This repository has been archived by the owner on Mar 16, 2022. It is now read-only.
Copied from cDNA_primer #17
Open
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
daligner.c:696:17: warning: ‘broot’ may be used uninitialized in this function [-Wmaybe-uninitialized]
free(broot);
warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
but with filter_p.c deleted, instead using a macro in filter.c old commits ----------- Add option "-m" for outputing "m4" like overlap summary data complie DB.c to DB.so to be called from python using ctypes python ctypes interface to read Dazzler Assembler read database and overlap database The DBLA_to_falcon.py generates output from an read db and overlap that can be sent to falcon_sense.py for generating consensus. For example, python DBLA_to_falcon.py yeast.1.las yeast.db | falcon_sense.py \ --min_cov 4 --output_multi --min_idt 0.70 --trim_size 10 \ --n_core 24 > preads.1.fa a note as an example the "3" should be "4" DBLib shosuld be DB.so mmm... forget something, fixing it experimental code to out data for using falcon_sense.py to generate consensus. fix various bugs for output format and reverse complement issues allowing more flexible ends / hard code length threshold cut add threholds for the read length to control what reads get corrected Two experimental to drive the jobs from the output from HPCdaligner on a SGE cluster DAPipe.py: running the daligner jobs LAPipe.py: sort / merge / doing error corrections relax the condition for proper overlapping the original one is too strigent for error correction add experimental code for reducing data sizes copied filter.c over filter_p.c, then copied change from other branch - cd squash corresponding to merge commit ef58b19 plus "Cosmetic mods" (remove -m option) edited Makefile to compile LA4Falcon ERR make proper overlapping detection more strict Add DB2Falcon.c and modify Makefile accordingly copied a correction from DAZZ_DB/DB2fasta.c - cd add missing LA4Falcon as targets ERR properly trimming the DB before dumping the sequences to get the id mapping right. change fopen to use mmap mode for reading When a read is detected as contained reads within other reads, it will ouput "* *" and ignore the rest of the bread. The fc_consensus.py should catch it and ignore to precess the aread as seed reads. Since the error corrected reads will be contained with other reads, this should reduce the computation time for those reads which has no impact in the string graph construction. add "s" option to skip contained reads add some testing code to output alignment from Gene's alinger Cosmetic mods (typos, etc.) mapping read_id to dalinger internal ID Adapt FALCON specific code for the newer version of Daligner modify the code for Gene's new struct free the memory properly must not put foo.h on command-line This actually breaks clang (and on my mac, gcc is actually clang) with this obscure error message: clang: error: cannot specify -o when generating multiple output files
* simpler _p * relative to DAZZ_DB, for now * README_PB
simpler GNUmakefile
mobs will call this.
for generating consensus. This limits innecessary I/O without much lost in my test. Some repeats might be lost but the overall efficiency for getting the useful information is higher.
…vement For read that has many repeat hit, we only output top n supporting reads sorted by overlapping lengths. This reduces the I/O load outputing many redundant sequences for highly repeatitive sequences with minimum effect on other region of a genome.
…OUNT to catch potential more longer overlap if avilable
…orting reads, fix for the last read
…vement Used this new modification for NIST Trio Child assembly. It works on-par with the previous version but with much better I/O performance and less useless computation during the consensus stage. I am merging the code.
Not really MT bug. Simple buffer over-run caused one thread to write into next. Root cause was logic error in dividing hits into threads when nhits < NTHREADS. Fixes PacificBiosciences#9
Fix apparent MT bug.
Soon, we can drop VERY_VERBOSE altogether.
cDNA_primer/pbtranscript-tofu/external_daligner/DALIGNER-d4aa4871122b35ac92e2cc13d9b1b1e9c5b5dc5c-ICEmod/LA4Ice.c
|
Liz (@Magdoll), This might need changes. I have no idea. But it definitely builds. |
|
Magdoll@ |
|
thanks i'll give it a try |
pb-cdunn
force-pushed
the
master
branch
4 times, most recently
from
029bfa8
to
3f1b474
Compare
pb-cdunn
pushed a commit
that referenced
this pull request
Mar 9, 2018
…nate-buffer to develop * commit '87189252aa9b3c216e12aad904c86a545735d125': Minor fix to null-terminate buffer (properly, I think)
Sign up for free
to subscribe to this conversation on GitHub.
Already have an account?
Sign in.
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
cDNA_primer/pbtranscript-tofu/external_daligner/DALIGNER-d4aa4871122b35ac92e2cc13d9b1b1e9c5b5dc5c-ICEmod/LA4Ice.c