Prepare/tsb reference grch37

.github/workflows/ci.yml

@@ -55,15 +55,14 @@ jobs:
       uses: actions/cache@v4
       with:
         path: ./src/
-        key: ${{ runner.os }}-src-grch37
-        restore-keys: |
-          ${{ runner.os }}-src-
+        key: ${{ runner.os }}-src-grch37-6eb14374
 
-    - name: Download GRCh37.tar.gz if not present
+    - name: Download corrected GRCh37 archive if not present
       run: |
         if [ ! -f ./src/GRCh37.tar.gz ]; then
           wget --connect-timeout=10 --tries=20 ftp://alexandrovlab-ftp.ucsd.edu/pub/tools/SigProfilerMatrixGenerator/GRCh37.tar.gz -P ./src/
         fi
+        echo '6eb14374fbaabe4b1f4c15bc9ca8d2cb58025ce73776864632ef6308bd19aaa3  ./src/GRCh37.tar.gz' | sha256sum --check
 
     - name: Install package with tests
       run: |

.github/workflows/release.yml

@@ -41,9 +41,34 @@ jobs:
       run: |
         python -m twine check dist/*
 
-    - name: Verify GRCh38 reference resources
+    - name: Verify reference resources
       run: |
-        python -c "import glob, zipfile; wheel=glob.glob('dist/*.whl')[0]; names=[name.rsplit('/', 1)[-1] for name in zipfile.ZipFile(wheel).namelist()]; assert not any('GRCh38_TSBv2' in name for name in names); assert sum(name.startswith(('context_counts_GRCh38_Legacy_', 'context_distribution_GRCh38_Legacy_')) for name in names) == 48; assert sum(name.startswith(('context_counts_GRCh38_', 'context_distribution_GRCh38_')) and 'GRCh38_Legacy_' not in name for name in names) == 48"
+        python - <<'PY'
+        import glob
+        import zipfile
+
+        wheel = glob.glob("dist/*.whl")[0]
+        context_prefix = (
+            "SigProfilerMatrixGenerator/references/chromosomes/"
+            "context_distributions/"
+        )
+        with zipfile.ZipFile(wheel) as archive:
+            names = set(archive.namelist())
+            manifest_name = context_prefix + "context_table_manifest.txt"
+            assert manifest_name in names
+            expected = {
+                line.strip()
+                for line in archive.read(manifest_name).decode("utf-8").splitlines()
+                if line.strip() and not line.startswith("#")
+            }
+            observed = {
+                name.removeprefix(context_prefix)
+                for name in names
+                if name.startswith(context_prefix) and name.endswith(".csv")
+            }
+        assert expected == observed
+        assert not any("_TSBv2" in name or "_pending" in name for name in names)
+        PY
 
     - name: Verify package version
       run: |

CHANGELOG.md

@@ -10,12 +10,22 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 - Register `GRCh38_Legacy` with the chromosome checksums and context tables from
   the previously distributed GRCh38 reference so historical results remain
   reproducible.
+- Register `GRCh37_Legacy` against a copy of the untouched historical archive
+  named `GRCh37_Legacy.tar.gz`
+  archive and preserve its supporting tables for reproducible older analyses.
+- Record the exact Ensembl GRCh37 FASTA and annotation sources, checksums, and
+  retained historical transcript scope used to rebuild the corrected reference.
 
 ### Changed
 - Promote the corrected transcription-strand reference to the default `GRCh38`
   identity, including validated strand-aware whole-genome and exome context-count
   and distribution tables. Existing installations of the former `GRCh38`
   reference must be reinstalled after upgrading.
+- Promote corrected GRCh37 transcription-strand labels and strand-dependent
+  opportunity tables to the default `GRCh37` identity.
+- Resolve logical reference names to their physical archive filenames and
+  stage archive extraction so a historical internal directory can be safely
+  installed under a distinct Legacy identity.
 
 ### Fixed
 - Rebuild SBS context-distribution tables from the shared five-base opportunity
@@ -44,10 +54,13 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
   retaining the CNV48 schema (from `fix/facets-cnv48-tcn1-loh`).
 
 ### Reference Data
-- `GRCh38.tar.gz` now contains the corrected transcription-strand reference.
-  The previously distributed data is preserved as `GRCh38_Legacy.tar.gz`.
-  Both archives must be published under these exact filenames before network
-  installation can succeed.
+- Corrected `GRCh38` continues to resolve to its already-published
+  `GRCh38.tar.gz`; the separately registered `GRCh38_Legacy` archive remains
+  available for old analyses.
+- Corrected `GRCh37` resolves to `GRCh37.tar.gz`.
+  `GRCh37_Legacy` resolves to `GRCh37_Legacy.tar.gz` with the historical bytes.
+  Older MatrixGenerator releases cannot verify the corrected archive under
+  the original name and should upgrade before reinstalling.
 
