Merge branch 'master' into vcf_writing

poseidon-framework · Feb 5, 2025 · 6ccbba2 · 6ccbba2
2 parents 317922a + 64b586d
commit 6ccbba2
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Showing 6 changed files with 18 additions and 7 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,5 +1,7 @@
 - V 1.7.0.0:
     - Added support for (optionally gzipped) VCF output in forge and genoconvert.
+- V 1.6.2.2:
+    - Fixed a small bug that prevented calculation of checksums for genotype data in `rectify`.
 - V 1.6.2.1:
     - Switch to GHC 9.6.6 and a new resolver version.
 - V 1.6.2.0:

diff --git a/src/Poseidon/CLI/Rectify.hs b/src/Poseidon/CLI/Rectify.hs
@@ -122,14 +122,14 @@ updateChecksums checksumSetting pac = do
                     case gFileSpec of
                         GenotypeEigenstrat gf gfc sf sfc if_ ifc -> do
                             [genoChkSum, snpChkSum, indChkSum] <-
-                                sequence [testAndGetChecksum f c | (f, c) <- zip [gf, sf, if_] [gfc, sfc, ifc]]
+                                sequence [testAndGetChecksum (d </> f) c | (f, c) <- zip [gf, sf, if_] [gfc, sfc, ifc]]
                             return $ GenotypeEigenstrat gf genoChkSum sf snpChkSum if_ indChkSum
                         GenotypePlink gf gfc sf sfc if_ ifc -> do
                             [genoChkSum, snpChkSum, indChkSum] <-
-                                sequence [testAndGetChecksum f c | (f, c) <- zip [gf, sf, if_] [gfc, sfc, ifc]]
+                                sequence [testAndGetChecksum (d </> f) c | (f, c) <- zip [gf, sf, if_] [gfc, sfc, ifc]]
                             return $ GenotypePlink gf genoChkSum sf snpChkSum if_ indChkSum
                         GenotypeVCF gf gfc -> do
-                            genoChkSum <- testAndGetChecksum gf gfc
+                            genoChkSum <- testAndGetChecksum (d </> gf) gfc
                             return $ GenotypeVCF gf genoChkSum
                 else return gFileSpec
             newJannoChkSum <-

diff --git a/test/PoseidonGoldenTests/GoldenTestCheckSumFile.txt b/test/PoseidonGoldenTests/GoldenTestCheckSumFile.txt
@@ -52,11 +52,11 @@ d8d1e5dd679ae256c40340e726a0cdc5 genoconvert init_vcf/Schiffels_vcf/geno.bim
 a9fcb59cb933d8f183f3c3f6fbf2e213 genoconvert genoconvert/zip_roundtrip/Schiffels_2016.fam
 72c7a584feefddb31f817c205355dd14 rectify init/Schiffels/POSEIDON.yml
 4aeae97cfc44b55b2a8005425d786148 rectify init/Schiffels/CHANGELOG.md
-da981f8d52f60ec4d96865b224648c92 rectify init/Schiffels/POSEIDON.yml
+925e402351afd974403402d141abe342 rectify init/Schiffels/POSEIDON.yml
 3bb396e099d5b8771a3409f5fe85d70b rectify init/Schiffels/CHANGELOG.md
-dc322649188ce2995cea8a46a7f97f3e rectify init/Schiffels/POSEIDON.yml
+b9216f365108c5c5c66f78cceb2eb09a rectify init/Schiffels/POSEIDON.yml
 3bb396e099d5b8771a3409f5fe85d70b rectify init/Schiffels/CHANGELOG.md
-a61f78b4e9b7e3c7e00ec7bc6aaab95b rectify init/Schiffels/POSEIDON.yml
+ebf0b456d5e09686ee7131db06848104 rectify init/Schiffels/POSEIDON.yml
 3bb396e099d5b8771a3409f5fe85d70b rectify init/Schiffels/CHANGELOG.md
 083fe7ef4206c979356a3a2454d780b1 rectify init/Schiffels/Schiffels.janno
 2757f727e02dd6453fffe68c4c6ec4c8 forge forge/ForgePac1/POSEIDON.yml
@@ -134,7 +134,7 @@ b4f71aff4fbc11594008c3811781cc43 forge forge/ForgePac21/ForgePac21.bib
 d4a05cfef045648238a94a9d621cf667 chronicle chronicle/chronicle1.yml
 b43da4d5734371c0648553120f812466 timetravel timetravel/Lamnidis_2018-1.0.0/POSEIDON.yml
 8d57ce1a1ab28c0d8a5f391dd790a59c timetravel timetravel/Lamnidis_2018-1.0.1/POSEIDON.yml
-a61f78b4e9b7e3c7e00ec7bc6aaab95b timetravel timetravel/Schiffels-1.1.1/POSEIDON.yml
+ebf0b456d5e09686ee7131db06848104 timetravel timetravel/Schiffels-1.1.1/POSEIDON.yml
 1ab24c45ef3a13e0fb34afac7a21dca8 timetravel timetravel/Schmid_2028-1.0.0/POSEIDON.yml
 8d57ce1a1ab28c0d8a5f391dd790a59c fetch fetch/by_package/Lamnidis_2018-1.0.1/POSEIDON.yml
 1ab24c45ef3a13e0fb34afac7a21dca8 fetch fetch/by_package/Schmid_2028-1.0.0/POSEIDON.yml

