From 6e2c9fe42a71124c333d2c30032a37de3ea00efc Mon Sep 17 00:00:00 2001 From: Jethro Rainford Date: Wed, 4 Jan 2023 14:52:04 +0000 Subject: [PATCH 1/3] add --panel_filters to readme --- README.md | 1 + 1 file changed, 1 insertion(+) diff --git a/README.md b/README.md index 06fd6bf3..1a330151 100644 --- a/README.md +++ b/README.md @@ -116,6 +116,7 @@ The `coverage_report_single.py` script generates the full HTML report. It requir -n / --sample_name: name for title of report (optional; gene_stats file name will be used if not given) -o / --output: name for output report (optional; sample name will be used if not given) -p / --panel: panel bed file used for initial annotation, name will be displayed in summary of report (optional) +--panel_filters: preset filters of genes / transcripts to set for the full gene plots, these will be presented in a drop down menu for filtering the plots. These should be passed as key:value pairs of panel name to display in the drop down and a comma separated list of gene symbols to filter with (i.e. panel1:gene1,gene2,gene3...) -l / --limit: number of genes at which to limit including full gene plots, large numbers of genes may take a long time to generate the plots (optional) -m / --summary: boolean flag to add clinical report summary text in summary section, includes list of all genes with transcripts (optional; default False) --cores: Number of CPU cores to utilise, for larger numbers of genes this will drastically reduce run time. If not given will use maximum available From 76b57dc47109b0ac5730d21b7793a54205764929 Mon Sep 17 00:00:00 2001 From: Jethro Rainford Date: Wed, 4 Jan 2023 14:52:44 +0000 Subject: [PATCH 2/3] readme --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 1a330151..1513eb84 100644 --- a/README.md +++ b/README.md @@ -116,9 +116,9 @@ The `coverage_report_single.py` script generates the full HTML report. It requir -n / --sample_name: name for title of report (optional; gene_stats file name will be used if not given) -o / --output: name for output report (optional; sample name will be used if not given) -p / --panel: panel bed file used for initial annotation, name will be displayed in summary of report (optional) ---panel_filters: preset filters of genes / transcripts to set for the full gene plots, these will be presented in a drop down menu for filtering the plots. These should be passed as key:value pairs of panel name to display in the drop down and a comma separated list of gene symbols to filter with (i.e. panel1:gene1,gene2,gene3...) -l / --limit: number of genes at which to limit including full gene plots, large numbers of genes may take a long time to generate the plots (optional) -m / --summary: boolean flag to add clinical report summary text in summary section, includes list of all genes with transcripts (optional; default False) +--panel_filters: preset filters of genes / transcripts to set for the full gene plots, these will be presented in a drop down menu for filtering the plots. These should be passed as key:value pairs of panel name to display in the drop down and a comma separated list of gene symbols to filter with (i.e. panel1:gene1,gene2,gene3...) (optional) --cores: Number of CPU cores to utilise, for larger numbers of genes this will drastically reduce run time. If not given will use maximum available From 8622efcb0e0bde4ce8b7b89c9ea4b709764671e0 Mon Sep 17 00:00:00 2001 From: Jethro Rainford Date: Wed, 4 Jan 2023 14:54:59 +0000 Subject: [PATCH 3/3] =?UTF-8?q?=C9=98mbA=C9=98=E1=B4=99=20=C9=98TAbqU?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 1513eb84..54109293 100644 --- a/README.md +++ b/README.md @@ -118,7 +118,7 @@ The `coverage_report_single.py` script generates the full HTML report. It requir -p / --panel: panel bed file used for initial annotation, name will be displayed in summary of report (optional) -l / --limit: number of genes at which to limit including full gene plots, large numbers of genes may take a long time to generate the plots (optional) -m / --summary: boolean flag to add clinical report summary text in summary section, includes list of all genes with transcripts (optional; default False) ---panel_filters: preset filters of genes / transcripts to set for the full gene plots, these will be presented in a drop down menu for filtering the plots. These should be passed as key:value pairs of panel name to display in the drop down and a comma separated list of gene symbols to filter with (i.e. panel1:gene1,gene2,gene3...) (optional) +--panel_filters: preset filters of genes / transcripts to set for the full gene plots, these will be presented in a drop down menu for filtering the plots. These should be passed as key:value pairs of panel name to display in the drop down and a comma separated list of gene symbols to filter with (i.e. panel1:gene1,gene2,gene3...) (optional) --cores: Number of CPU cores to utilise, for larger numbers of genes this will drastically reduce run time. If not given will use maximum available