 ## [1.3.6] - 2025-10-28
 

README.md

@@ -83,7 +83,7 @@ View the table below for the full list of parameters.
 | ------ | ----------- | ----------- | ----------- |
 | Required |  |  |  |
 |  | project | String | The name of the project. |
-|  | reference_genome | String | The name of the reference genome. Full list of genomes under **Supported Genomes** section. Supported values include the following: {c_elegans, dog, ebv, GRCh37, GRCh38, GRCh38_Legacy, mm9, mm10, mm39, rn6, yeast} |
+|  | reference_genome | String | The name of the reference genome. Full list of genomes under **Supported Genomes** section. Supported values include the following: {c_elegans, dog, ebv, GRCh37, GRCh37_Legacy, GRCh38, GRCh38_Legacy, mm9, mm10, mm39, rn6, yeast} |
 |  | path_to_input_files | String | The path to the input files. |
 | Optional |  |  |  |
 |  | exome | Boolean | Downsamples mutational matrices to the exome regions of the genome. Default value False. |
@@ -235,6 +235,11 @@ references use the same GRCh38 DNA sequence.
 GRCh37.p13 [GRCh37] (Genome Reference Consortium Human Reference 37), INSDC
 Assembly GCA_000001405.14, Feb 2009. Released April 2011. Last updated September 2013. This genome was downloaded from ENSEMBL database version 93.37.
 
+`GRCh37` uses the corrected transcription-strand reference for new analyses.
+Use `GRCh37_Legacy` only to reproduce results generated with the historical
+pre-correction archive. Both identities use the same GRCh37.p13 DNA assembly;
+strand-independent contexts are unchanged.
+
 GRCm39 [mm39] (Genome Reference Consortium Mouse Reference 39), INSDC
 Assembly GCA_000001635.9, Jun 2020. Last updated August 2020. This genome was downloaded from ENSEMBL database version 103.
 
@@ -255,7 +260,7 @@ CanFam3.1 [dog] GCA_000002285.2, Sep 2011. Last updated Jun 2019. This genome wa
 
 WBcel235 [c_elegans] GCA_000002985.3, Oct 2014. Last updated Jan 2019. This genome was downloaded from ENSEMBL database version 100.
 
-*One can specify "_havana" to the end of the genome to include annotations in t-cell receptor genes and IG clusters (available for GRCh37, GRCh38, and mm10).
+*One can specify "_havana" to the end of the genome to include annotations in t-cell receptor genes and IG clusters (available for GRCh37, GRCh38, and mm10). These historical Havana references are known to contain the pre-correction transcription-strand boundary and overlap defect. No corrected Havana archives are currently available. MatrixGenerator emits a runtime warning and continues so that historical analyses remain reproducible; transcription-strand-aware results may be affected.*
 
 **LOG FILES**
 

SigProfilerMatrixGenerator/controllers/cli_controller.py

@@ -53,7 +53,7 @@ def parse_arguments_install(args: List[str]) -> argparse.Namespace:
     parser = argparse.ArgumentParser(description="Install reference genome files.")
     parser.add_argument(
         "genome",
-        help="The reference genome to install. Supported genomes include {c_elegans, dog, ebv, GRCh37, GRCh38, GRCh38_Legacy, mm9, mm10, mm39, rn6, rn7, yeast}.",
+        help="The reference genome to install. Supported genomes include {c_elegans, dog, ebv, GRCh37, GRCh37_Legacy, GRCh38, GRCh38_Legacy, mm9, mm10, mm39, rn6, rn7, yeast}.",
     )
     parser.add_argument(
         "-l",
@@ -86,7 +86,7 @@ def parse_arguments_matrix_generator(args: List[str]) -> argparse.Namespace:
     parser.add_argument("project", help="The name of the project.")
     parser.add_argument(
         "reference_genome",
-        help="The name of the reference genome. Supported values {c_elegans, dog, ebv, GRCh37, GRCh38, GRCh38_Legacy, mm9, mm10, mm39, rn6, rn7, yeast}.",
+        help="The name of the reference genome. Supported values {c_elegans, dog, ebv, GRCh37, GRCh37_Legacy, GRCh38, GRCh38_Legacy, mm9, mm10, mm39, rn6, rn7, yeast}.",
     )
     parser.add_argument("path_to_input_files", help="The path to the input files.")
 

