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daviesrobwhitwham
daviesrob
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whitwham
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Change sort order for trio-dnm3 test file
The trio-dnm3.1.out file was sorted using `-k4,4g`, which is an extension to the POSIX specification. While widely supported, it isn't available everywhere leading to test failures on some platforms. As the ordering isn't that important for the purposes of the test, the easiest solution is to sort it by the filename in the first column instead.
1 parent f3e12f6 commit 7813ff9

2 files changed

Lines changed: 37 additions & 36 deletions

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‎test/trio-dnm3.1.out‎

Lines changed: 35 additions & 35 deletions
Original file line numberDiff line numberDiff line change
@@ -1,49 +1,49 @@
1-
dnm21.vcf chr16:28606650 - -inf . . 61 0 100 11,7 0,0 18,0 T,C 0 . . . . .
2-
dnm23.vcf chr9:41644187 - -inf . . 88 0 100 29,4 0,0 20,0 T,A 0 . . . . .
3-
dnm38.vcf chrX:49689611 - -inf . . 33 0 50 4,8 0,0 1,1 T,C 0 . . . . .
4-
dnm17.vcf chrX:141906066 - -544.123 . . 66 0 26 29,57 77,0 168,59 C,G 1 . . . . .
1+
dnm01.vcf chr8:120811802 o -0.764704 . . 18 0 0 9,2,0 71,0,1 56,0,1 G,T,A 1 . . . . .
2+
dnm06.vcf chr6:32522150 - -1.7168 . . 100 0 0 0,26,0,0 1,0,9,0 23,0,0,1 T,G,A,C 1 . . . . .
3+
dnm07.vcf chr9:19094217 --unk -7.01979 . . 62 0 0 4,8,1 3,0,0 13,0,0 G,A,T 1 . . . . .
4+
dnm09.vcf chr2:219571274 - -17.5276 . . 50 0 0 3,5,1,1 9,0,8,2 11,0,4,4 A,G,T,C 1 . . . . .
5+
dnm10.vcf chr8:30846433 o -0.000201919 . . 41 0 0 41,29,1 69,0,0 52,0,0 C,G,T 1 . . . . .
6+
dnm11.vcf chr10:104250407 - -74.5666 . . 66 3 11 19,37 28,1 78,10 G,C 1 . . . . .
57
dnm12.vcf chr6:32581812 - -330.706 . . 31 8 16 110,50 206,19 140,27 A,C 1 . . . . .
8+
dnm13.vcf chrX:68112092 - -17.7637 . . 100 0 0 8,0 0,5 0,1 G,C 0 . . . . .
9+
dnm14.vcf chr12:27401766 - -11.8629 . . 100 0 0 0,14 4,0 5,0 G,A 1 . . . . .
610
dnm15.vcf chr6:32581810 - -124.562 . . 18 11 0 178,40 174,22 36,0 T,G 1 . . . . .
711
dnm16.vcf chr6:32761865 - -88.0806 . . 19 11 0 101,0,24 59,66,16 91,0,0 G,C,A 2 . . . . .
8-
dnm11.vcf chr10:104250407 - -74.5666 . . 66 3 11 19,37 28,1 78,10 G,C 1 . . . . .
9-
dnm13.vcf chrX:68112092 - -17.7637 . . 100 0 0 8,0 0,5 0,1 G,C 0 . . . . .
10-
dnm09.vcf chr2:219571274 - -17.5276 . . 50 0 0 3,5,1,1 9,0,8,2 11,0,4,4 A,G,T,C 1 . . . . .
12+
dnm17.vcf chrX:141906066 - -544.123 . . 66 0 26 29,57 77,0 168,59 C,G 1 . . . . .
1113
dnm18.vcf chr11:71527372 - -15.1104 . . 24 4 0 116,37,1 149,7,0 101,0,1 T,C,G 1 . . . . .
12-
dnm22.vcf chr11:71527372 - -15.1104 . . 24 4 0 116,37,1 149,7,0 101,0,1 T,C,G 1 . . . . .
13-
dnm32.vcf chrM:9899 - -13.155 . . 37 0 2 198,117,1,0 319,0,0,1 313,8,0,0 T,C,A,G 1 . . . . .
14-
dnm14.vcf chr12:27401766 - -11.8629 . . 100 0 0 0,14 4,0 5,0 G,A 1 . . . . .
15-
dnm41.vcf chr1:930055 - -9.54764 . . 100 0 0 0,6 4,0 1,0 C,G 1 . . . . .
