tests.bash

#!/bin/bash

set -e

samFile=$(tempfile).sam
bamFile=${samFile%.sam}.bam
sortBamFile=${samFile%.sam}_sort.bam
#qname flag rname pos mapq cigar mcrap mpos isize seq qual tags
echo "@HD	VN:1.0	SO:coordinate	
@SQ	SN:chr1	LN:1000
read01	99	chr1	10	40	10M	=	18	0	TTCCTTTCCT	IIIIIIIIII
read02	1	chr1	11	35	11M	=	1	0	ACACACACACA	>>>>>>>>>>>
read03	1	chr1	10	40	10M	=	1	0	ACACACACAC	>>>>>>>>>>
read01	147	chr1	19	40	10M	=	1	0	GGGGGTTTTT	>>>>>>>>>>
">$samFile
samtools/samtools view -bS $samFile >$bamFile 2>/dev/null
samtools/samtools sort -f $bamFile $sortBamFile
samtools/samtools index $sortBamFile

samFile2=$(tempfile).sam
bamFile2=${samFile2%.sam}.bam
sortBamFile2=${samFile2%.sam}_sort.bam
#qname flag rname pos mapq cigar mcrap mpos isize seq qual tags
echo "@HD	VN:1.0	SO:coordinate	
@SQ	SN:chr1	LN:1000
read01	99	chr1	10	40	10M	=	18	0	ACACACACAC	>>>>>>>>>>
read02	1	chr1	10	35	8M20D2M	=	1	0	ACACACACAC	>>>>>>>>>>
read03	1	chr1	50	40	10M	=	1	0	ACACACACAC	>>>>>>>>>>
read01	147	chr1	19	40	10M	=	1	0	GGGGGTTTTT	>>>>>>>>>>
read04	0	chr1	100	30	10M	=	1	0	GGGGGTTTTT	>>>>>>>>>>
read05	16	chr1	100	30	10M	=	1	0	GGGGGTTTTT	>>>>>>>>>>
read06	16	chr1	101	31	10M	=	1	0	GGGGGTTTTT	>>>>>>>>>>
read07	16	chr1	102	32	10M	=	1	0	GGGGGTTTTT	>>>>>>>>>>
">$samFile2
samtools/samtools view -bS $samFile2 >$bamFile2 2>/dev/null
samtools/samtools sort -f $bamFile2 $sortBamFile2
samtools/samtools index $sortBamFile2 

bedFile=$(tempfile).bed
echo "chr1	19	20	region1
chr1	24	25	region2">$bedFile

bedFile2=$(tempfile).bed
echo "chr1	1	25	region1
chr1	24	25	region2">$bedFile2

bedFile3=$(tempfile).bed
touch $bedFile3

bedFile4=$(tempfile).bed
echo "chrZ	1	25	region1
chrZ	24	25	region2">$bedFile4

bedFile5=$(tempfile).bed
echo "chr1	1	15	region1	-
chr1	24	25	region2	+">$bedFile5

bedFile6=$(tempfile).bed
echo "chr1	104	105	region1	-
chr1	104	105	region2	+
chr1	104	105	region2	*">$bedFile6

echo "Testing bedCount"
./bedCount 2>/dev/null && { echo "Missing files did not fail"; exit 1; }
./bedCount -h |grep Usage >/dev/null|| { echo "-h did not generate usage"; exit 1; }
./bedCount -Z 2>/dev/null&& { echo "Weird arg did not fail"; exit 1; }
./bedCount -$'\05' 2>/dev/null&& { echo "Weird arg did not fail"; exit 1; }
./bedCount -b $bedFile 2>/dev/null&& { echo "bed no bam did not fail"; exit 1; }
./bedCount -b $bedFile3 $sortBamFile  2>/dev/null&& { echo "empty bed did not fail"; exit 1; }
./bedCount -b $bedFile4 $sortBamFile  2>/dev/null&& { echo "all bad chr did not fail"; exit 1; }
./bedCount -b $bedFile $sortBamFile  2>/dev/null|grep "	0$"|wc -l|grep '^2$' >/dev/null|| { echo "Unexpected bedCount output for bamFile with 0 left after border"; exit 1; }
./bedCount -b ${bedFile2}.NOTAREALFILE $sortBamFile $sortBamFile2 -B 0 -G 2>/dev/null&& { echo "non-existent bed did not fail"; exit 1; }
./bedCount -b $bedFile $sortBamFile $sortBamFile2 -B 0 2>/dev/null|head -1|grep "chr1:20-20	chr1:20-20	1	1" >/dev/null|| { echo "Unexpected output with 0 border"; exit 1; }
./bedCount -b $bedFile $sortBamFile $sortBamFile2 -B 0 -s 2>/dev/null|head -1|grep "chr1:20-20	chr1:20-20	2	1" >/dev/null|| { echo "Unexpected output with 0 border and not require pair"; exit 1; }
./bedCount -b $bedFile $sortBamFile $sortBamFile2 -B 0 -s -G 2>/dev/null|tail -1|grep "GLOBAL	GLOBAL	2	1" >/dev/null|| { echo "Unexpected output with 0 border and not require pair and global"; exit 1; }
./bedCount -b $bedFile2 $sortBamFile $sortBamFile2 -B 0 -s -G 2>/dev/null|tail -1|grep "GLOBAL	GLOBAL	3	2" >/dev/null|| { echo "Unexpected output with 0 border and not require pair and global"; exit 1; }
./bedCount -b $bedFile2 $sortBamFile $sortBamFile2 -B 0 -G 2>/dev/null|tail -1|grep "GLOBAL	GLOBAL	1	1" >/dev/null|| { echo "Unexpected output with 0 border and pair and global"; exit 1; }
./bedCount -b $bedFile2 $sortBamFile $sortBamFile2 -B 0 -G -t 2 -v 2>/dev/null|tail -1|grep "GLOBAL	GLOBAL	1	1" >/dev/null|| { echo "Unexpected output 2 threads"; exit 1; }
./bedCount -b $bedFile2 $sortBamFile $sortBamFile2 -B 0 -s -Q 35 2>/dev/null|head -1|grep "chr1:2-25	chr1:2-25	3	2" >/dev/null|| { echo "Unexpected out with Q35"; exit 1; }
./bedCount -b $bedFile2 $sortBamFile $sortBamFile2 -B 0 -s -Q 36 2>/dev/null|head -1|grep "chr1:2-25	chr1:2-25	2	1" >/dev/null|| { echo "Unexpected with Q36"; exit 1; }
./bedCount -b $bedFile5 $sortBamFile $sortBamFile2 -B 0 2>/dev/null|head -1|grep "chr1:2-15	chr1:2-15	0	0" >/dev/null|| { echo "Unexpected result with strand"; exit 1; }
./bedCount -b $bedFile5 $sortBamFile $sortBamFile2 -B 0 2>/dev/null|tail -1|grep "chr1:25-25	chr1:25-25	1	1" >/dev/null|| { echo "Unexpected result with strand"; exit 1; }
#check strand and single end
./bedCount -b $bedFile6 $sortBamFile $sortBamFile2 -B 0 -G 2>/dev/null|tail -1|grep "GLOBAL	GLOBAL	0	0" >/dev/null|| { echo "Global sum not zero when all unpaired reads"; exit 1; }
./bedCount -b $bedFile6 $sortBamFile $sortBamFile2 -B 0 -G -s 2>/dev/null|tail -1|grep "GLOBAL	GLOBAL	0	4" >/dev/null|| { echo "Global sum not correct when all unpaired reads"; exit 1; }
./bedCount -b $bedFile6 $sortBamFile $sortBamFile2 -B 0 -s 2>/dev/null|cut -f 4|paste -sd ',' -|grep "^3,1,4$">/dev/null|| { echo "Counts not correct with single end stranded reads"; exit 1; }

