From 64ed292d5b3bcb021791d5a9fadaa95f2a59ff47 Mon Sep 17 00:00:00 2001 From: Aaron Date: Fri, 30 Mar 2012 11:01:09 -0400 Subject: [PATCH] add omitted test dirs for "make test" --- test/coverage/one_block.bam.bai | Bin 0 -> 96 bytes test/coverage/one_block.sam | 3 ++ test/coverage/sam-w-del.bam.bai | Bin 0 -> 96 bytes test/coverage/sam-w-del.sam | 3 ++ test/coverage/test-coverage.sh | 35 +++++++++++++++++++++++ test/coverage/three_blocks.bam.bai | Bin 0 -> 96 bytes test/coverage/three_blocks.sam | 3 ++ test/coverage/three_blocks_match.bed | 1 + test/coverage/three_blocks_match_1bp.bed | 1 + test/coverage/three_blocks_nomatch.bed | 1 + test/coverage/two_blocks.bam.bai | Bin 0 -> 96 bytes test/coverage/two_blocks.sam | 3 ++ test/merge/a.full.bed | 9 ++++++ 13 files changed, 59 insertions(+) create mode 100644 test/coverage/one_block.bam.bai create mode 100644 test/coverage/one_block.sam create mode 100644 test/coverage/sam-w-del.bam.bai create mode 100644 test/coverage/sam-w-del.sam create mode 100644 test/coverage/test-coverage.sh create mode 100644 test/coverage/three_blocks.bam.bai create mode 100644 test/coverage/three_blocks.sam create mode 100644 test/coverage/three_blocks_match.bed create mode 100644 test/coverage/three_blocks_match_1bp.bed create mode 100644 test/coverage/three_blocks_nomatch.bed create mode 100644 test/coverage/two_blocks.bam.bai create mode 100644 test/coverage/two_blocks.sam create mode 100644 test/merge/a.full.bed diff --git a/test/coverage/one_block.bam.bai b/test/coverage/one_block.bam.bai new file mode 100644 index 0000000000000000000000000000000000000000..0cb055b291408c0ef41010d67958293df0311741 GIT binary patch literal 96 wcmZ>A^kigYU|?VZVoxCk1`wNpAq7k_FuVfOUXvj5=;9EyP^CZ$RWC#w05|0Y4FCWD literal 0 HcmV?d00001 diff --git a/test/coverage/one_block.sam b/test/coverage/one_block.sam new file mode 100644 index 00000000..48408220 --- /dev/null +++ b/test/coverage/one_block.sam @@ -0,0 +1,3 @@ +@HD VN:1.0 GO:none SO:coordinate +@SQ SN:chr1 LN:1000 +one_blocks 16 chr1 1 40 30M * 0 0 GAAGGCCACCGCCGCGGTTATTTTCCTTCA CCCDDB?=FJIIJIGFJIJHIJJJJJJJJI MD:Z:50 \ No newline at end of file diff --git a/test/coverage/sam-w-del.bam.bai b/test/coverage/sam-w-del.bam.bai new file mode 100644 index 0000000000000000000000000000000000000000..eccb935b786ffac1a629e01faa26518bcb78fc30 GIT binary patch literal 96 wcmZ>A^kigYU|?VZVoxCk1`wNpAq7k_Fgyg)UXvj5=;9EyP^CZ$RWC#w05ll{`v3p{ literal 0 HcmV?d00001 diff --git a/test/coverage/sam-w-del.sam b/test/coverage/sam-w-del.sam new file mode 100644 index 00000000..887b745d --- /dev/null +++ b/test/coverage/sam-w-del.sam @@ -0,0 +1,3 @@ +@HD VN:1.0 GO:none SO:coordinate +@SQ SN:chr1 LN:1000 +one_bp_del 16 chr1 1 40 10M1D10M * 0 0 GAAGGCCACCGCCGCGCCGC CCCDDB?