1614
dnm19.vcf chr2:165310656 --unk -8.82426 . . 100 0 0 0,9 2,0 7,0 T,A 1 . . . . .
17-
dnm36.vcf chr16:58041597 o-ma -7.22407 . . 49 0 0 30,33,4 58,0,0 43,0,0 G,A,T 1 . . . . .
18-
dnm07.vcf chr9:19094217 --unk -7.01979 . . 62 0 0 4,8,1 3,0,0 13,0,0 G,A,T 1 . . . . .
1915
dnm20.vcf chr7:98949906 --unk -6.33187 . . 70 0 0 8,19 4,0 17,0 C,T 1 . . . . .
20-
dnm30.vcf chr19:13978125 o-mosaic -3.16171 . . 13 0 0 14,2 24,0 26,0 G,A 1 . . . . .
21-
dnm27.vcf chr17:81536135 o-mosaic -2.37269 . . 10 0 0 26,3 45,0 39,0 G,A 1 . . . . .
16+
dnm21.vcf chr16:28606650 - -inf . . 61 0 100 11,7 0,0 18,0 T,C 0 . . . . .
17+
dnm22.vcf chr11:71527372 - -15.1104 . . 24 4 0 116,37,1 149,7,0 101,0,1 T,C,G 1 . . . . .
18+
dnm23.vcf chr9:41644187 - -inf . . 88 0 100 29,4 0,0 20,0 T,A 0 . . . . .
2219
dnm24.vcf chr19:54775322 - -1.90049 . . 13 0 0 109,17 95,0 86,0 G,C 1 . . . . .
23-
dnm06.vcf chr6:32522150 - -1.7168 . . 100 0 0 0,26,0,0 1,0,9,0 23,0,0,1 T,G,A,C 1 . . . . .
24-
dnm28.vcf chr16:2210587 o-mosaic -1.70308 . . 13 0 0 28,4 62,0 43,0 G,C 1 . . . . .
25-
dnm45.vcf chr17:38802154 o-mosaic -1.3055 . . 16 0 0 48,9,0 71,0,0 65,0,1 G,A,T 1 . . . . .
2620
dnm25.vcf chr3:48419708 o-mosaic -1.17026 . . 16 0 0 56,11,1 80,0,0 70,0,0 C,G,T 1 . . . . .
27-
dnm42.vcf chr1:151306305 o-mosaic -1.07353 . . 17 0 0 59,12,1 66,0,0 58,0,0 A,C,T 1 . . . . .
28-
dnm01.vcf chr8:120811802 o -0.764704 . . 18 0 0 9,2,0 71,0,1 56,0,1 G,T,A 1 . . . . .
21+
dnm26.vcf chr19:43071662 o -5.06194e-07 . . 51 0 0 38,39 117,0 101,0 C,A 1 . . . . .
22+
dnm27.vcf chr17:81536135 o-mosaic -2.37269 . . 10 0 0 26,3 45,0 39,0 G,A 1 . . . . .
23+
dnm28.vcf chr16:2210587 o-mosaic -1.70308 . . 13 0 0 28,4 62,0 43,0 G,C 1 . . . . .
2924
dnm29.vcf chr1:39901935 --unk -0.457031 . . 23 0 0 10,3 22,0 26,0 G,C 1 . . . . .
30-
dnm40.vcf chr1:35192655 o -0.336011 . . 23 0 0 62,18 92,0 67,0 G,A 1 . . . . .
31-
dnm51.vcf chr11:62604250 o-pdp -0.253838 . . 46 0 0 13,11 15,0 23,0 G,A 1 . . . . .
32-
dnm50.vcf chr1:39452137 o-mosaic -0.209761 . . 26 0 0 17,6 31,0 25,0 C,T 1 . . . . .
33-
dnm53.vcf chr18:31466562 --unk -0.206326 . . 29 0 0 37,15 57,0 48,0 T,G 1 . . 65 0 0
25+
dnm30.vcf chr19:13978125 o-mosaic -3.16171 . . 13 0 0 14,2 24,0 26,0 G,A 1 . . . . .
26+
dnm31.vcf chr7:114922376 o -0.124865 . . 50 0 5 17,17 30,0 20,1 G,A 1 . . . . .
27+
dnm32.vcf chrM:9899 - -13.155 . . 37 0 2 198,117,1,0 319,0,0,1 313,8,0,0 T,C,A,G 1 . . . . .
3428
dnm33.vcf chr6:32518660 - -0.176899 . . 27 0 5 40,15 23,0 42,2 T,C 1 . . . . .
29+
dnm34.vcf chr16:90035660 o -2.39592e-05 . . 45 3 0 44,36 67,2 82,0 C,T 1 . . . . .
30+
dnm35.vcf chr2:95951365 - -0.00159963 . . 38 4 0 60,36 45,2 64,0 G,A 1 . . . . .
31+
dnm36.vcf chr16:58041597 o-ma -7.22407 . . 49 0 0 30,33,4 58,0,0 43,0,0 G,A,T 1 . . . . .
3532
dnm37.vcf chr19:54751586 - -0.172621 . . 57 0 3 3,4 16,0 28,1 G,A 1 . . . . .
36-
dnm43.vcf chr7:74097029 o -0.144411 . . 48 0 0 15,14 16,0 48,0 G,A 1 . . . . .