echo "Testing bam2depth"
./bam2depth 2>/dev/null && { echo "Missing files did not fail"; exit 1; }
./bam2depth -h |grep Usage >/dev/null|| { echo "-h did not generate usage"; exit 1; }
./bam2depth -Z 2>/dev/null&& { echo "Weird arg did not fail"; exit 1; }
./bam2depth -$'\05' 2>/dev/null&& { echo "Weird arg did not fail"; exit 1; }
./bam2depth $sortBamFile |head -1|grep "chr1	10	2" >/dev/null|| { echo "Unexpected output for bamFile"; exit 1; }
./bam2depth $sortBamFile -r chr1:19-20|head -1|grep "chr1	19	4" >/dev/null|| { echo "Unexpected output for region"; exit 1; }
./bam2depth $sortBamFile -b $bedFile|head -1|grep "chr1	20	2" >/dev/null|| { echo "Unexpected start output for bedFile"; exit 1; }
./bam2depth $sortBamFile -b $bedFile|tail -1|grep "chr1	25	1" >/dev/null|| { echo "Unexpected end output for bedFile"; exit 1; }
./bam2depth $sortBamFile -r chr1:10-11 -Q 35|tail -1|grep "chr1	11	3" >/dev/null|| { echo ">35 map Q count messed up"; exit 1; }
./bam2depth $sortBamFile -r chr1:10-11 -Q 36|tail -1|grep "chr1	11	2" >/dev/null|| { echo ">36 map Q count messed up"; exit 1; }
./bam2depth $sortBamFile -r chr1:11-19 -d100|head -1|grep "chr1	11	3" >/dev/null|| { echo "Max depth count messed up"; exit 1; }
./bam2depth $sortBamFile $sortBamFile2 -r chr1:10-11 |tail -1|grep "chr1	11	3	2" >/dev/null|| { echo "Multiple depth count messed up"; exit 1; }
./bam2depth $sortBamFile $sortBamFile2 -r chr1:10-11 -q 40 |tail -1|grep "chr1	11	1	0" >/dev/null|| { echo "Multiple depth count with base qual messed up"; exit 1; }
./bam2depth $sortBamFile $sortBamFile2 -r chr1:10-11 -q 41 |tail -1|grep "chr1	11	0	0" >/dev/null|| { echo "Multiple depth count with base qual messed up"; exit 1; }
./bam2depth $sortBamFile $sortBamFile2 -r 'chr1:10-11*' |tail -1|grep "chr1	11	3	2" >/dev/null|| { echo "Stranded region messed up"; exit 1; }
./bam2depth $sortBamFile $sortBamFile2 -r 'chr1:10-11+' |tail -1|grep "chr1	11	3	2" >/dev/null|| { echo "Stranded region messed up"; exit 1; }
./bam2depth $sortBamFile $sortBamFile2 -r 'chr1:10-11-' |tail -1|grep "chr1	11	0	0" >/dev/null|| { echo "Stranded region messed up"; exit 1; }
echo "All clear"

rm $bedFile1 $bedFile2 $bedFile3 $bedFile4 $bedFile5 $bedFile6
rm $bamFile $bamFile2 $sortBamFile $sortBamFile2 $samFile $samFile2

exit 0