bigdatagenomics/adam — pull request #155 by cchng (2014-02-28 07:50:08+00:00)
Title: Identifier consistency & formatting cleanup Issue #126

The commits fix issue [#162](https://github.com/bigdatagenomics/adam/issues/126).

Adam --> ADAM for all file contents and file names.
Variation --> Variant for all file contents and file names.
```
find . \( ! -regex '.*/\..*' \) -type f -print0 |xargs -0 sed -i '' 's/Adam/ADAM/g'
find . \( ! -regex '.*/\..*' \) -type f -print0 |xargs -0 sed -i '' 's/Variation/Variant/g'
find . -type f -name '*Adam*' | while read filename ; do git mv --force $filename `echo $filename | sed 's/Adam/ADAM/g'`; done
```
Checked with:
```
grep -r "Adam"
grep -r "Variation"
find . -type f -name '*Adam*'
find . -type f -name '*Variation*'
```
Imports are alphabetized with bash "sort"
Checked with:
```
for file in $(find . -name '*.scala' -or -name '*.java'); do
DIFF_OUT=`diff <(grep "^import" $file) <(grep "^import" $file |sort)`
if [[ -n $DIFF_OUT ]]; then
echo $file
fi
done
```
All scala code reformatted with https://github.com/mdr/scalariform/wiki/Command-line-tool

I'm not sure if adam runs on a laptop computer, so I have not done any tests.