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]

* thegenemyers#20

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

…ang length)

…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.

resolves PacificBiosciences#10

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