Replaced email addresses by URL to the website or to mailing lists
License update
Throw exception when trf dies (Thibaut's fix).
- Added option 'padded_nonref' which returns all non-reference sequences padded with N's to match the corresponding full length of the reference chromosome for the given non-reference sequence. Only works if 'include_duplicates' is disabled.
- Implemented option 'padded_human_Chr_Y' for human GRCh38.
Chromosome Y header changed to match the other sequences format.
Added a clone analysis script.

Will clone analyses in the db and config files. By default the script expects a pipeline style db. It will clone from one analysis (already present in the db) to a set of new logic names specified in the input file. By default it will clone the entry in the analysis table, the input id type and any rules of the original analysis. A set of config files can be specified on the second line of the input file. If present the analysis entry in these configs will be cloned to the new logic names in the input file. Configs that are being cloned will be backed up by the script, however it is recommended that you back them up if you haven't checked them into git.

Optional flags include: -no_rules (don't clone rules), -not_pipeline_db (don't clone rules or input id type), -just_config (don't touch the db tables and only clone in configs). Consult the help to see all options.

Care should be taken when cloning analyses, especially for rules and paths to output dirs in BatchQueue.pm. For BatchQueue.pm output paths, remove the output path (if present) from the analysis being cloned and make sure the default path is set. Cloned analyses will then use the default output dir path with their logic name appended onto them.
updated deprecated call
* added --sourcepass option to allow use of password-protected
  source mysql instances
replace_stops_with_introns rewritten to allow more cases like stops at the start and end of exons, stops on two exons at the same time. It does not remove tiny exons now. It replaces the stop with an intron and/or moves the translation start and end if necessary. Only for transcripts containing 1 stop. A exception will be thrown if there are more stops.
Updated config parsing.

This update deals with scenarios where the config hash has an opening bracket on a separate line.

Also added some throws for when things aren't parsed correctly or nothing is parsed.

Removed  as it is unused.
Fixed eponine offset on reverse strand
Merge branch 'master', remote-tracking branch 'origin'
Migration of new merge code.
Move of code and docs from (cvs) ensembl personal ak4 to (git) ensembl-analysis/scripts/Merge
Bug fix: stop length taken into account when splitting features into two exons.
Commented out some unwanted logic about one and two bases exons.
Bug fix: padded haplotype coordinates in the headers are now dumped correctly starting at 1 and finishing at the end of the full length of the chromosome including the haplotype (rather than starting/ending at the start/end of the hap sequence within the chromosome).
Merge branch 'master' of https://github.com/Ensembl/ensembl-analysis
replace_stops_with_introns bug fixes:
- fp start and end are now calculated by taking the strand into account
- it supports DnaDnaAlignFeatures (cdna2genome-like analyses)
Re-implemented some of the changes from the experimental branch, do not use this commit
Updated merge code.
The following changes have been implemented:
1) The code warns about Havana pseudogenes that have more than one transcript
2) The code tags any Havana genes that have a transcript with attribute gene_cluster.
   In this scenario, any Ensembl genes that have overlapping transcripts are either
   merged or the transcript/gene is thrown out
3) If the Havana xref tag info is not present in the config file then it throws
4) If the Havana gene is a pseudogene a check is now present to see if the Ensembl
   transcript that is being copied in is ccds, if it is then the Ensembl transcript
   takes precedence and the biotype of the gene is updated
5) If the Havana gene is non-coding, but not a pseudogene, and the Ensembl transcript
   being copied is coding, the exon phases are now stripped if the Ensembl transcript
   is not ccds (this is in addition to the translation being removed)
6) If the biotype of the Havana gene is bad, at the moment that's TEC or artifact,
   then skip storing the Havana gene and throw out any overlapping Ensembl genes. In
   both cases a warning is printed showing the gene stable ids of anything affected
Updated merge.pl
Removed an incorrect print and fixed some indentation