From c66024665459c440c3b985e878646c4fd1eb7cb1 Mon Sep 17 00:00:00 2001 From: Rob Davies Date: Mon, 22 Jun 2026 12:10:31 +0100 Subject: [PATCH] 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. --- test/trio-dnm3.1.out | 70 +++++++++++++++++++++--------------------- test/trio-dnm3/test.sh | 3 +- 2 files changed, 37 insertions(+), 36 deletions(-) diff --git a/test/trio-dnm3.1.out b/test/trio-dnm3.1.out index dc2d824bd..01e92c030 100644 --- a/test/trio-dnm3.1.out +++ b/test/trio-dnm3.1.out @@ -1,49 +1,49 @@ -dnm21.vcf chr16:28606650 - -inf . . 61 0 100 11,7 0,0 18,0 T,C 0 . . . . . -dnm23.vcf chr9:41644187 - -inf . . 88 0 100 29,4 0,0 20,0 T,A 0 . . . . . -dnm38.vcf chrX:49689611 - -inf . . 33 0 50 4,8 0,0 1,1 T,C 0 . . . . . -dnm17.vcf chrX:141906066 - -544.123 . . 66 0 26 29,57 77,0 168,59 C,G 1 . . . . . +dnm01.vcf chr8:120811802 o -0.764704 . . 18 0 0 9,2,0 71,0,1 56,0,1 G,T,A 1 . . . . . +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 . . . . . +dnm07.vcf chr9:19094217 --unk -7.01979 . . 62 0 0 4,8,1 3,0,0 13,0,0 G,A,T 1 . . . . . +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 . . . . . +dnm10.vcf chr8:30846433 o -0.000201919 . . 41 0 0 41,29,1 69,0,0 52,0,0 C,G,T 1 . . . . . +dnm11.vcf chr10:104250407 - -74.5666 . . 66 3 11 19,37 28,1 78,10 G,C 1 . . . . . dnm12.vcf chr6:32581812 - -330.706 . . 31 8 16 110,50 206,19 140,27 A,C 1 . . . . . +dnm13.vcf chrX:68112092 - -17.7637 . . 100 0 0 8,0 0,5 0,1 G,C 0 . . . . . +dnm14.vcf chr12:27401766 - -11.8629 . . 100 0 0 0,14 4,0 5,0 G,A 1 . . . . . dnm15.vcf chr6:32581810 - -124.562 . . 18 11 0 178,40 174,22 36,0 T,G 1 . . . . . dnm16.vcf chr6:32761865 - -88.0806 . . 19 11 0 101,0,24 59,66,16 91,0,0 G,C,A 2 . . . . . -dnm11.vcf chr10:104250407 - -74.5666 . . 66 3 11 19,37 28,1 78,10 G,C 1 . . . . . -dnm13.vcf chrX:68112092 - -17.7637 . . 100 0 0 8,0 0,5 0,1 G,C 0 . . . . . -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 . . . . . +dnm17.vcf chrX:141906066 - -544.123 . . 66 0 26 29,57 77,0 168,59 C,G 1 . . . . . dnm18.vcf chr11:71527372 - -15.1104 . . 24 4 0 116,37,1 149,7,0 101,0,1 T,C,G 1 . . . . . -dnm22.vcf chr11:71527372 - -15.1104 . . 24 4 0 116,37,1 149,7,0 101,0,1 T,C,G 1 . . . . . -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 . . . . . -dnm14.vcf chr12:27401766 - -11.8629 . . 100 0 0 0,14 4,0 5,0 G,A 1 . . . . . -dnm41.vcf chr1:930055 - -9.54764 . . 100 0 0 0,6 4,0 1,0 C,G 1 . . . . . dnm19.vcf chr2:165310656 --unk -8.82426 . . 100 0 0 0,9 2,0 7,0 T,A 1 . . . . . -dnm36.vcf chr16:58041597 o-ma -7.22407 . . 49 0 0 30,33,4 58,0,0 43,0,0 G,A,T 1 . . . . . -dnm07.vcf chr9:19094217 --unk -7.01979 . . 