37-
dnm52.vcf chr11:64320638 o-pdp -0.144198 . . 56 0 0 12,15 16,0 34,0 G,A 1 . . . . .
38-
dnm31.vcf chr7:114922376 o -0.124865 . . 50 0 5 17,17 30,0 20,1 G,A 1 . . . . .
33+
dnm38.vcf chrX:49689611 - -inf . . 33 0 50 4,8 0,0 1,1 T,C 0 . . . . .
3934
dnm39.vcf chr6:31356309 - -0.121649 . . 100 4 3 0,5 24,1 37,1 G,C 1 . . . . .
40-
dnm49.vcf chr21:39312993 - -0.10072 . . 29 0 0 22,9 21,0 23,0 G,C 1 . . . . .
41-
dnm54.vcf chr2:232380380 o -0.00690831 . . 51 0 0 34,35,0 41,0,36 74,0,0 A,C,G 1 . . 3 4 0
42-
dnm48.vcf chr3:195783381 - -0.00176814 . . 54 0 0 19,22 16,0 27,0 G,C 1 . . . . .
43-
dnm35.vcf chr2:95951365 - -0.00159963 . . 38 4 0 60,36 45,2 64,0 G,A 1 . . . . .
44-
dnm10.vcf chr8:30846433 o -0.000201919 . . 41 0 0 41,29,1 69,0,0 52,0,0 C,G,T 1 . . . . .
45-
dnm46.vcf chr9:137114271 o -3.01723e-05 . . 45 0 2 27,22 54,0 65,1 C,T 1 . . . . .
46-
dnm34.vcf chr16:90035660 o -2.39592e-05 . . 45 3 0 44,36 67,2 82,0 C,T 1 . . . . .
35+
dnm40.vcf chr1:35192655 o -0.336011 . . 23 0 0 62,18 92,0 67,0 G,A 1 . . . . .
36+
dnm41.vcf chr1:930055 - -9.54764 . . 100 0 0 0,6 4,0 1,0 C,G 1 . . . . .
37+
dnm42.vcf chr1:151306305 o-mosaic -1.07353 . . 17 0 0 59,12,1 66,0,0 58,0,0 A,C,T 1 . . . . .
38+
dnm43.vcf chr7:74097029 o -0.144411 . . 48 0 0 15,14 16,0 48,0 G,A 1 . . . . .
4739
dnm44.vcf chr18:76910115 o -8.46558e-07 . . 50 0 1 46,46,0 39,0,0 88,1,1 T,A,G 1 . . . . .
48-
dnm26.vcf chr19:43071662 o -5.06194e-07 . . 51 0 0 38,39 117,0 101,0 C,A 1 . . . . .
40+
dnm45.vcf chr17:38802154 o-mosaic -1.3055 . . 16 0 0 48,9,0 71,0,0 65,0,1 G,A,T 1 . . . . .
41+
dnm46.vcf chr9:137114271 o -3.01723e-05 . . 45 0 2 27,22 54,0 65,1 C,T 1 . . . . .
4942
dnm47.vcf chrX:136240391 o -2.09988e-08 . . 100 0 0 0,37 26,0 61,0 C,T 1 . . . . .
43+
dnm48.vcf chr3:195783381 - -0.00176814 . . 54 0 0 19,22 16,0 27,0 G,C 1 . . . . .
44+
dnm49.vcf chr21:39312993 - -0.10072 . . 29 0 0 22,9 21,0 23,0 G,C 1 . . . . .
45+
dnm50.vcf chr1:39452137 o-mosaic -0.209761 . . 26 0 0 17,6 31,0 25,0 C,T 1 . . . . .
46+
dnm51.vcf chr11:62604250 o-pdp -0.253838 . . 46 0 0 13,11 15,0 23,0 G,A 1 . . . . .
47+
dnm52.vcf chr11:64320638 o-pdp -0.144198 . . 56 0 0 12,15 16,0 34,0 G,A 1 . . . . .
48+
dnm53.vcf chr18:31466562 --unk -0.206326 . . 29 0 0 37,15 57,0 48,0 T,G 1 . . 65 0 0
49+
dnm54.vcf chr2:232380380 o -0.00690831 . . 51 0 0 34,35,0 41,0,36 74,0,0 A,C,G 1 . . 3 4 0

‎test/trio-dnm3/test.sh‎

Lines changed: 2 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -3,8 +3,9 @@
33
cd "$(dirname "${BASH_SOURCE[0]}")"
44

55
BCFTOOLS=${1:-bcftools}
6+
export LC_ALL=C
67

78
for x in *.vcf; do
89
"$BCFTOOLS" +trio-dnm3 -p 1X:child,dad,mom $x | "$BCFTOOLS" query -uf$x'\t%CHROM:%POS\t%EXP\t[ %DNM]\t[ %VAF]\t[ %AD]\t%REF,%ALT\t[ %VA]\t[ %SP]';
9-
done | sort -k3,3g -k4,4g -k3,3d | sed 's,fp,-, ; s,tp,o,'
10+
done | sort | sed 's,fp,-, ; s,tp,o,'
1011

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