diff --git a/public/gentrap/src/main/resources/nl/lumc/sasc/biopet/pipelines/gentrap/scripts/pdf_report.py b/public/gentrap/src/main/resources/nl/lumc/sasc/biopet/pipelines/gentrap/scripts/pdf_report.py
index 5206e98cf6ceb6896e1d2668f30b34e02b812036..9cdcaf95194ab29449e11a5ec24ade29417345c4 100755
--- a/public/gentrap/src/main/resources/nl/lumc/sasc/biopet/pipelines/gentrap/scripts/pdf_report.py
+++ b/public/gentrap/src/main/resources/nl/lumc/sasc/biopet/pipelines/gentrap/scripts/pdf_report.py
@@ -422,9 +422,9 @@ class GentrapLib(object):
# insert size metrics files
self.inserts_metrics_files = summary.get("bammetrics", {}).get("files", {}).get("insert_size_metrics", {})
# rna metrics files and stats
+ self.rna_metrics_files = summary.get("gentrap", {}).get("files", {}).get("rna_metrics", {})
_rmetrics = summary.get("gentrap", {}).get("stats", {}).get("rna_metrics", {})
if _rmetrics:
- self.rna_metrics_files = summary.get("gentrap", {}).get("files", {}).get("rna_metrics", {})
self.rna_metrics = {k: v for k, v in _rmetrics.items() }
pf_bases = float(_rmetrics["pf_bases"])
exonic_bases = int(_rmetrics.get("coding_bases", 0)) + int(_rmetrics.get("utr_bases", 0))
@@ -461,10 +461,15 @@ class GentrapSample(object):
self.libs = \
{l: GentrapLib(self.run, self, l, summary["libraries"][l]) \
for l in self.lib_names}
+ self.is_paired_end = summary.get("gentrap", {}).get("stats", {}).get("pipeline", {})["all_paired"]
+ # mapping metrics settings
+ self.aln_metrics = summary.get("bammetrics", {}).get("stats", {}).get("alignment_metrics", {})
+ # insert size metrics files
+ self.inserts_metrics_files = summary.get("bammetrics", {}).get("files", {}).get("insert_size_metrics", {})
# rna metrics files and stats
+ self.rna_metrics_files = summary.get("gentrap", {}).get("files", {}).get("rna_metrics", {})
_rmetrics = summary.get("gentrap", {}).get("stats", {}).get("rna_metrics", {})
if _rmetrics:
- self.rna_metrics_files = summary.get("gentrap", {}).get("files", {}).get("rna_metrics", {})
self.rna_metrics = {k: v for k, v in _rmetrics.items() }
pf_bases = float(_rmetrics["pf_bases"])
exonic_bases = int(_rmetrics.get("coding_bases", 0)) + int(_rmetrics.get("utr_bases", 0))
diff --git a/public/gentrap/src/main/resources/nl/lumc/sasc/biopet/pipelines/gentrap/templates/pdf/lib_mapping.tex b/public/gentrap/src/main/resources/nl/lumc/sasc/biopet/pipelines/gentrap/templates/pdf/lib_mapping.tex
index 0d862bc9b649157cef7fe5640fbc1948681968fe..50fd3606d01c5a6f5ca0d451725def487e9307ef 100644
--- a/public/gentrap/src/main/resources/nl/lumc/sasc/biopet/pipelines/gentrap/templates/pdf/lib_mapping.tex
+++ b/public/gentrap/src/main/resources/nl/lumc/sasc/biopet/pipelines/gentrap/templates/pdf/lib_mapping.tex
@@ -77,7 +77,6 @@
=))
((* endif *))
-((* if lib.sample.libs|length > 1 *))
\subsubsection{RNA-specific metrics}
\IfFileExists{((( lib.rna_metrics_files.output_chart.path )))}
@@ -111,5 +110,3 @@
\hline
\end{tabular}
\end{center}
-
-((* endif *))
diff --git a/public/gentrap/src/main/resources/nl/lumc/sasc/biopet/pipelines/gentrap/templates/pdf/sample.tex b/public/gentrap/src/main/resources/nl/lumc/sasc/biopet/pipelines/gentrap/templates/pdf/sample.tex
