From 06f253a19c05569492ed08e11bf8fbb421122b0a Mon Sep 17 00:00:00 2001 From: "Stephanie M. Gogarten" Date: Fri, 6 Sep 2024 14:50:23 -0700 Subject: [PATCH] change data type to float to allow large integers --- CHANGELOG.md | 10 +++++++++ GREGoR_data_model.json | 50 ++++++++++++++++++++++++------------------ 2 files changed, 39 insertions(+), 21 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 896497e..2a51cf4 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -18,6 +18,16 @@ |called_variants_nanopore |chrom |added; not required | |called_variants_pac_bio |chrom |added; not required | |called_variants_optical_mapping |chrom |added; not required | +|aligned_nanopore |num_reads |changed data type to float for large number support | +|aligned_nanopore |num_bases |changed data type to float for large number support | +|aligned_nanopore |num_aligned_reads |changed data type to float for large number support | +|aligned_nanopore |num_aligned_bases |changed data type to float for large number support | +|aligned_nanopore |read_length_mean |changed data type to float | +|aligned_pac_bio |num_reads |changed data type to float for large number support | +|aligned_pac_bio |num_bases |changed data type to float for large number support | +|aligned_pac_bio |num_aligned_reads |changed data type to float for large number support | +|aligned_pac_bio |num_aligned_bases |changed data type to float for large number support | +|aligned_pac_bio |read_length_mean |changed data type to float | ## 1.5.2 diff --git a/GREGoR_data_model.json b/GREGoR_data_model.json index ccdd3fb..33ea412 100644 --- a/GREGoR_data_model.json +++ b/GREGoR_data_model.json @@ -345,7 +345,7 @@ "data_type": "enumeration", "enumerations": ["SNV", "INDEL", "SV", "CNV", "RE", "MEI", "STR"], "multi_value_delimiter": "|", - "examples": "SNV/INDEL", + "examples": "SNV|CNV", "notes": "SNV: single nucelotide variants\nINDEL: short insertion/deletions (<50bp)\nRE: repeat elements\nSV: structural variants, including copy number variants and mobile element insertions" }, { @@ -1548,37 +1548,41 @@ { "column": "num_reads", "description": "Total reads (before/ignoring alignment)", - "data_type": "integer", - "examples": "11946552" + "data_type": "float", + "examples": "11946552", + "notes": "float type required for large number, but value entered should be an integer" }, { "column": "num_bases", "description": "Number of bases (before/ignoring alignment)", - "data_type": "integer", - "examples": "101126719147" + "data_type": "float", + "examples": "101126719147", + "notes": "float type required for large number, but value entered should be an integer" }, { "column": "read_length_mean", "description": "Mean length of all reads (before/ignoring alignment)", - "data_type": "integer", + "data_type": "float", "examples": "18232" }, { "column": "num_aligned_reads", "description": "Total aligned reads", - "data_type": "integer", - "examples": "10751896" + "data_type": "float", + "examples": "10751896", + "notes": "float type required for large number, but value entered should be an integer" }, { "column": "num_aligned_bases", "description": "Number of bases in aligned reads", - "data_type": "integer", - "examples": "91014047232" + "data_type": "float", + "examples": "91014047232", + "notes": "float type required for large number, but value entered should be an integer" }, { "column": "aligned_read_length_mean", "description": "Mean length of aligned reads", - "data_type": "integer", + "data_type": "float", "examples": "18104" }, { @@ -1973,37 +1977,41 @@ { "column": "num_reads", "description": "Total reads (before/ignoring alignment)", - "data_type": "integer", - "examples": "11946552" + "data_type": "float", + "examples": "11946552", + "notes": "float type required for large number, but value entered should be an integer" }, { "column": "num_bases", "description": "Number of bases (before/ignoring alignment)", - "data_type": "integer", - "examples": "101126719147" + "data_type": "float", + "examples": "101126719147", + "notes": "float type required for large number, but value entered should be an integer" }, { "column": "read_length_mean", "description": "Mean length of all reads (before/ignoring alignment)", - "data_type": "integer", + "data_type": "float", "examples": "18232" }, { "column": "num_aligned_reads", "description": "Total aligned reads", - "data_type": "integer", - "examples": "10751896" + "data_type": "float", + "examples": "10751896", + "notes": "float type required for large number, but value entered should be an integer" }, { "column": "num_aligned_bases", "description": "Number of bases in aligned reads", - "data_type": "integer", - "examples": "91014047232" + "data_type": "float", + "examples": "91014047232", + "notes": "float type required for large number, but value entered should be an integer" }, { "column": "aligned_read_length_mean", "description": "Mean length of aligned reads", - "data_type": "integer", + "data_type": "float", "examples": "18104" }, {