From 2bbe31c0185ccc64fffa62ae4309e5598cd66a81 Mon Sep 17 00:00:00 2001 From: Ksenia Lavrichenko Date: Mon, 27 Jul 2026 21:34:11 +0200 Subject: [PATCH 1/2] Add cramino test data for #3603 --- .../cramino/PKD1_bead_test1_B.cramino.txt | 213 ++++++++++++++++++ .../toy_estimated_identity.cramino.txt | 30 +++ .../cramino/toy_no_contigs.cramino.txt | 23 ++ data/modules/cramino/toy_ubam.cramino.txt | 14 ++ 4 files changed, 280 insertions(+) create mode 100644 data/modules/cramino/PKD1_bead_test1_B.cramino.txt create mode 100644 data/modules/cramino/toy_estimated_identity.cramino.txt create mode 100644 data/modules/cramino/toy_no_contigs.cramino.txt create mode 100644 data/modules/cramino/toy_ubam.cramino.txt diff --git a/data/modules/cramino/PKD1_bead_test1_B.cramino.txt b/data/modules/cramino/PKD1_bead_test1_B.cramino.txt new file mode 100644 index 00000000..4a21b6b4 --- /dev/null +++ b/data/modules/cramino/PKD1_bead_test1_B.cramino.txt @@ -0,0 +1,213 @@ +File name PKD1_bead_test1_B_haplotagged.bam +Number of alignments 20564409 +% from total alignments 96.04 +Number of reads 20235704 +Yield [Gb] 15.34 +Mean coverage 4.95 +Yield [Gb] (>25kb) 1.89 +N50 633 +N75 527 +Median length 539.00 +Mean length 746.19 + +Median identity 99.41 +Mean identity 99.02 +Modal identity 100.0 + + + +# Normalized read count per chromosome + +chr1 0.84 +chr10 0.86 +chr11 0.83 +chr11_KI270721v1_random 0.32 +chr12 0.83 +chr13 0.76 +chr14 0.70 +chr14_GL000009v2_random 2.32 +chr14_GL000194v1_random 2.75 +chr14_GL000225v1_random 9.89 +chr14_KI270722v1_random 1.38 +chr14_KI270723v1_random 2.86 +chr14_KI270724v1_random 2.36 +chr14_KI270725v1_random 0.85 +chr14_KI270726v1_random 0.09 +chr15 0.69 +chr15_KI270727v1_random 0.41 +chr16 0.88 +chr16_KI270728v1_random 0.41 +chr17 0.82 +chr17_GL000205v2_random 2.25 +chr17_KI270729v1_random 2.92 +chr17_KI270730v1_random 1.33 +chr18 0.83 +chr19 0.80 +chr1_KI270706v1_random 1.18 +chr1_KI270707v1_random 1.09 +chr1_KI270708v1_random 0.55 +chr1_KI270709v1_random 16.18 +chr1_KI270710v1_random 1.41 +chr1_KI270711v1_random 2.24 +chr1_KI270712v1_random 1.00 +chr1_KI270713v1_random 2.45 +chr1_KI270714v1_random 0.69 +chr2 0.84 +chr20 0.86 +chr21 0.78 +chr22 0.64 +chr22_KI270731v1_random 0.62 +chr22_KI270732v1_random 2.46 +chr22_KI270733v1_random 7.82 +chr22_KI270734v1_random 0.92 +chr22_KI270735v1_random 2.87 +chr22_KI270736v1_random 2.10 +chr22_KI270737v1_random 0.69 +chr22_KI270738v1_random 1.24 +chr22_KI270739v1_random 0.47 +chr2_KI270715v1_random 0.64 +chr2_KI270716v1_random 0.31 +chr3 0.86 +chr3_GL000221v1_random 1.75 +chr4 0.84 +chr4_GL000008v2_random 1.53 +chr5 0.83 +chr5_GL000208v1_random 1.36 +chr6 0.83 +chr7 0.83 +chr8 0.83 +chr9 0.73 +chr9_KI270717v1_random 0.42 +chr9_KI270718v1_random 1.25 +chr9_KI270719v1_random 1.29 +chr9_KI270720v1_random 1.51 +chrM 71.44 +chrUn_GL000195v1 1.40 +chrUn_GL000213v1 0.31 +chrUn_GL000214v1 2.26 +chrUn_GL000216v2 5.17 +chrUn_GL000218v1 1.08 +chrUn_GL000219v1 2.27 +chrUn_GL000220v1 9.71 +chrUn_GL000224v1 5.20 +chrUn_GL000226v1 22.07 +chrUn_KI270302v1 0.59 +chrUn_KI270303v1 0.56 +chrUn_KI270304v1 0.22 +chrUn_KI270305v1 0.91 +chrUn_KI270310v1 9.72 +chrUn_KI270311v1 1.41 +chrUn_KI270315v1 0.11 +chrUn_KI270316v1 0.17 +chrUn_KI270317v1 0.05 +chrUn_KI270320v1 2.95 +chrUn_KI270322v1 0.31 +chrUn_KI270329v1 0.94 +chrUn_KI270330v1 17.16 +chrUn_KI270333v1 93.62 +chrUn_KI270334v1 4.80 +chrUn_KI270335v1 1.04 +chrUn_KI270336v1 42.45 +chrUn_KI270337v1 112.98 +chrUn_KI270338v1 0.34 +chrUn_KI270340v1 18.49 +chrUn_KI270362v1 0.76 +chrUn_KI270363v1 1.21 +chrUn_KI270364v1 0.60 +chrUn_KI270366v1 0.75 +chrUn_KI270371v1 0.17 +chrUn_KI270372v1 0.52 +chrUn_KI270373v1 0.25 +chrUn_KI270374v1 0.23 +chrUn_KI270375v1 0.36 +chrUn_KI270376v1 0.21 +chrUn_KI270378v1 0.23 +chrUn_KI270379v1 0.23 +chrUn_KI270381v1 0.38 +chrUn_KI270382v1 0.20 +chrUn_KI270383v1 0.07 +chrUn_KI270384v1 0.59 +chrUn_KI270385v1 0.37 +chrUn_KI270386v1 0.14 +chrUn_KI270387v1 0.16 +chrUn_KI270388v1 0.30 +chrUn_KI270390v1 0.20 +chrUn_KI270391v1 0.08 +chrUn_KI270392v1 0.13 +chrUn_KI270393v1 0.47 +chrUn_KI270394v1 0.50 +chrUn_KI270395v1 2.55 +chrUn_KI270396v1 0.06 +chrUn_KI270411v1 8.60 +chrUn_KI270412v1 1.24 +chrUn_KI270414v1 0.49 +chrUn_KI270417v1 1.07 +chrUn_KI270418v1 0.57 +chrUn_KI270419v1 0.71 +chrUn_KI270420v1 2.15 +chrUn_KI270422v1 0.93 +chrUn_KI270423v1 2.36 +chrUn_KI270424v1 0.17 +chrUn_KI270425v1 0.13 +chrUn_KI270429v1 3.04 +chrUn_KI270435v1 1.69 +chrUn_KI270438v1 29.54 +chrUn_KI270442v1 2.38 +chrUn_KI270448v1 1.57 +chrUn_KI270465v1 20.30 +chrUn_KI270466v1 163.50 +chrUn_KI270467v1 185.90 +chrUn_KI270468v1 1.56 +chrUn_KI270507v1 2.95 +chrUn_KI270508v1 3.93 +chrUn_KI270509v1 3.52 +chrUn_KI270510v1 3.93 +chrUn_KI270511v1 1.77 +chrUn_KI270512v1 2.16 +chrUn_KI270515v1 3.58 +chrUn_KI270516v1 2.62 +chrUn_KI270517v1 3.55 +chrUn_KI270518v1 2.89 +chrUn_KI270519v1 1.96 +chrUn_KI270521v1 0.88 +chrUn_KI270522v1 0.60 +chrUn_KI270528v1 0.69 +chrUn_KI270529v1 2.11 +chrUn_KI270530v1 1.01 +chrUn_KI270538v1 1.86 +chrUn_KI270539v1 0.37 +chrUn_KI270544v1 4.55 +chrUn_KI270548v1 0.46 +chrUn_KI270579v1 0.99 +chrUn_KI270580v1 3.53 +chrUn_KI270581v1 0.88 +chrUn_KI270582v1 0.95 +chrUn_KI270583v1 4.87 +chrUn_KI270584v1 3.96 +chrUn_KI270587v1 1.39 +chrUn_KI270588v1 2.23 +chrUn_KI270589v1 1.65 +chrUn_KI270590v1 5.97 +chrUn_KI270591v1 4.20 +chrUn_KI270593v1 1.68 +chrUn_KI270741v1 0.92 +chrUn_KI270742v1 2.46 +chrUn_KI270743v1 0.85 +chrUn_KI270744v1 4.45 +chrUn_KI270745v1 0.62 +chrUn_KI270746v1 2.42 +chrUn_KI270747v1 0.41 +chrUn_KI270748v1 0.66 +chrUn_KI270749v1 1.38 +chrUn_KI270750v1 1.25 +chrUn_KI270751v1 2.96 +chrUn_KI270753v1 1.28 +chrUn_KI270754v1 2.29 +chrUn_KI270755v1 0.61 +chrUn_KI270756v1 0.90 +chrUn_KI270757v1 2.54 +chrX 0.81 +chrY 0.02 + +Path /work/aligned_reads/PKD1_bead_test1_B/PKD1_bead_test1_B_haplotagged.bam +Creation time NA diff --git a/data/modules/cramino/toy_estimated_identity.cramino.txt b/data/modules/cramino/toy_estimated_identity.cramino.txt new file mode 100644 index 00000000..2ea9ce48 --- /dev/null +++ b/data/modules/cramino/toy_estimated_identity.cramino.txt @@ -0,0 +1,30 @@ +File name toy_estimated_identity.bam +Number of alignments 5000 +% from total alignments 98.50 +Number of reads 4950 +Yield [Gb] 0.05 +Mean coverage 1.20 +Yield [Gb] (>25kb) 0.01 +N50 11000 +N75 8500 +Median length 9800.00 +Mean length 10100.25 + +Median est. identity 98.70 +Mean est. identity 98.40 +Modal est. identity 99.0 + + + +# Normalized read count per chromosome + +chr1 0.95 +chr2 1.02 +chrX 0.48 +chrY 0.01 +chrM 85.30 +chr1_KI270706v1_random 1.10 +chrUn_KI270333v1 42.00 + +Path /work/toy_estimated_identity.bam +Creation time NA diff --git a/data/modules/cramino/toy_no_contigs.cramino.txt b/data/modules/cramino/toy_no_contigs.cramino.txt new file mode 100644 index 00000000..ee02eaa2 --- /dev/null +++ b/data/modules/cramino/toy_no_contigs.cramino.txt @@ -0,0 +1,23 @@ +File name toy_no_contigs.bam +Number of alignments 200 +% from total alignments 100.00 +Number of reads 200 +Yield [Gb] 0.001 +Mean coverage 0.00 +Yield [Gb] (>25kb) 0.00 +N50 800 +N75 650 +Median length 700.00 +Mean length 720.10 + +Median identity 95.20 +Mean identity 94.80 +Modal identity 96.0 + + + +# Warning - no contigs found in BAM file! + + +Path /work/toy_no_contigs.bam +Creation time NA diff --git a/data/modules/cramino/toy_ubam.cramino.txt b/data/modules/cramino/toy_ubam.cramino.txt new file mode 100644 index 00000000..1f4ea111 --- /dev/null +++ b/data/modules/cramino/toy_ubam.cramino.txt @@ -0,0 +1,14 @@ +File name toy_ubam.bam +Number of alignments 1000 +% from total alignments 100.00 +Number of reads 1000 +Yield [Gb] 0.01 +Mean coverage 0.00 +Yield [Gb] (>25kb) 0.00 +N50 12000 +N75 9000 +Median length 10500.00 +Mean length 10800.50 + +Path /work/toy_ubam.bam +Creation time NA From cf78c0883ecf4a1258ef21a17ab40ac3dae9a22c Mon Sep 17 00:00:00 2001 From: Ksenia Lavrichenko Date: Mon, 27 Jul 2026 21:37:39 +0200 Subject: [PATCH 2/2] Rename real sample fixture and scrub identifying fields --- ...t1_B.cramino.txt => example_aligned_karyotype.cramino.txt} | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) rename data/modules/cramino/{PKD1_bead_test1_B.cramino.txt => example_aligned_karyotype.cramino.txt} (97%) diff --git a/data/modules/cramino/PKD1_bead_test1_B.cramino.txt b/data/modules/cramino/example_aligned_karyotype.cramino.txt similarity index 97% rename from data/modules/cramino/PKD1_bead_test1_B.cramino.txt rename to data/modules/cramino/example_aligned_karyotype.cramino.txt index 4a21b6b4..89e35afa 100644 --- a/data/modules/cramino/PKD1_bead_test1_B.cramino.txt +++ b/data/modules/cramino/example_aligned_karyotype.cramino.txt @@ -1,4 +1,4 @@ -File name PKD1_bead_test1_B_haplotagged.bam +File name example_aligned.bam Number of alignments 20564409 % from total alignments 96.04 Number of reads 20235704 @@ -209,5 +209,5 @@ chrUn_KI270757v1 2.54 chrX 0.81 chrY 0.02 -Path /work/aligned_reads/PKD1_bead_test1_B/PKD1_bead_test1_B_haplotagged.bam +Path /work/aligned_reads/example_aligned/example_aligned.bam Creation time NA