=FJIIJIGIIJIG MD:Z:50 diff --git a/test/coverage/test-coverage.sh b/test/coverage/test-coverage.sh new file mode 100644 index 00000000..969e1c1c --- /dev/null +++ b/test/coverage/test-coverage.sh @@ -0,0 +1,35 @@ +BT=../../bin/bedtools + +check() +{ + if diff $1 $2; then + echo ok + else + echo fail + fi +} + +########################################################### +########################################################### +# BAM files # +########################################################### +########################################################### +samtools view -Sb one_block.sam > one_block.bam 2>/dev/null +samtools view -Sb two_blocks.sam > two_blocks.bam 2>/dev/null +samtools view -Sb three_blocks.sam > three_blocks.bam 2>/dev/null +samtools view -Sb sam-w-del.sam > sam-w-del.bam 2>/dev/null + + + +################################################################## +# Test three blocks without -split +################################################################## +# echo " coverage.t1...\c" +# echo \ +# "chr1 0 50 1" > exp +# $BT coverage -abam three_blocks.bam -b three_blocks_nomatch.bed > obs +# check obs exp +# rm obs exp + + +rm *.bam \ No newline at end of file diff --git a/test/coverage/three_blocks.bam.bai b/test/coverage/three_blocks.bam.bai new file mode 100644 index 0000000000000000000000000000000000000000..c66d8f26184bfd73a6baf14f2169ad4ee9ab2dcd GIT binary patch literal 96 wcmZ>A^kigYU|?VZVoxCk1`wNpAq7k_FuVuTUXvj5=;9EyP^CZ$RWC#w06GB$7XSbN literal 0 HcmV?d00001 diff --git a/test/coverage/three_blocks.sam b/test/coverage/three_blocks.sam new file mode 100644 index 00000000..9bf1a627 --- /dev/null +++ b/test/coverage/three_blocks.sam @@ -0,0 +1,3 @@ +@HD VN:1.0 GO:none SO:coordinate +@SQ SN:chr1 LN:1000 +three_blocks 16 chr1 1 40 10M10N10M10N10M * 0 0 GAAGGCCACCGCCGCGGTTATTTTCCTTCA CCCDDB?=FJIIJIGFJIJHIJJJJJJJJI MD:Z:50 diff --git a/test/coverage/three_blocks_match.bed b/test/coverage/three_blocks_match.bed new file mode 100644 index 00000000..33123c2f --- /dev/null +++ b/test/coverage/three_blocks_match.bed @@ -0,0 +1 @@ +chr1 0 50 three_blocks_match 0 + 0 0 0 3 10,10,10, 0,20,40, diff --git a/test/coverage/three_blocks_match_1bp.bed b/test/coverage/three_blocks_match_1bp.bed new file mode 100644 index 00000000..de8b10d2 --- /dev/null +++ b/test/coverage/three_blocks_match_1bp.bed @@ -0,0 +1 @@ +chr1 10 60 three_blocks_nomatch 0 + 0 0 0 3 11,10,10, 0,20,40, diff --git a/test/coverage/three_blocks_nomatch.bed b/test/coverage/three_blocks_nomatch.bed new file mode 100644 index 00000000..1835260e --- /dev/null +++ b/test/coverage/three_blocks_nomatch.bed @@ -0,0 +1 @@ +chr1 10 60 three_blocks_nomatch 0 + 0 0 0 3 10,10,10, 0,20,40, diff --git a/test/coverage/two_blocks.bam.bai b/test/coverage/two_blocks.bam.bai new file mode 100644 index 0000000000000000000000000000000000000000..e2f6dc8ad52caaccb59b4580f44414ef3d3ea1c8 GIT binary patch literal 96 wcmZ>A^kigYU|?VZVoxCk1`wNpAq7k_FuVoRUXvj5=;9EyP^CZ$RWC#w068fI6951J literal 0 HcmV?d00001 diff --git a/test/coverage/two_blocks.sam b/test/coverage/two_blocks.sam new file mode 100644 index 00000000..a28928ab --- /dev/null +++ b/test/coverage/two_blocks.sam @@ -0,0 +1,3 @@ +@HD VN:1.0 GO:none SO:coordinate +@SQ SN:chr1 LN:1000 +two_blocks 16 chr1 1 40 15M10N15M * 0 0 GAAGGCCACCGCCGCGGTTATTTTCCTTCA CCCDDB?=FJIIJIGFJIJHIJJJJJJJJI MD:Z:50 \ No newline at end of file diff --git a/test/merge/a.full.bed b/test/merge/a.full.bed new file mode 100644 index 00000000..f877fca8 --- /dev/null +++ b/test/merge/a.full.bed @@ -0,0 +1,9 @@ +chr1 10 20 a1 1 + +chr1 30 40 a2 2 + +chr1 40 50 a3 3 - +chr1 45 100 a4 4 + +chr2 10 20 a1 5 + +chr2 30 40 a2 6 + +chr2 42 50 a3 7 + +chr2 45 100 a4 8 - +