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These assist with TestIteratedSortedAlignment2.
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
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