62 0 0 4,8,1 3,0,0 13,0,0 G,A,T 1 . . . . . dnm20.vcf chr7:98949906 --unk -6.33187 . . 70 0 0 8,19 4,0 17,0 C,T 1 . . . . . -dnm30.vcf chr19:13978125 o-mosaic -3.16171 . . 13 0 0 14,2 24,0 26,0 G,A 1 . . . . . -dnm27.vcf chr17:81536135 o-mosaic -2.37269 . . 10 0 0 26,3 45,0 39,0 G,A 1 . . . . . +dnm21.vcf chr16:28606650 - -inf . . 61 0 100 11,7 0,0 18,0 T,C 0 . . . . . +dnm22.vcf chr11:71527372 - -15.1104 . . 24 4 0 116,37,1 149,7,0 101,0,1 T,C,G 1 . . . . . +dnm23.vcf chr9:41644187 - -inf . . 88 0 100 29,4 0,0 20,0 T,A 0 . . . . . dnm24.vcf chr19:54775322 - -1.90049 . . 13 0 0 109,17 95,0 86,0 G,C 1 . . . . . -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 . . . . . -dnm28.vcf chr16:2210587 o-mosaic -1.70308 . . 13 0 0 28,4 62,0 43,0 G,C 1 . . . . . -dnm45.vcf chr17:38802154 o-mosaic -1.3055 . . 16 0 0 48,9,0 71,0,0 65,0,1 G,A,T 1 . . . . . dnm25.vcf chr3:48419708 o-mosaic -1.17026 . . 16 0 0 56,11,1 80,0,0 70,0,0 C,G,T 1 . . . . . -dnm42.vcf chr1:151306305 o-mosaic -1.07353 . . 17 0 0 59,12,1 66,0,0 58,0,0 A,C,T 1 . . . . . -dnm01.vcf chr8:120811802 o -0.764704 . . 18 0 0 9,2,0 71,0,1 56,0,1 G,T,A 1 . . . . . +dnm26.vcf chr19:43071662 o -5.06194e-07 . . 51 0 0 38,39 117,0 101,0 C,A 1 . . . . . +dnm27.vcf chr17:81536135 o-mosaic -2.37269 . . 10 0 0 26,3 45,0 39,0 G,A 1 . . . . . +dnm28.vcf chr16:2210587 o-mosaic -1.70308 . . 13 0 0 28,4 62,0 43,0 G,C 1 . . . . . dnm29.vcf chr1:39901935 --unk -0.457031 . . 23 0 0 10,3 22,0 26,0 G,C 1 . . . . . -dnm40.vcf chr1:35192655 o -0.336011 . . 23 0 0 62,18 92,0 67,0 G,A 1 . . . . . -dnm51.vcf chr11:62604250 o-pdp -0.253838 . . 46 0 0 13,11 15,0 23,0 G,A 1 . . . . . -dnm50.vcf chr1:39452137 o-mosaic -0.209761 . . 26 0 0 17,6 31,0 25,0 C,T 1 . . . . . -dnm53.vcf chr18:31466562 --unk -0.206326 . . 29 0 0 37,15 57,0 48,0 T,G 1 . . 65 0 0 +dnm30.vcf chr19:13978125 o-mosaic -3.16171 . . 13 0 0 14,2 24,0 26,0 G,A 1 . . . . . +dnm31.vcf chr7:114922376 o -0.124865 . . 50 0 5 17,17 30,0 20,1 G,A 1 . . . . . +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 . . . . . dnm33.vcf chr6:32518660 - -0.176899 . . 27 0 5 40,15 23,0 42,2 T,C 1 . . . . . +dnm34.vcf chr16:90035660 o -2.39592e-05 . . 45 3 0 44,36 67,2 82,0 C,T 1 . . . . . +dnm35.vcf chr2:95951365 - -0.00159963 . . 38 4 0 60,36 45,2 64,0 G,A 1 . . . . . +dnm36.vcf chr16:58041597 o-ma -7.22407 . . 49 0 0 30,33,4 58,0,0 43,0,0 G,A,T 1 . . . . . dnm37.vcf chr19:54751586 - -0.172621 . . 57 0 3 3,4 16,0 28,1 G,A 1 . . . . . -dnm43.vcf chr7:74097029 o -0.144411 . . 48 0 0 15,14 16,0 48,0 G,A 1 . . . . . -dnm52.vcf chr11:64320638 o-pdp -0.144198 . . 