diff --git a/test/intersect/bed3.bed b/test/intersect/bed3.bed new file mode 100644 index 0000000000000000000000000000000000000000..d6c80bc6d33f8a72df31745e36b65f8364603dbb --- /dev/null +++ b/test/intersect/bed3.bed @@ -0,0 +1 @@ +chr1 10 20 diff --git a/test/intersect/bed4.bed b/test/intersect/bed4.bed new file mode 100644 index 0000000000000000000000000000000000000000..d7d228733ee88e87f3ef2561cb2179cf1f1dc46f --- /dev/null +++ b/test/intersect/bed4.bed @@ -0,0 +1 @@ +chr1 10 20 345.7 diff --git a/test/intersect/bed5.bed b/test/intersect/bed5.bed new file mode 100644 index 0000000000000000000000000000000000000000..614b75270ea36b219946392b47310bbe0ca37406 --- /dev/null +++ b/test/intersect/bed5.bed @@ -0,0 +1 @@ +chr1 10 20 345.7 why? diff --git a/test/intersect/bed6.bed b/test/intersect/bed6.bed new file mode 100644 index 0000000000000000000000000000000000000000..8382fe1f0bcb75fca6a4c05195807a07662324b0 --- /dev/null +++ b/test/intersect/bed6.bed @@ -0,0 +1 @@ +chr1 10 20 345.7 why? 11 diff --git a/test/intersect/bed6.strand.bed b/test/intersect/bed6.strand.bed new file mode 100644 index 0000000000000000000000000000000000000000..6c6e21e4f235c76b6fa49390f0d31c81fd9c5f06 --- /dev/null +++ b/test/intersect/bed6.strand.bed @@ -0,0 +1 @@ +chr1 10 20 345.7 why? - diff --git a/test/intersect/bed6.strand2.bed b/test/intersect/bed6.strand2.bed new file mode 100644 index 0000000000000000000000000000000000000000..e5d0d25f8fe10cb3f93a943f063f623b2f3b953a --- /dev/null +++ b/test/intersect/bed6.strand2.bed @@ -0,0 +1,2 @@ +chr1 10 20 345.7 why? - +chr1 11 21 345.7 why? + diff --git a/test/intersect/bedplus.bed b/test/intersect/bedplus.bed new file mode 100644 index 0000000000000000000000000000000000000000..f2d698465ce246e2542e2f0dfc8d72ebcba3fe86 --- /dev/null +++ b/test/intersect/bedplus.bed @@ -0,0 +1 @@ +chr1 10 20 345.7 why? 11 foo bar biz 11 bang bop 99 diff --git a/test/intersect/test-intersect.sh b/test/intersect/test-intersect.sh index b363499d51e71cf5fbbf17bde734e613f48d57e5..40e2ec487651044a4c43baa0877e63547555eaa4 100644 --- a/test/intersect/test-intersect.sh +++ b/test/intersect/test-intersect.sh @@ -304,6 +304,86 @@ echo \ $BT intersect -abam one_block.bam -b c.bed -wo -bed > obs check obs exp +################################################################## +# Test BED3 with BED3 +################################################################## +echo " intersect.t28...\c" +echo \ +"chr1^I10^I20^Ichr1^I10^I20" > exp +$BT intersect -a bed3.bed -b bed3.bed -wa -wb | cat -t > obs +check obs exp + +################################################################## +# Test BED4 with BED3 +################################################################## +echo " intersect.t29...\c" +echo \ +"chr1^I10^I20^I345.7^Ichr1^I10^I20" > exp +$BT intersect -a bed4.bed -b bed3.bed -wa -wb | cat -t > obs +check obs exp + +################################################################## +# Test BED5 with BED3 +################################################################## +echo " intersect.t30...\c" +echo \ +"chr1^I10^I20^I345.7^Iwhy?^Ichr1^I10^I20" > exp +$BT intersect -a bed5.bed -b bed3.bed -wa -wb | cat -t > obs +check obs exp + +################################################################## +# Test BED6 (without a proper strand) with BED3 +################################################################## +echo " intersect.t31...\c" +echo \ +"chr1^I10^I20^I345.7^Iwhy?^I11^Ichr1^I10^I20" > exp +$BT intersect -a bed6.bed -b bed3.bed -wa -wb | cat -t > obs +check obs exp + +################################################################## +# Test BED6 (with a strand) with BED3 +################################################################## +echo " intersect.t32...\c" +echo \ +"chr1^I10^I20^I345.7^Iwhy?^I-^Ichr1^I10^I20" > exp +$BT intersect -a bed6.strand.bed -b bed3.bed -wa -wb | cat -t > obs +check obs exp + +################################################################## +# Test BED PLUS with BED3 +################################################################## +echo " intersect.t33...\c" +echo \ +"chr1^I10^I20^I345.7^Iwhy?^I11^Ifoo^Ibar^Ibiz^I11^Ibang^Ibop^I99^Ichr1^I10^I20" > exp +$BT intersect -a bedplus.bed -b bed3.bed -wa -wb | cat -t > obs +check obs exp + +################################################################## +# Test for strand matches with BED3 +################################################################## +echo " intersect.t34...\c" +echo \ +"chr1^I10^I20^I345.7^Iwhy?^I11^Ichr1^I10^I20^I345.7^Iwhy?^I-" > exp +$BT intersect -a bed6.bed -b bed6.strand.bed -wa -wb | cat -t > obs +check obs exp + +################################################################## +# Test for strand matches with BED3 +################################################################## +echo " intersect.t35...\c" +echo \ +"chr1^I10^I20^I345.7^Iwhy?^I-^Ichr1^I10^I20^I345.7^Iwhy?^I-" > exp +$BT intersect -a bed6.strand.bed -b bed6.strand2.bed -wa -wb -s | cat -t > obs +check obs exp + +################################################################## +# Test for strand matches with BED3 +################################################################## +echo " intersect.t36...\c" +echo \ +"chr1^I10^I20^I345.7^Iwhy?^I-^Ichr1^I11^I21^I345.7^Iwhy?^I+" > exp +$BT intersect -a bed6.strand.bed -b bed6.strand2.bed -wa -wb -S | cat -t > obs +check obs exp rm obs exp