From 8f292e936772df6161a84834a219080af5d3cc1d Mon Sep 17 00:00:00 2001 From: Ryan Welch Date: Sat, 5 Aug 2023 13:08:07 -0400 Subject: [PATCH] Removed unnecessary MetaSTAAR parameters --- core/src/MetastaarSummaryStatisticsLoader.cpp | 5 ----- core/src/MetastaarSummaryStatisticsLoader.h | 7 +------ core/src/pywrapper.cpp | 3 --- 3 files changed, 1 insertion(+), 14 deletions(-) diff --git a/core/src/MetastaarSummaryStatisticsLoader.cpp b/core/src/MetastaarSummaryStatisticsLoader.cpp index 075d058..d945c17 100644 --- a/core/src/MetastaarSummaryStatisticsLoader.cpp +++ b/core/src/MetastaarSummaryStatisticsLoader.cpp @@ -60,9 +60,6 @@ MetastaarParquetMetadata read_parquet_metadata(const string& s) { extract_parquet_value(s, meta, "nrows", spstoull_uint64, pq_meta.nrows, true); extract_parquet_value(s, meta, "ncols", spstoull_uint64, pq_meta.ncols, true); extract_parquet_value(s, meta, "cov_maf_cutoff", spstod, pq_meta.cov_maf_cutoff, true); - extract_parquet_value(s, meta, "pos_start", spstoull_uint64, pq_meta.pos_start); - extract_parquet_value(s, meta, "pos_end", spstoull_uint64, pq_meta.pos_end); - extract_parquet_value(s, meta, "pos_mid", spstoull_uint64, pq_meta.pos_mid, true); extract_parquet_value(s, meta, "region_start", spstoull_uint64, pq_meta.region_start); extract_parquet_value(s, meta, "region_mid", spstoull_uint64, pq_meta.region_mid); extract_parquet_value(s, meta, "region_end", spstoull_uint64, pq_meta.region_end); @@ -70,8 +67,6 @@ MetastaarParquetMetadata read_parquet_metadata(const string& s) { if (pq_meta.nrows < 0 || pq_meta.ncols < 0) throw_ldserver_exception("nrows or ncols in parquet metadata were invalid", {}, "parquet file was: %s", {s}); if (pq_meta.cov_maf_cutoff < 0 || pq_meta.cov_maf_cutoff > 1) throw_ldserver_exception("cov_maf_cutoff should be >= 0 and <= 1", {}, "parquet file was: %s", {s}); - if (pq_meta.pos_start <= 0) throw_ldserver_exception("pos_start should be > 0", {}, "parquet file was: %s", {s}); - if (pq_meta.pos_end <= 0) throw_ldserver_exception("pos_end should be > 0", {}, "parquet file was: %s", {s}); if (pq_meta.region_start <= 0) throw_ldserver_exception("region_start should be > 0", {}, "parquet file was: %s", {s}); if (pq_meta.region_mid <= 0) throw_ldserver_exception("region_mid should be > 0", {}, "parquet file was: %s", {s}); if (pq_meta.region_end <= 0) throw_ldserver_exception("region_end should be > 0", {}, "parquet file was: %s", {s}); diff --git a/core/src/MetastaarSummaryStatisticsLoader.h b/core/src/MetastaarSummaryStatisticsLoader.h index 74f8675..f180abd 100644 --- a/core/src/MetastaarSummaryStatisticsLoader.h +++ b/core/src/MetastaarSummaryStatisticsLoader.h @@ -14,9 +14,7 @@ mid, and end position (sometimes referred to as "region" start, mid, end.) Each segment though may or may not contain genetic variants, depending on the particular dataset. There may be no known - variants there, or the genotyping array did not have variants typed there, etc. We record below for each segment the position - of the first actual variant seen in the file (pos_start), the position of the middle variant (pos_mid), and the position - of the final variant (pos_end). + variants there, or the genotyping array did not have variants typed there, etc. The score files look like: GtU @@ -58,9 +56,6 @@ Segment──►3│..xxx.│ struct MetastaarParquetMetadata { std::string filepath; std::string chrom; - uint64_t pos_start = 0; - uint64_t pos_end = 0; - uint64_t pos_mid = 0; uint64_t region_start = 0; uint64_t region_mid = 0; uint64_t region_end = 0; diff --git a/core/src/pywrapper.cpp b/core/src/pywrapper.cpp index b63d553..48375f4 100644 --- a/core/src/pywrapper.cpp +++ b/core/src/pywrapper.cpp @@ -275,9 +275,6 @@ BOOST_PYTHON_MODULE(pywrapper) { boost::python::class_>("MetastaarParquetMetadata") .def_readwrite("filepath", &MetastaarParquetMetadata::filepath) .def_readwrite("chrom", &MetastaarParquetMetadata::chrom) - .def_readwrite("pos_start", &MetastaarParquetMetadata::pos_start) - .def_readwrite("pos_end", &MetastaarParquetMetadata::pos_end) - .def_readwrite("pos_mid", &MetastaarParquetMetadata::pos_mid) .def_readwrite("region_start", &MetastaarParquetMetadata::region_start) .def_readwrite("region_mid", &MetastaarParquetMetadata::region_mid) .def_readwrite("region_end", &MetastaarParquetMetadata::region_end)