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#!/bin/sh
# Copyright (C) 2015, 2018 Genome Research Ltd.
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in
# all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
# THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
# DEALINGS IN THE SOFTWARE.
#
# -----------------------------------------------------------------------------
# Author: James Bonfield.
#
# This cross validation script is designed to run the htslib test_view
# and cramtools.jar CRAM implementations to test compatibility between
# implementations.
#
# The test set may contain many dubious and ambiguous SAM cases, such as
# single base reads (is that quality "*" really meaning Q9 or no quality?).
# Some of these may fail one or the other implementations and be acceptable
# in the short-term, so to spot more important regressions we can tag
# specific cases as being known-pass or known-fail.
# -----------------------------------------------------------------------------
#
vers=3.0
cramtools_jar=$HOME/work/cram/cramtools/cramtools-$vers.jar
test_view="./test_view -o VERSION=$vers"
cramtools="/software/bin/java -Xmx4000m -jar $cramtools_jar"
cramtools="/software/bin/java -Xmx4000m -jar $cramtools_jar"
run_out() {
out=$1; shift
echo "$@ > $out"
$@ > $out
}
run() {
echo "$@"
$@
}
sam_to_Ccram() {
run_out _tmp.cram $test_view -C -t $1 $2
#run_out _tmp.cram $HOME/io_lib/trunk/build.seq3/progs/scramble -r $1 -O CRAM $2
if [ $? != 0 ]
then
crash=`expr $crash + 1`
false
fi
}
Ccram_to_sam() {
run_out _tmp.sam $test_view -i REFERENCE=$1 _tmp.cram
#run_out _tmp.sam $HOME/io_lib/trunk/build.seq3/progs/scramble -r $1 _tmp.cram
if [ $? != 0 ]
then
crash=`expr $crash + 1`
false
fi
}
sam_to_Jcram() {
run $cramtools cram -R $1 -I $2 -O _tmp.cram -n -Q --capture-all-tags
if [ $? != 0 ]
then
crash=`expr $crash + 1`
false
fi
}
Jcram_to_sam() {
run $cramtools bam -R $1 -I _tmp.cram -O _tmp.sam
if [ $? != 0 ]
then
crash=`expr $crash + 1`
false
fi
}
compare_sam() {
#run ./compare_sam.pl $i _tmp.sam -nomd -notemplate -unknownrg -Baux
run ./compare_sam.pl $i _tmp.sam -nomd -Baux
if [ $? != 0 ]
then
fails=`expr $fails + 1`
false
fi
}
trials=0
fails=0
crash=0
files=`ls -1 *#*.sam`
# Restrict to known workers from SAM->CRAM->CRAM in cramtools
#files="auxf#values.sam c1#bounds.sam c1#noseq.sam c1#pad1.sam c1#pad2.sam c1#pad3.sam c1#unknown.sam ce#1.sam ce#2.sam ce#5b.sam ce#large_seq.sam ce#tag_depadded.sam ce#tag_padded.sam ce#unmap.sam ce#unmap1.sam ce#unmap2.sam xx#large_aux.sam xx#large_aux2.sam xx#pair.sam xx#rg.sam xx#unsorted.sam"
for i in $files
do
r=`echo $i | sed 's/#.*/.fa/'`
echo "=== $i"
# C to C
trials=`expr $trials + 1`
sam_to_Ccram $r $i && Ccram_to_sam $r && compare_sam $i _tmp.sam
# Java to Java
trials=`expr $trials + 1`
sam_to_Jcram $r $i && Jcram_to_sam $r && compare_sam $i _tmp.sam
# C to Java
trials=`expr $trials + 1`
sam_to_Ccram $r $i && Jcram_to_sam $r && compare_sam $i _tmp.sam
# Java to C
trials=`expr $trials + 1`
sam_to_Jcram $r $i && Ccram_to_sam $r && compare_sam $i _tmp.sam
done
# Overcounts failures as an early fail can lead to 1 or 2 more fails.
echo ""
echo ============
echo No. tests: $trials
echo No. diffs: $fails
echo No. crash: $crash
|
