecc9b704a2
Author: minillinim <[email protected]>
Date: Mon Apr 30 16:50:58 2012 +1000
Changed default color scheme
commit bea2b63b275212426c32a474375bd7ff08e987f5
Author: minillinim <[email protected]>
Date: Mon Apr 30 15:42:25 2012 +1000
Fixed a bug which let similar spacers get through. Should reduce the number of spacers and DRs quite a bitsy...
commit 422fb6b4eb09e3d652a40c0f84d4a7336ae8a9cf
Merge: 2e8fb47 ddea4e0
Author: ctSkennerton <[email protected]>
Date: Sun Apr 29 22:15:45 2012 +1000
Merge branch 'master' of github.com:ctSkennerton/crass
commit 2e8fb47b4feeba4c657ed27d3b1eb174748c8c07
Author: ctSkennerton <[email protected]>
Date: Sun Apr 29 22:14:44 2012 +1000
some small updates to the documentation
commit ddea4e0c4873d4e1434d12214d779284e356bf17
Author: ctSkennerton <[email protected]>
Date: Sun Apr 29 16:25:34 2012 +1000
updated version to 0.2.8
commit 63a79ee4a7aa6b70976ac17edd1042dc9c4e97f6
Author: ctSkennerton <[email protected]>
Date: Sun Apr 29 16:22:34 2012 +1000
Added in an extra test in NodeManager::genreateFlankers whereby a spacer instance must be a cap node in the graph for it to be considered
commit eb28dcd06e1bb6b793aa563123bcc51dcf45356e
Author: ctSkennerton <[email protected]>
Date: Sun Apr 29 15:42:53 2012 +1000
updated version to 0.2.7
commit 846ac751c33d7ddbbda64ca1c008190d9144572a
Author: ctSkennerton <[email protected]>
Date: Sun Apr 29 00:56:41 2012 +1000
Fixed a bug in WorkHorse::removeLowConfidenceNodeManagers that was causing some node managers to not get deleted when they should have been
commit c53120dc833a0d60fe2f59c59fec5af658848239
Merge: faa8884 dc89c00
Author: ctSkennerton <[email protected]>
Date: Sun Apr 29 00:25:30 2012 +1000
Merge branch 'spacer_length_investigation' of github.com:ctSkennerton/crass into spacer_length_investigation
commit dc89c00ad419dd65fe4ed845bfe9116dd9ee40c3
Merge: 75d7db2 3c7002f
Author: ctSkennerton <[email protected]>
Date: Sun Apr 29 00:11:27 2012 +1000
Merge branch 'master' into spacer_length_investigation
commit a09473ccb96f4107e09d79a1e882525761022426
Author: ctSkennerton <[email protected]>
Date: Fri Apr 27 23:02:06 2012 +1000
added in some updated information about crisprtools in the man page
commit faa88846cde01e0177141f5a419f62f96fd6149a
Author: ctSkennerton <[email protected]>
Date: Thu Apr 26 15:46:08 2012 +1000
Fixed a compiler bug and upped the version number
commit 3c7002fa8bdc2b026c8f17fc1000d1d56be5c1f2
Merge: dfad298 631f487
Author: ctSkennerton <[email protected]>
Date: Thu Apr 26 15:39:17 2012 +1000
Merge branch 'search_singleton'
commit dfad298e532e33eab982ceaaefa63a01917186f3
Author: ctSkennerton <[email protected]>
Date: Thu Apr 26 15:30:07 2012 +1000
fixed a typo that was preventing crisprtools extract from extracting flankers
commit 631f48723ff1dc38169b8bd268844983d9a7e96d
Merge: a11e6a9 6d7387f
Author: ctSkennerton <[email protected]>
Date: Wed Apr 25 15:20:53 2012 +1000
Merge branch 'search_singleton' of github.com:ctSkennerton/crass into search_singleton
commit a11e6a9f67d75fb59270fdf13b248c503fb5eeb3
Author: ctSkennerton <[email protected]>
Date: Wed Apr 25 15:20:03 2012 +1000
fixed up some #ifdef statement positioning so that code doesn't get accidentally compiled
commit 6d7387ff62d745598195ac954d01d60d1db5bf41
Author: ctSkennerton <[email protected]>
Date: Wed Apr 25 15:17:34 2012 +1000
added in a report format as basic output for the debugger
commit 9718ec98a3d3f5b714851cbf4cdeb6a136edc83f
Author: ctSkennerton <[email protected]>
Date: Wed Apr 25 13:29:46 2012 +1000
Added in a help msg for search debugger
commit f37a787c6b4a899c914ef4db0e31949362d898b3
Author: ctSkennerton <[email protected]>
Date: Wed Apr 25 12:50:36 2012 +1000
The singleton debugger is now linked into NodeManager, WorkHorse and libcrispr so that when crass is compiled with SEARCH_SINGLETON particular reads can be tracked
commit 04bf829ebd8390eee26f5c28794c483107888baf
Author: ctSkennerton <[email protected]>
Date: Wed Apr 25 10:30:37 2012 +1000
Changed the search debugger into a singleton
commit cd99f35b6af823b6dd07b59f851c7fe03a22c1aa
Author: ctSkennerton <[email protected]>
Date: Tue Apr 24 23:08:35 2012 +1000
added in a new class just for debugging and begun linking it in with the rest of the code
commit d18ea74d867653881ae92d1ea1c4e567fd935dad
Author: ctSkennerton <[email protected]>
Date: Tue Apr 24 01:14:34 2012 +1000
Changed the way in which streams are set so that the default output is to std::cout
commit 8b7acd69686a9560910f4e78803a71c92b15a84d
Author: ctSkennerton <[email protected]>
Date: Mon Apr 23 21:58:52 2012 +1000
added in extra tests when parsing input files so that non-xml files will not cause segmentation faults. such issues are now properly caught. resolves issue #47
commit 278048ae10d9333b984316e8bbb5ce39e9f154f0
Author: ctSkennerton <[email protected]>
Date: Mon Apr 23 21:32:27 2012 +1000
SanitiseTool::processOptions will now throw an error if no option is given. A new shortcut option has been added for sanitising all features. Fixes issue #46
commit 4519f1e28c5fbb378535953d024083a0d365e189
Author: ctSkennerton <[email protected]>
Date: Mon Apr 23 21:10:58 2012 +1000
added print statement for debugging
commit 75d7db2c491447be1c35bae008c199f4568ebbb3
Author: ctSkennerton <[email protected]>
Date: Mon Apr 23 21:01:58 2012 +1000
Fixed a test in WorkHorse::removeLowConfidenceNodeManagers
commit d74693080582f531adae0977e8e6e464ea079506
Merge: 6dbf4b6 8c6ac3e
Author: ctSkennerton <[email protected]>
Date: Mon Apr 23 20:54:04 2012 +1000