From 23ef8303ff9899bbc4292768db4d70b59decb10f Mon Sep 17 00:00:00 2001 From: Kieron Taylor Date: Mon, 26 Feb 2024 15:53:19 +0000 Subject: [PATCH 1/2] Update PacBioProductMetrics definition to include new per-product metrics --- lang_qc/db/mlwh_schema.py | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/lang_qc/db/mlwh_schema.py b/lang_qc/db/mlwh_schema.py index 9b7ededb..5f307623 100644 --- a/lang_qc/db/mlwh_schema.py +++ b/lang_qc/db/mlwh_schema.py @@ -579,6 +579,30 @@ class PacBioProductMetrics(Base): index=True, comment="The final QC outcome of the product as 0(failed), 1(passed) or NULL", ) + hifi_read_bases = Column( + mysqlBIGINT(unsigned=True), nullable=True, comment="The number of HiFi bases" + ) + hifi_num_reads = Column( + mysqlINTEGER(unsigned=True), nullable=True, comment="The number of HiFi reads" + ) + hifi_read_length_mean = Column( + mysqlSMALLINT(unsigned=True), nullable=True, comment="The mean HiFi read length" + ) + barcode_quality_score = Column( + mysqlSMALLINT(unsigned=True), + nullable=True, + comment="The mean barcode HiFi quality score", + ) + hifi_read_quality_mean = Column( + mysqlSMALLINT(unsigned=True), + nullable=True, + comment="The mean HiFi base quality", + ) + hifi_bases_percent = Column( + mysqlFLOAT(), + nullable=True, + comment="The HiFi bases expressed as a percentage of the total HiFi bases", + ) pac_bio_run_well_metrics = relationship( "PacBioRunWellMetrics", back_populates="pac_bio_product_metrics" From 08cf2eed23daf05dcebccd28afa5721c37f6313e Mon Sep 17 00:00:00 2001 From: Kieron Taylor Date: Wed, 28 Feb 2024 17:36:33 +0000 Subject: [PATCH 2/2] Incorrect type for hifi_read_length_mean --- lang_qc/db/mlwh_schema.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/lang_qc/db/mlwh_schema.py b/lang_qc/db/mlwh_schema.py index 5f307623..bc1ea86a 100644 --- a/lang_qc/db/mlwh_schema.py +++ b/lang_qc/db/mlwh_schema.py @@ -586,7 +586,7 @@ class PacBioProductMetrics(Base): mysqlINTEGER(unsigned=True), nullable=True, comment="The number of HiFi reads" ) hifi_read_length_mean = Column( - mysqlSMALLINT(unsigned=True), nullable=True, comment="The mean HiFi read length" + mysqlINTEGER(unsigned=True), nullable=True, comment="The mean HiFi read length" ) barcode_quality_score = Column( mysqlSMALLINT(unsigned=True), @@ -594,7 +594,7 @@ class PacBioProductMetrics(Base): comment="The mean barcode HiFi quality score", ) hifi_read_quality_mean = Column( - mysqlSMALLINT(unsigned=True), + mysqlINTEGER(unsigned=True), nullable=True, comment="The mean HiFi base quality", )