From 04828d1afb070eaf00070cb02b97bc938f4d56ba Mon Sep 17 00:00:00 2001 From: Ari Frantz Date: Tue, 25 Aug 2026 10:23:48 -0400 Subject: [PATCH 1/3] commit FASTA --- test/fixtures/reference/gencode.v50.BCR_ABL1.transcripts.fa | 3 +++ 1 file changed, 3 insertions(+) create mode 100644 test/fixtures/reference/gencode.v50.BCR_ABL1.transcripts.fa diff --git a/test/fixtures/reference/gencode.v50.BCR_ABL1.transcripts.fa b/test/fixtures/reference/gencode.v50.BCR_ABL1.transcripts.fa new file mode 100644 index 000000000..659daaa14 --- /dev/null +++ b/test/fixtures/reference/gencode.v50.BCR_ABL1.transcripts.fa @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:f25546f7e1ef28fba36dc906fa783109a3850d3134eab6ad790395352b22e9a1 +size 104005 From 8a93a8b78e45ba9f7b79492e1293f2a1b78860b1 Mon Sep 17 00:00:00 2001 From: Ari Frantz Date: Tue, 25 Aug 2026 10:26:52 -0400 Subject: [PATCH 2/3] README --- test/fixtures/reference/README.md | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/test/fixtures/reference/README.md b/test/fixtures/reference/README.md index 1bca8c115..f8462d96a 100644 --- a/test/fixtures/reference/README.md +++ b/test/fixtures/reference/README.md @@ -20,6 +20,10 @@ Unheadered 2 column TSV file containing genelengths with `gene_name` labels from Gencode v31 release GTF (or GFFv2) file, subsetted to only contain annotations for `chrY` and `chrM`. Gzipped. +## gencode.v50.BCR_ABL1.transcripts.fa + +Gencode v50 release protein-coding transcript sequences FASTA, subsetted to only contain sequences from the genes BCR and ABL1. + ## GRCh38.chr1_chr19.dict Sequence dictionary for GRCh38 reference containing `chr1` and `chr19` only From a5299aee05f97a65bd6344dd9b67c76abed8d32a Mon Sep 17 00:00:00 2001 From: Ari Frantz Date: Tue, 25 Aug 2026 10:29:45 -0400 Subject: [PATCH 3/3] gzip FASTA --- test/fixtures/reference/README.md | 4 ++-- test/fixtures/reference/gencode.v50.BCR_ABL1.transcripts.fa | 3 --- .../fixtures/reference/gencode.v50.BCR_ABL1.transcripts.fa.gz | 3 +++ 3 files changed, 5 insertions(+), 5 deletions(-) delete mode 100644 test/fixtures/reference/gencode.v50.BCR_ABL1.transcripts.fa create mode 100644 test/fixtures/reference/gencode.v50.BCR_ABL1.transcripts.fa.gz diff --git a/test/fixtures/reference/README.md b/test/fixtures/reference/README.md index f8462d96a..f6b948dc6 100644 --- a/test/fixtures/reference/README.md +++ b/test/fixtures/reference/README.md @@ -20,9 +20,9 @@ Unheadered 2 column TSV file containing genelengths with `gene_name` labels from Gencode v31 release GTF (or GFFv2) file, subsetted to only contain annotations for `chrY` and `chrM`. Gzipped. -## gencode.v50.BCR_ABL1.transcripts.fa +## gencode.v50.BCR_ABL1.transcripts.fa.gz -Gencode v50 release protein-coding transcript sequences FASTA, subsetted to only contain sequences from the genes BCR and ABL1. +Gencode v50 release protein-coding transcript sequences FASTA, subsetted to only contain sequences from the genes BCR and ABL1. Gzipped. ## GRCh38.chr1_chr19.dict diff --git a/test/fixtures/reference/gencode.v50.BCR_ABL1.transcripts.fa b/test/fixtures/reference/gencode.v50.BCR_ABL1.transcripts.fa deleted file mode 100644 index 659daaa14..000000000 --- a/test/fixtures/reference/gencode.v50.BCR_ABL1.transcripts.fa +++ /dev/null @@ -1,3 +0,0 @@ -version https://git-lfs.github.com/spec/v1 -oid sha256:f25546f7e1ef28fba36dc906fa783109a3850d3134eab6ad790395352b22e9a1 -size 104005 diff --git a/test/fixtures/reference/gencode.v50.BCR_ABL1.transcripts.fa.gz b/test/fixtures/reference/gencode.v50.BCR_ABL1.transcripts.fa.gz new file mode 100644 index 000000000..e1dbed572 --- /dev/null +++ b/test/fixtures/reference/gencode.v50.BCR_ABL1.transcripts.fa.gz @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:1f7d5eaacd432840dd78f02fa23bfa43626c1356b2b644fba0c4cb66643bec66 +size 16006