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#!/bin/bash
test -e ssshtest || wget -q https://raw.githubusercontent.com/ryanlayer/ssshtest/master/ssshtest
. ssshtest
set -o nounset
go build -o ./gsort_linux_amd64 cmd/gsort/gsort.go
run check_usage ./gsort_linux_amd64
assert_exit_code 255
assert_in_stderr "Usage"
run check_funky ./gsort_linux_amd64 example/a.bed example/3Y21.genome
assert_exit_code 0
assert_equal "$(cut -f 1 $STDOUT_FILE | perl -pe 's/\n//')" "3Y2111"
assert_equal "$(cut -f 2 $STDOUT_FILE | perl -pe 's/\n//')" "12342224233145567556"
assert_equal "$(cut -f 3 $STDOUT_FILE | perl -pe 's/\n//')" "12353335555255668566"
run check_funky_with_remap ./gsort_linux_amd64 -c example/remapchr.txt example/chra.bed example/3Y21.genome
assert_equal "$(cut -f 1 $STDOUT_FILE | perl -pe 's/\n//')" "3Y2111"
run check_normal ./gsort_linux_amd64 example/a.bed example/123Y.genome
assert_exit_code 0
exp="1 1 2
1 4556 5566
1 7556 8566
2 4233 5555
3 1234 1235
Y 222 333"
assert_equal "$(cat $STDOUT_FILE)" "$exp"
run check_bed_header ./gsort_linux_amd64 example/track-browser.bed example/123Y.genome
assert_exit_code 0
exp="track name=\"ItemRGBDemo\" description=\"Item RGB demonstration\" visibility=2 itemRgb=\"On\"
browser position chr7:127471196-127495720
browser hide all
1 127473530 127474697 Pos3 0 + 127473530 127474697 255,0,0
1 127474697 127475864 Pos4 0 + 127474697 127475864 255,0,0
1 127478198 127479365 Neg3 0 - 127478198 127479365 0,0,255
1 127479365 127480532 Pos5 0 + 127479365 127480532 255,0,0
1 127480532 127481699 Neg4 0 - 127480532 127481699 0,0,255
2 127475864 127477031 Neg1 0 - 127475864 127477031 0,0,255
2 127477031 127478198 Neg2 0 - 127477031 127478198 0,0,255
Y 127471196 127472363 Pos1 0 + 127471196 127472363 255,0,0
Y 127472363 127473530 Pos2 0 + 127472363 127473530 255,0,0"
assert_equal "$(cat $STDOUT_FILE)" "$exp"
run check_gff_parent ./gsort_linux_amd64 --parent test.gff test.gff.genome
assert_exit_code 0
exp="##gff-version 3
##sequence-region CHROM1 1 20386
###
###
CHROM1 Cufflinks mRNA 1473 16154 . - . ID=XLOC_228.2;description=228
CHROM1 Cufflinks mRNA 1473 16386 . - . ID=XLOC_228.3
CHROM1 Cufflinks exon 1473 1814 . - . Parent=XLOC_228.2
CHROM1 Cufflinks exon 1473 12024 . - . Parent=XLOC_228.3
CHROM1 Cufflinks exon 11626 12574 . - . Parent=XLOC_228.2
CHROM1 Cufflinks exon 12615 12721 . - . Parent=XLOC_228.3
CHROM1 Cufflinks exon 12695 12721 . - . Parent=XLOC_228.2
CHROM1 Cufflinks exon 13637 13726 . - . Parent=XLOC_228.2
CHROM1 Cufflinks exon 13637 13726 . - . Parent=XLOC_228.3
CHROM1 Cufflinks exon 15329 15408 . - . Parent=XLOC_228.2
CHROM1 Cufflinks exon 15329 16386 . - . Parent=XLOC_228.3
CHROM1 Cufflinks exon 15994 16154 . - . Parent=XLOC_228.2"
assert_equal "$(cat $STDOUT_FILE)" "$exp"
run check_vcf_like_sort ./gsort_linux_amd64 test.vcf-like.tsv test.vcf-like.genome
assert_exit_code 0
exp="#chrom pos ref alt strand gene_symbol prediction class score
1 12623 A C + DDX11L9 benign neutral 0.386
1 12624 T C + DDX11L9 possiblydamaging deleterious 0.89
1 12625 G A + DDX11L9 possiblydamaging deleterious 0.769
1 12626 C G + DDX11L9 benign neutral 0
1 12627 C G + DDX11L9 benign neutral 0
12 78791 A G + DKFZp434K1323 possiblydamaging deleterious 0.713
12 78792 T A + DKFZp434K1323 possiblydamaging deleterious 0.932
12 78793 G A + DKFZp434K1323 possiblydamaging deleterious 0.851
12 78794 A C + DKFZp434K1323 possiblydamaging deleterious 0.895
Y 59356108 G T + WASH1 benign neutral 0.026
Y 59356110 A G + WASH1 benign neutral 0
Y 59356111 G C + WASH1 possiblydamaging deleterious 0.501
Y 59356112 C A + WASH1 benign neutral 0.003
Y 59356113 A G + WASH1 benign neutral 0.004
Y 59356113 A C + WASH1 possiblydamaging deleterious 0.952
Y 59356114 G A + WASH1 possiblydamaging deleterious 0.736"
assert_equal "$(cat $STDOUT_FILE)" "$exp"
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