SigProfilerMatrixGenerator/references/chromosomes/context_distributions/context_counts_GRCh37_24.csv

@@ -1,9 +1,9 @@
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-N:C,40866161,7985883,49000698,55662130,39484694,45017298,43187770,38617751,33225332,34321485,29148120,28857004,28755961,27486024,24607397,20137609,16852480,18589259,15177324,17886893,11273471,14051563,8502866,7522636
-N:T,63650029,12361715,70063558,83527595,61602936,73868815,67701633,59627494,48922902,51477355,42854201,40867499,42123360,40880260,39977346,29895128,23256604,24239421,18994161,27699952,13166310,18263361,13066958,8366112
-T:C,9095150,230777,21340790,18807930,18035421,13425054,13477673,13945462,14280320,11929599,10604057,12950754,12638874,12319323,5818552,6985911,8877473,6753335,10447004,5523864,7599792,5100222,3118983,4551626
-T:T,13297376,367590,29084262,28080243,26311585,21176234,20030569,20983761,20291516,17221825,14674422,18001477,17076740,17485644,9010275,9622347,12017150,7674175,12065753,8087506,7618301,6066676,4229815,4920819
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-U:T,14137294,1242422,31626715,30291863,28740515,20477441,19496057,20046265,22449976,16494980,12794205,17509630,17080205,18377978,9734605,12308911,11596208,11310116,10973154,9055519,7710538,8768128,3209927,4744103
+B:C,246624,14539,397369,362777,659964,299079,277443,350457,308467,233679,147407,303396,330165,416457,38796,327831,270516,332967,366185,111550,379509,139574,228937,136566
+B:T,338903,19205,484793,494772,910629,451756,366421,477747,417068,304510,183523,389327,403042,550466,59225,399071,382769,351750,380548,137699,395887,150521,294159,121245
+N:C,40865874,7985871,48999966,55661724,39484366,45017052,43187510,38617406,33225009,34321247,29147789,28856737,28755526,27485680,24607274,20137397,16852265,18589003,15176938,17886797,11272973,14051353,8502790,7522457
+N:T,63649567,12361681,70062484,83526903,61602398,73868379,67701157,59626955,48922450,51476996,42853829,40867103,42122729,40879732,39977171,29894845,23256310,24239023,18993606,27699804,13165654,18263094,13066845,8365918
+T:C,9428257,507154,22810433,20372005,18989636,13513542,13660145,13974602,15204542,11674630,10407793,13028962,12968858,12941100,6249671,7999349,8885065,8365270,10135564,5977481,7771169,6153658,2858484,4641562
+T:T,13071540,753830,28998278,27851564,26294800,19929032,18831010,19619749,20405561,16129324,13051329,16816326,16337488,17118377,8946824,10397951,11228837,9039657,10965987,8181821,7289947,7082770,3527285,4572985
+U:C,9138393,485989,21833134,19465955,18189325,12946934,13093463,13364224,14570601,11177034,9936407,12417929,12450274,12408784,5931723,7634501,8468106,8044780,9749593,5726497,7565742,5912643,2744691,4444593
+U:T,14361314,856216,31694012,30468727,28665985,21635858,20578087,21363886,22299901,17571470,14415198,18634865,17761402,18680749,9779174,11498591,12350854,9922283,12026757,8935508,7968082,7751883,3883387,5089143

SigProfilerMatrixGenerator/references/chromosomes/context_distributions/context_counts_GRCh37_24_exome.csv

@@ -1,9 +1,9 @@
 ,X,Y,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,MT,M
-B:C,21846,719,52085,36352,62005,17256,20461,45509,29355,20072,22834,27862,55421,35876,4206,37862,15662,54751,59928,11372,49097,16942,17010,14373,0,0
-B:T,24773,546,44891,37330,60987,18177,18691,39053,27649,17903,20749,24561,49562,31795,4387,36269,16936,43573,48130,10793,36557,12831,14657,10708,0,0
-N:C,20245,1544,14280,20162,10851,7489,5599,11525,46580,9784,8241,12387,25706,9276,3224,47548,11953,13634,13558,3250,22065,5275,1886,11639,0,0
-N:T,24005,1756,13692,20848,8440,8960,6252,14017,34844,8539,8367,11340,25067,9782,4633,45933,12026,10280,11306,3352,19366,5092,1926,9205,0,0
-T:C,472883,13260,1411964,893817,769109,415325,511983,671974,565733,446619,559379,503887,800874,722534,215635,420535,469118,567757,909257,161628,1007408,376304,130465,340074,0,0
-T:T,487260,17100,1334966,1005761,782907,517983,535767,708854,554678,436552,516824,513590,703469,718406,258178,411267,469031,443508,751104,191571,710508,300928,126078,245328,0,0
-U:C,492445,21156,1440224,859956,730705,470279,639299,643376,600469,390434,572856,520770,813369,689944,204547,385963,439194,691322,811454,191174,994884,385054,141353,326043,0,0
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