This directory contains simulated data we use to check sequence variations for Goby alignments.
The simulated data contains an example of each type of variation that can be represented with Goby
and makes it easy to check visually that the Goby IGV code works as expected.

The simulated data is produced as described in the following.


The index is "small-synth.fa". The reads are "seq-var-reads.fa".

To create the gsnap index, first create compact-reads from the files

   java -jar goby.jar -m fasta-to-compact -d -o small-synth.compact-reads small-synth.fa
   java -jar goby.jar -m fasta-to-compact -d -o seq-var-reads.compact-reads seq-var-reads.fa

Create the GSNAP index

   mkdir SMALL_SYNTH_DB-gsnap
   cd SMALL_SYNTH_DB-gsnap
   ../../gmap-icb/util/gmap_setup -d index -B ../../gmap-icb/util ../small-synth.fa
   make -f Makefile.index coords
   make -f Makefile.index gmapdb
   # The following augments the index for Bisulfite, not necessary
   ../../gmap-icb/src/cmetindex -d index -D . -F .
   cd ..

Align the output. To make the output useful for debugging, make sure to
compile goby-ccp with debugging enabled by editing the top of C_Alignments.cc
and set
    #define C_WRITE_API_WRITE_ALIGNMENT_DEBUG

Align command:

   # unthreaded with 6 mismatches allowed
   ../gmap-icb/src/gsnap -t 0 -m 6 -A goby --goby-output seq-var-reads-gsnap -D SMALL_SYNTH_DB-gsnap -d index seq-var-reads.compact-reads > seq-var-reads-gsnap.exec-output.txt

Finally, since the iterator we are testing requires a SORTED alignment run

   java -jar goby.jar -m sort -d -o sorted-seq-var-reads-gsnap seq-var-reads-gsnap.entries
