Peter Johansson committed [r1239] on SVN

latest results

Peter Johansson committed [r2266] on Code

rewriting vcf_dnv_call such that the bam iterator is recycled rather than creating a new pileup object for every locus analysed.

Peter Johansson committed [r2265] on Code

limit number of reads used to 256.

Peter Johansson committed [r2264] on Code

make LENDI job single-threaded.

Peter Johansson committed [r2263] on Code

avoid debug output

Peter Johansson committed [r2262] on Code

reimplement vcf_dnv_call

Peter Johansson committed [r2261] on Code

set --native-pair-hmm-thread=1 in tests

Peter Johansson committed [r2260] on Code

new function make_alleles(1).

Peter Johansson committed [r2259] on Code

remove outdated test.

Peter Johansson committed [r2258] on Code

use $TMPDIR and prefer double-digit format for walltime.

Peter Johansson committed [r2257] on Code

add some asserts in vcf_dnv_call.

Peter Johansson committed [r2256] on Code

make MNV single-threaded by executing tools in serial against disk rather than piping tools.

Peter Johansson committed [r1238] on SVN

results

Peter Johansson committed [r1237] on SVN

Nov

Peter Johansson committed [r2255] on Code

vcf_dnv_call assumed no indels; fix that by basically ignore them and to make things easier within the pipeline, split multi-allelic entries.

Peter Johansson committed [r1236] on SVN

QF draw.

Peter Johansson committed [r2254] on Code

reduce MNV walltime to 2hrs per sample.

Peter Johansson committed [r1235] on SVN

league cup results.

Peter Johansson committed [r2253] on Code

only request 1 cpu for MNV jobs

Peter Johansson committed [r2252] on Code

increase memory request for HaplotypeCaller.

Peter Johansson committed [r1234] on SVN

Peter Johansson committed [r1233] on SVN

more results

Peter Johansson committed [r2251] on Code

redict from file rather than using bcftools.

Peter Johansson committed [r1232] on SVN

Peter Johansson committed [r2250] on Code

increase logging freq.

Peter Johansson committed [r2249] on Code

increase memory fro HaplotypeCaller.

Peter Johansson committed [r2248] on Code

fix test dependency

Peter Johansson committed [r2247] on Code

increase mem request after crash.

Peter Johansson committed [r2246] on Code

remove unused variable.

Peter Johansson committed [r2245] on Code

update copyright years.

Peter Johansson committed [r2244] on Code

correct typo in message

Peter Johansson committed [r2243] on Code

fix test failures against yat trunk.

Peter Johansson committed [r2242] on Code

update pbs requests for bam2fastq pipeline

Peter Johansson committed [r2241] on Code

increase memory request

Peter Johansson committed [r1231] on SVN

again basic skeleton

Peter Johansson committed [r1230] on SVN

basic features

Peter Johansson committed [r1229] on SVN

seed of a program

Peter Johansson committed [r1228] on SVN

remove old code

Peter Johansson committed [r2240] on Code

avoid deprecate warnings

Peter Johansson committed [r1227] on SVN

add factor analysis in europe output.

Peter Johansson committed [r1226] on SVN

results

Peter Johansson committed [r2239] on Code

add missing svn props

Peter Johansson committed [r1225] on SVN

October update.

Peter Johansson committed [r1224] on SVN

Thursday football.

Peter Johansson committed [r1223] on SVN

results

Peter Johansson committed [r1222] on SVN

mark table segments with colours in europe output.

Peter Johansson committed [r1221] on SVN

Peter Johansson committed [r2238] on Code

avoid default value [4] for number of threads.

Peter Johansson committed [r1220] on SVN

Saturday football

Peter Johansson committed [r1219] on SVN

calculate a hashkey of current position.

Peter Johansson committed [r1218] on SVN

EL matchday 1

Peter Johansson committed [r2237] on Code

add RAC1 from AMGP SMG list.

Peter Johansson committed [r2236] on Code

add known UM genes PLCB4, CYSLTR2, and EIF1AX.

Peter Johansson committed [r2235] on Code

only check mpos and mtid for paired data.

Peter Johansson committed [r2234] on Code

avoid throwing char const*

Peter Johansson committed [r2233] on Code

fix typo

Peter Johansson committed [r1217] on SVN

league cup 4R draw.

Peter Johansson committed [r2232] on Code

increase memory request after crash 26705868.

Peter Johansson committed [r2231] on Code

remove debug output.

Peter Johansson committed [r2230] on Code

temporary super cautious version.

Peter Johansson committed [r2229] on Code

lift out bam validator to a separate class.

Peter Johansson committed [r2228] on Code

make constructor public.

Peter Johansson committed [r1216] on SVN

Sunday results.

Peter Johansson committed [r1215] on SVN

first version

Peter Johansson committed [r1214] on SVN

init connect4

Peter Johansson committed [r1213] on SVN

work on factor analysis for european tournaments.

Peter Johansson committed [r1212] on SVN

move builtin tests to a macro hosted in yat.

Peter Johansson committed [r2227] on Code

pipeline align: error out if log indicates serious error.

Peter Johansson committed [r1211] on SVN

update for CL matchweek 1

Peter Johansson committed [r1210] on SVN

more results

Peter Johansson committed [r1209] on SVN

tweak output and add some results.

Peter Johansson committed [r2226] on Code

jack up memory request for mane job after upgrade.

Peter Johansson committed [r1208] on SVN

results

Peter Johansson committed [r2225] on Code

increase memory usage for PILEUP job

Peter Johansson committed [r2224] on Code

Peter Johansson committed [r2223] on Code

get rid of obsolete PP forks

Peter Johansson committed [r2222] on Code

continue clean-up

Peter Johansson committed [r2221] on Code

use yat 0.22 instead

Peter Johansson committed [r2220] on Code

remove files no longer needed since we require yat 0.22

Peter Johansson committed [r2219] on Code

remove source no longer needed

Peter Johansson committed [r2218] on Code

Peter Johansson committed [r2217] on Code

pipeline align: set walltimes based on size of input fastq file.

Peter Johansson committed [r2216] on Code

remove PP fork.

Peter Johansson committed [r2215] on Code

remove index wrappers

Peter Johansson committed [r2214] on Code

remove PP forks.

Peter Johansson committed [r2213] on Code

remove PP forks.

Peter Johansson committed [r2212] on Code

remove PP forks.

Peter Johansson committed [r2211] on Code

get rid of PP forks no longer needed.

Peter Johansson committed [r2210] on Code

remove MatrixBase

Peter Johansson committed [r2209] on Code

require yat 0.22

Peter Johansson committed [r2208] on Code

new function filesize

Peter Johansson committed [r1207] on SVN

set baseline i.e. avoid simulating early-stage matches.

Peter Johansson committed [r2207] on Code

fix typo

Peter Johansson committed [r1206] on SVN

add output for most important matches.

Peter Johansson committed [r1205] on SVN

playoff results

Peter Johansson committed [r1204] on SVN

remove obsolete files and add seed for FactorAnalysis class.

Peter Johansson committed [r1203] on SVN

remove obsolete files.

Peter Johansson committed [r2206] on Code

fix typo

Peter Johansson committed [r2205] on Code

correction of r2204

Peter Johansson committed [r2204] on Code

add missing dependency for test.