[ENSCORESW-2508]. Somehow (difficult to find exactly where) output is emitted without newline at the end, which is
then attached the result of the test, e.g. [last line of output]ok 17 ...
TAP fails because the parsed output is expecting the ok/not ok string at the beginning of the line.

bugfix: not all users require a password

Create PULL_REQUEST_TEMPLATE.md

[ENSCORESW-2230]. Checking whether the same fragment is mapped to a different seq_region relies on checking
whether the last target coordinate has been previously set and is on a different seq region. When looping
sequentially over the mapped fragments, these are checked whether they need to be considered and if they need not,
the loop was jumping to the next fragment, but only AFTER having registered the to be skipped fragment as the
last seen target coordinate.
A subsequent step might be considering a fragment on the same seq_region of the previously discarded fragment,
but now the check of whether the last target coordinate has been previously set and is on a different seq region
fails and so it might fail to detect the same source fragment is mapped to a different assembly bit, which happens
in the particular cases on chr10 reported in the issue.

WARNING: this change addresses the issue, as can be seen by the following output:

Found chromosome:GRCh38:10:96229321:96229901:1
Retrieved 2 projected bits
1-581 - chromosome:GRCh37:10:97989077:97989657:1
582-1162 - chromosome:GRCh37:HG339_PATCH:98024843:98025423:1

but does not entirely solve problems. As it can be seen, the coordinates of the fragments in the slice of the
source coordinate system and projected to two different seq_regions are deemed to be sequential where is reality
they are overlapping (the same).

NOTE: switching to the experimental branch as it is at this stage solves the two problems simulaneously:
- the interval tree just detects and then consider two overlapping fragments hence it does not have to loop
over irrelevant fragments which might compromise the logic; even if this is the case, the code in the experimental
branch already skips irrelevant fragments at the beginning of the loop;
- the coordinates of the projected bits in the original coordinate systems are already being correctly returned
by virtue of a previous fix [ENSCORESW-2289].

This is the output obtained with the new branch:

1-581 - chromosome:GRCh37:10:97989077:97989657:1
1-581 - chromosome:GRCh37:HG339_PATCH:98024843:98025423:1

[ENSCORESW-2428]. This is the full template with an added section about testing and improved formatting.

Extra parameters for the REST endpoint 'overlap/translation'. Will be…

Extra parameters for the REST endpoint 'overlap/translation'. Will be needed for a mapping to the PDB coordinates in a tool/feature using it

updates to Exon is_coding routine to handle cases where the coding region boundry falls within the exon boundry - ENSCORESW-2465

Removed special treatment for funcgen adaptors, coord systems have be…

This script has been replaced with https://github.com/Ensembl/ensembl-production/blob/master/scripts/copy_database.pl

Updates to add align_type column to dna_align_feature and protein_align_feature tables to support multiple align types and remove external_data column from dna_align_feature table - ENSCORESW-1937