amplikyzer
==========

TODO:
- Erklaerung der Optionen
- Manual, Aufbau des LOCI files
- 

Improvements:
#- %-sign looks funny in plots. why? workaround? other font?
#- font problem with % -- pehaps use Agg backend for pdf
#- Some of the user output of analyze, statistics, align, methylation goes to stderr instead of stdout.
- fill more homopolymer gaps in alignments ('aggressively fill gaps')
- small letters after long homopolymers are probably wrong.
#- report discarded/used/total number of reads, report good-read-coverage for each CpG.
- use matplotlib for analysis diagnostic plots (at the moment it it gnuplot).
- use matplotlib for analysis diagnostic plots (at the moment it is gnuplot).
#- Use Cython for further speed-ups
#- font size on y-axis when there are many MIDs
#- add option --showpositions to show CpG positions, otherwise just number them 1..n
#- specify SNPs with IUPAC amiguity codes
- Sortierug bei comparative nach Gesamtethylierung (standard), alternativ nach eigener MID-Vorgabe
- Sortierung nach Methylierung auch umgekehrt (indiv, comparative)
#- Comparative-Plot und indiv-Plot: Positionen der CpGs einfach durch Nummern ersetzen
#- "samples" statt "analyses"
#- Schriftart bei comparative ab 22 kleiner
#- Option fuer Schriftgroesse
#- Standardeinstellung bei comparative: pdf
- Allele im Dateinamen von comparative
- Im Titel statt N oder NN besser: "complete"
- in comparative: Man will im selben Plot eine Zeile fuer Allele A, G, N
#- CpGs die durch SNPs enstehen, richtig behandeln: Fall NG, wobei N ein C sein kann: Spalte immer vorsehen.
#- Wenn man 2 Allele zusammen sehen will, mit amg codes arbeiten (Y statt N): Y ist C oder T


Feature requests:
- find interesting variants (rare! 0.1%, distinguish from seq errors)
- find in-frame deletions (more than 1 read, length = 3n)
- map (patient,locus) to (mid,locus)

Notes:
- Description of CWF format and other formats:
  http://454.com/my454/documentation/gs-flx-system/emanuals.asp



geniegui
========

- New "--exec" option to call exec() instead of using a new child process directly
#- why are global options so far to the right (amplikyzer)?
#- Why doesn't the option panel expand when the window is re-sized?


mamaslemonpy
============
- Allow general alphabet
- perhaps a --path option?
- one-error ms

