1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
|
#! /bin/sh
# Regression tests
cd $(dirname $0)
PATH=../bin:$PATH
r=maf-convert
maf1=SRR359290-1k.maf
maf2=bs100.maf
{
$r -h
head -n999 $maf1 | $r axt
maf-convert axt toprev.maf
head -n999 $maf1 | $r blast
head -n999 $maf1 | $r -l100 blast
$r blast $maf2
$r -l120 blast frameshift-new.maf
tail -n8 frameshift-new.maf | maf-swap | $r blast
tail -n8 frameshift-new.maf | $r -s2 blast
$r -l159 blast herv30.maf
$r -l120 blast HERVS71A.maf # test ambiguous N bases
$r blasttab $maf2
$r blasttab+ frameshift-new.maf
$r -s2 blasttab frameshift-new.maf
maf-cut DF0000170.5:633-798 herv30.maf | $r blasttab # gaps at edges
maf-cut DF0000170.5:633-798 herv30.maf | $r -s2 blasttab # gaps at edges
head -n999 $maf1 | $r chain
$r gff 102.maf
$r -J1e9 gff 102.maf
$r -J1e9 -s2 gff 102.maf
$r gff frameshift-new.maf
$r -J1e9 -s2 bed 102.maf
$r html -l100 $maf2
head -n999 $maf1 | $r -n html
head -n999 $maf1 | $r psl
head -n999 $maf1 | $r -p psl
$r psl $maf2
$r -j1e9 psl 102.maf
$r -j1e9 -s2 psl 102.maf
$r -J1e9 psl 102.maf
$r psl 90089.maf
$r psl frameshift-old.maf
$r psl frameshift-new.maf
$r -s1 psl frameshift-new.maf
$r -n sam $maf2
head -n999 $maf1 | $r -r 'ID:1 PL:ILLUMINA SM:x' sam
$r -d sam $maf1
$r -j1e9 sam 90089.maf 102.maf
$r sam toprev.maf
$r sam homSap-monDom.maf
head -n999 $maf1 | $r -n tab
head -n999 $maf1 | $r tab
$r -n tab frameshift-new.maf
} | diff -u maf-convert-test.out -
|
