diff --git a/CHANGELOG.md b/CHANGELOG.md index c1a6e4d34..382a34e0b 100644 --- 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 index 725838110..32abbde6c 100644 --- 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 index 64a8192c1..4643fd23e 100644 --- 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 index 1e71dd7f9..a184e9eb7 100644 --- 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 index 1e71dd7f9..a184e9eb7 100644 --- 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 index 1e71dd7f9..a184e9eb7 100644 --- 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