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Created with Raphaël 2.2.05Mar2128Feb27262322212019161514131211987652131Jan2926252423221917161512111098543221Dec201918161513128765130Nov29282724222120181716141310987632131Oct30272625242320191817161312104228Sep272625222120191815141312117654131Aug30292118171614119832131Jul282721191712111097654330Jun292827262322Change the order of the argument for the run() method in the sub-classesMake checksums smaller; use the file size and only the first sixStore checksums of files as ":checksum1:checksum2:checksum3" and thenLogical error fixed.- Added transform method to BaseAlignFeature so that if a simple transformUse filename given to us, not static 'interpro.xml'.rm debug outputGet rid of a couple of warnings.Also update usage() sub for -unzip.Do not decompress gzipped files (new default behaviour).fixed DAS to do the right thing!removed shoutsShouldn't have been in branch 43bug fix for wrong level being usedUse while/shift instead of foreach to reduce memory requirements.removed print statementadded support in negative strandremoved reverse sequence, it is already in the negative strandmodified to add proper coverage for negative strandThis commit was manufactured by cvs2svn to create branch 'branch-modified slices in negative strandmake sure varsplic stuff done after uniprot as they are dependent on themmodified line to add strain object in StrainSliceadded coverage information to return allele featuresBUG FIX: transcript_xrefs needed to be initialised per transcript not per geneRemoved duplicate entry for monodelphis which was causing xref_mapper.pl to die.modified when returning sequence in negative strandadded reference strain in the get_all_Slices callreturns sequence for reference strainMade Felix's ditag_* changes (patch_43_44_b.sql)Changed analysis_id and external_db_id columns to SMALLINT (patch_43_44_a.sql).Change types of analysis_id and external_db_id columns.Felix's ditag table patch.Added documentation for -health_check optionadded oligo_array probe_setsize warning and individual probe_setsize countAllow the Xref parsers to read gzip compressed files through a zcatadded healthcheck modeadd source type to the keyinsert followed by delete warning message now only printed once.modified last character end of slice