updated seqlib

test/t/00_region_and_target_handling.t

@@ -0,0 +1,145 @@
+#!/usr/bin/env bash
+# vi: set ft=sh :
+
+test=$(dirname $0)/..
+root=$(dirname $0)/../..
+
+source $test/test-simple-bash/lib/test-simple.bash \
+    tests 11
+
+PATH=$root/bin:$PATH
+
+ref=$test/$(basename $0).ref
+alt=$test/$(basename $0).alt
+bam=$test/$(basename $0).bam
+bed=$test/$(basename $0).bed
+vcf=$test/$(basename $0).vcf
+
+trap 'rm -f $ref* $alt $bam* $bed $vcf' EXIT
+
+# 01234567890	start
+# ATCGGCTAAAA	ref
+# GTTAGGTTAAC	alt
+# 12345678901	end
+
+cat >$ref <<REF
+>ref
+ATCGGCTAAAA
+REF
+samtools faidx $ref
+
+cat >$alt <<ALT
+>alt
+GTTAGGTTAAC
+ALT
+
+samtools view -S -b - >$bam <<SAM
+@HD	VN:1.5	SO:coordinate
+@SQ	SN:ref	LN:11
+alt	0	ref	1	30	1X1=2X1=1X1=1X2=1X	*	0	0	GTTAGGTTAAC	*
+SAM
+samtools index $bam
+
+cat >$bed <<BED
+ref	0	1	first_base
+ref	2	4	third_and_fourth_base
+ref	5	6	sixth_base
+ref	7	8	eighth_base
+ref	10	11	eleventh base
+BED
+
+cat >$vcf <<VCF
+##fileformat=VCFv4.1
+##INFO=<ID=NAME,Number=0,Type=String,Description="Test name">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
+ref	1	.	A	G	1234	PASS	NAME=first base
+ref	2	.	T	.	1234	PASS	NAME=second base
+ref	3	.	C	T	1234	PASS	NAME=third base
+ref	4	.	G	A	1234	PASS	NAME=fourth base
+ref	5	.	G	.	1234	PASS	NAME=fifth base
+ref	6	.	C	G	1234	PASS	NAME=sixth base
+ref	7	.	T	.	1234	PASS	NAME=seventh base
+ref	8	.	A	T	1234	PASS	NAME=eighth base
+ref	9	.	A	.	1234	PASS	NAME=ninth base
+ref	10	.	A	.	1234	PASS	NAME=tenth base
+ref	11	.	A	C	1234	PASS	NAME=eleventh base
+VCF
+
+PS4='\n+ '
+
+function run_freebayes() {
+    ($root/bin/freebayes "$@" \
+        --haplotype-length 0 --min-alternate-count 1 \
+        --min-alternate-fraction 0 --pooled-continuous --report-monomorphic \
+        --ploidy 1 \
+        -f $ref $bam \
+        | grep -vE "^#" | cut -f1-5)
+}
+
+if [[ -n $TEST_DEBUG ]]; then
+    cat $ref >&2
+    cat $bed >&2
+    cat $vcf >&2
+    vcfannotate --bed $bed --key MATCH $vcf >&2
+    vcfintersect --bed $bed $vcf >&2
+    bedtools intersect -a $vcf -b $bed >&2
+fi
+
+
+output=$(run_freebayes --region ref:4-5 --region ref:6-7)
+ok [ -z "$output" ] "ref:4-5 ref:6-7 are empty" || echo "$output"
+
+output=$(run_freebayes --region ref:4 --region ref:6)
+ok [ -z "$output" ] "ref:4 ref:6 are empty" || echo "$output"
+
+expected=$(cat <<END
+ref	6	.	C	G
+ref	8	.	A	T
+END
+)
+output=$(run_freebayes --region ref:5-6 --region ref:7-8)
+ok [ "$output" == "$expected" ] "ref:5-6 ref:7-8" || echo "$output"
+
+output=$(run_freebayes --region ref:5 --region ref:7)
+ok [ "$output" == "$expected" ] "ref:5 ref:7" || echo "$output"
+
+expected=$(cat <<END
+ref	6	.	C	G
+ref	8	.	A	T
+ref	11	.	A	C
+END
+)
+output=$(run_freebayes --region ref:5-)
+ok [ "$output" == "$expected" ] "ref:5-" || echo "$output"
+
+expected=$(cat <<END
+ref	1	.	A	G
+ref	3	.	CG	TA
+ref	6	.	C	G
+ref	8	.	A	T
+ref	11	.	A	C
+END
+)
+output=$(run_freebayes)
+ok [ "$output" == "$expected" ] "full output" || echo "$output"
+
+output=$(run_freebayes --targets $bed)
+ok [ "$output" == "$expected" ] "--targets $bed" || echo "$output"
+
+output=$(run_freebayes --region ref)
+ok [ "$output" == "$expected" ] "--region ref" || echo "$output"
+
+# commas as separators: should really be 1,000
+expected=$(cat <<END
+ref	11	.	A	C
+END
+)
+output=$(run_freebayes --region ref:1,0)
+ok [ "$output" == "$expected" ] "ref:1,0-" || echo "$output"
+
+output=$(run_freebayes --region ref:1,0-1,1)
+ok [ "$output" == "$expected" ] "ref:1,0-1,1" || echo "$output"
+
+expected="ERROR(freebayes): Target region coordinates (ref 1 20) outside of reference sequence bounds (ref 11) terminating."
+output=$(run_freebayes --region ref:1-20 2>&1)
+ok [ "$output" == "$expected" ] "region outside of bounds error" || echo "$output"