diff options
Diffstat (limited to 'src/gemma_io.cpp')
| -rw-r--r-- | src/gemma_io.cpp | 39 |
1 files changed, 38 insertions, 1 deletions
diff --git a/src/gemma_io.cpp b/src/gemma_io.cpp index 76f8a35..fddfd79 100644 --- a/src/gemma_io.cpp +++ b/src/gemma_io.cpp @@ -641,8 +641,45 @@ bool ReadFile_fam(const string &file_fam, vector<vector<int>> &indicator_pheno, // Read bimbam mean genotype file, the first time, to obtain #SNPs for // analysis (ns_test) and total #SNP (ns_total). +/* +## Modified (Mutated) Parameters: + +1. **`indicator_idv`** (vector<int>&) + - Actually **not modified** - only read from to determine which individuals to include + +2. **`indicator_snp`** (vector<int>&) + - **Modified**: Cleared at the start (`indicator_snp.clear()`) + - Populated with 0s and 1s to indicate whether each SNP passes filters + - One entry per SNP in the genotype file + +3. **`mapRS2chr`** (map<string, string>&) + - **Not modified** - only read from to get chromosome info + +4. **`mapRS2bp`** (map<string, long int>&) + - **Not modified** - only read from to get base pair positions + +5. **`mapRS2cM`** (map<string, double>&) + - **Not modified** - only read from to get centimorgan positions + +6. **`snpInfo`** (vector<SNPINFO>&) + - **Modified**: Cleared at the start (`snpInfo.clear()`) + - Populated with SNPINFO structures for each SNP containing metadata (chr, rs, position, alleles, missingness, MAF, etc.) + +7. **`ns_test`** (size_t&) + - **Modified**: Set to 0 initially + - Incremented for each SNP that passes all filters + - Returns the count of SNPs that will be used for testing + +## Summary of Mutated Outputs: +- **`indicator_snp`**: Binary indicators for which SNPs passed filtering +- **`snpInfo`**: Complete metadata for all SNPs in the file +- **`ns_test`**: Count of SNPs passing filters + +The function returns a `bool` indicating success/failure, but the real outputs are these three modified reference parameters. +*/ + bool ReadFile_geno(const string &file_geno, const set<string> &setSnps, - const gsl_matrix *W, vector<int> &indicator_idv, + const gsl_matrix *W, const vector<int> &indicator_idv, vector<int> &indicator_snp, const double &maf_level, const double &miss_level, const double &hwe_level, const double &r2_level, map<string, string> &mapRS2chr, |