diff --git a/test/PoseidonGoldenTests/GoldenTestData/chronicle/Schiffels/POSEIDON.yml b/test/PoseidonGoldenTests/GoldenTestData/chronicle/Schiffels/POSEIDON.yml
@@ -12,8 +12,11 @@ lastModified: 1970-01-01
 genotypeData:
   format: EIGENSTRAT
   genoFile: geno.txt
+  genoFileChkSum: 0332344057c0c4dce2ff7176f8e1103d
   snpFile: snp.txt
+  snpFileChkSum: d76e3e7a8fc0f1f5e435395424b5aeab
   indFile: ind.txt
+  indFileChkSum: f77dc756666dbfef3bb35191ae15a167
   snpSet: Other
 jannoFile: Schiffels.janno
 jannoFileChkSum: 083fe7ef4206c979356a3a2454d780b1

diff --git a/test/PoseidonGoldenTests/GoldenTestData/init/Schiffels/POSEIDON.yml b/test/PoseidonGoldenTests/GoldenTestData/init/Schiffels/POSEIDON.yml
@@ -12,8 +12,11 @@ lastModified: 1970-01-01
 genotypeData:
   format: EIGENSTRAT
   genoFile: geno.txt
+  genoFileChkSum: 0332344057c0c4dce2ff7176f8e1103d
   snpFile: snp.txt
+  snpFileChkSum: d76e3e7a8fc0f1f5e435395424b5aeab
   indFile: ind.txt
+  indFileChkSum: f77dc756666dbfef3bb35191ae15a167
   snpSet: Other
 jannoFile: Schiffels.janno
 jannoFileChkSum: 083fe7ef4206c979356a3a2454d780b1

diff --git a/test/PoseidonGoldenTests/GoldenTestData/timetravel/Schiffels-1.1.1/POSEIDON.yml b/test/PoseidonGoldenTests/GoldenTestData/timetravel/Schiffels-1.1.1/POSEIDON.yml
@@ -12,8 +12,11 @@ lastModified: 1970-01-01
 genotypeData:
   format: EIGENSTRAT
   genoFile: geno.txt
+  genoFileChkSum: 0332344057c0c4dce2ff7176f8e1103d
   snpFile: snp.txt
+  snpFileChkSum: d76e3e7a8fc0f1f5e435395424b5aeab
   indFile: ind.txt
+  indFileChkSum: f77dc756666dbfef3bb35191ae15a167
   snpSet: Other
 jannoFile: Schiffels.janno
 jannoFileChkSum: 083fe7ef4206c979356a3a2454d780b1