56 0 0 12,15 16,0 34,0 G,A 1 . . . . . -dnm31.vcf chr7:114922376 o -0.124865 . . 50 0 5 17,17 30,0 20,1 G,A 1 . . . . . +dnm38.vcf chrX:49689611 - -inf . . 33 0 50 4,8 0,0 1,1 T,C 0 . . . . . dnm39.vcf chr6:31356309 - -0.121649 . . 100 4 3 0,5 24,1 37,1 G,C 1 . . . . . -dnm49.vcf chr21:39312993 - -0.10072 . . 29 0 0 22,9 21,0 23,0 G,C 1 . . . . . -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 -dnm48.vcf chr3:195783381 - -0.00176814 . . 54 0 0 19,22 16,0 27,0 G,C 1 . . . . . -dnm35.vcf chr2:95951365 - -0.00159963 . . 38 4 0 60,36 45,2 64,0 G,A 1 . . . . . -dnm10.vcf chr8:30846433 o -0.000201919 . . 41 0 0 41,29,1 69,0,0 52,0,0 C,G,T 1 . . . . . -dnm46.vcf chr9:137114271 o -3.01723e-05 . . 45 0 2 27,22 54,0 65,1 C,T 1 . . . . . -dnm34.vcf chr16:90035660 o -2.39592e-05 . . 45 3 0 44,36 67,2 82,0 C,T 1 . . . . . +dnm40.vcf chr1:35192655 o -0.336011 . . 23 0 0 62,18 92,0 67,0 G,A 1 . . . . . +dnm41.vcf chr1:930055 - -9.54764 . . 100 0 0 0,6 4,0 1,0 C,G 1 . . . . . +dnm42.vcf chr1:151306305 o-mosaic -1.07353 . . 17 0 0 59,12,1 66,0,0 58,0,0 A,C,T 1 . . . . . +dnm43.vcf chr7:74097029 o -0.144411 . . 48 0 0 15,14 16,0 48,0 G,A 1 . . . . . dnm44.vcf chr18:76910115 o -8.46558e-07 . . 50 0 1 46,46,0 39,0,0 88,1,1 T,A,G 1 . . . . . -dnm26.vcf chr19:43071662 o -5.06194e-07 . . 51 0 0 38,39 117,0 101,0 C,A 1 . . . . . +dnm45.vcf chr17:38802154 o-mosaic -1.3055 . . 16 0 0 48,9,0 71,0,0 65,0,1 G,A,T 1 . . . . . +dnm46.vcf chr9:137114271 o -3.01723e-05 . . 45 0 2 27,22 54,0 65,1 C,T 1 . . . . . dnm47.vcf chrX:136240391 o -2.09988e-08 . . 100 0 0 0,37 26,0 61,0 C,T 1 . . . . . +dnm48.vcf chr3:195783381 - -0.00176814 . . 54 0 0 19,22 16,0 27,0 G,C 1 . . . . . +dnm49.vcf chr21:39312993 - -0.10072 . . 29 0 0 22,9 21,0 23,0 G,C 1 . . . . . +dnm50.vcf chr1:39452137 o-mosaic -0.209761 . . 26 0 0 17,6 31,0 25,0 C,T 1 . . . . . +dnm51.vcf chr11:62604250 o-pdp -0.253838 . . 46 0 0 13,11 15,0 23,0 G,A 1 . . . . . +dnm52.vcf chr11:64320638 o-pdp -0.144198 . . 56 0 0 12,15 16,0 34,0 G,A 1 . . . . . +dnm53.vcf chr18:31466562 --unk -0.206326 . . 29 0 0 37,15 57,0 48,0 T,G 1 . . 65 0 0 +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 diff --git a/test/trio-dnm3/test.sh b/test/trio-dnm3/test.sh index 067d5c01f..7caf09378 100755 --- a/test/trio-dnm3/test.sh +++ b/test/trio-dnm3/test.sh @@ -3,8 +3,9 @@ cd "$(dirname "${BASH_SOURCE[0]}")" BCFTOOLS=${1:-bcftools} +export LC_ALL=C for x in *.vcf; do "$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]'; -done | sort -k3,3g -k4,4g -k3,3d | sed 's,fp,-, ; s,tp,o,' +done | sort | sed 's,fp,-, ; s,tp,o,'