index 39709550273ada4a8b0fd73d69b5e4982c883f57..b5f31e50efa563c748fa03ada85b61a6139510fe 100644
--- a/public/gentrap/src/main/resources/nl/lumc/sasc/biopet/pipelines/gentrap/templates/pdf/sample.tex
+++ b/public/gentrap/src/main/resources/nl/lumc/sasc/biopet/pipelines/gentrap/templates/pdf/sample.tex
@@ -1,7 +1,9 @@
\part{Sample "((( sample.name )))" Results}
\label{sample:(((sample.name)))}
+((* if sample.libs|length > 1 *))
((* include "sample_mapping.tex" *))
+((* endif *))
((* for lib in sample.libs.values() *))
((* include "lib.tex" *))
diff --git a/public/gentrap/src/main/resources/nl/lumc/sasc/biopet/pipelines/gentrap/templates/pdf/sample_mapping.tex b/public/gentrap/src/main/resources/nl/lumc/sasc/biopet/pipelines/gentrap/templates/pdf/sample_mapping.tex
index 5e3ab9da745896723197f78ca8ba0d9d428f3667..4ad4547277343f82d7e0412603c6311110ddb4b5 100644
--- a/public/gentrap/src/main/resources/nl/lumc/sasc/biopet/pipelines/gentrap/templates/pdf/sample_mapping.tex
+++ b/public/gentrap/src/main/resources/nl/lumc/sasc/biopet/pipelines/gentrap/templates/pdf/sample_mapping.tex
@@ -5,6 +5,78 @@
\indent
+% number + percentage of reads mapped to genome
+% number + percentage of properly paired reads
+\begin{center}
+ \captionof{table}{Mapping Overview}
+ \label{tab:bamstat-((( sample.name )))}
+ \setlength{\tabcolsep}{11pt}
+ ((* if sample.is_paired_end *))
+ \begin{tabular}{ l r r r }
+ \hline
+ \multirow{2}{*}{Parameter} & \multicolumn{1}{c}{All Pairs} & \multicolumn{1}{c}{First in Pairs} & \multicolumn{1}{c}{Second in Pairs} \\
+ & Value & Value & Value \\
+ \hline \hline
+ Total reads & ((( sample.aln_metrics.PAIR.total_reads|nice_int ))) & ((( sample.aln_metrics.FIRST_OF_PAIR.total_reads|nice_int ))) & ((( sample.aln_metrics.SECOND_OF_PAIR.total_reads|nice_int ))) \\
+ Mean read length & ((( sample.aln_metrics.PAIR.mean_read_length|nice_flt ))) & ((( sample.aln_metrics.FIRST_OF_PAIR.mean_read_length|nice_flt ))) & ((( sample.aln_metrics.SECOND_OF_PAIR.mean_read_length|nice_flt ))) \\
+ Strand balance & ((( sample.aln_metrics.PAIR.strand_balance|nice_flt ))) & ((( sample.aln_metrics.FIRST_OF_PAIR.strand_balance|nice_flt ))) & ((( sample.aln_metrics.SECOND_OF_PAIR.strand_balance|nice_flt ))) \\
+ \% Mapped to reference & ((( sample.aln_metrics.PAIR.pct_pf_reads_aligned|float2nice_pct )))\% & ((( sample.aln_metrics.FIRST_OF_PAIR.pct_pf_reads_aligned|float2nice_pct )))\% & ((( sample.aln_metrics.SECOND_OF_PAIR.pct_pf_reads_aligned|float2nice_pct )))\% \\
+ \% Mapped to reference (MAPQ >= 20) & ((( sample.aln_metrics.PAIR.pct_pf_reads_aligned|float2nice_pct )))\% & ((( sample.aln_metrics.FIRST_OF_PAIR.pct_pf_reads_aligned|float2nice_pct )))\% & ((( sample.aln_metrics.SECOND_OF_PAIR.pct_pf_reads_aligned|float2nice_pct )))\% \\
+ Mismatch rate & ((( sample.aln_metrics.PAIR.pf_mismatch_rate|float2nice_pct )))\% & ((( sample.aln_metrics.FIRST_OF_PAIR.pf_mismatch_rate|float2nice_pct )))\% & ((( sample.aln_metrics.SECOND_OF_PAIR.pf_mismatch_rate|float2nice_pct )))\% \\
+ Indel rate & ((( sample.aln_metrics.PAIR.pf_indel_rate|float2nice_pct )))\% & ((( sample.aln_metrics.FIRST_OF_PAIR.pf_indel_rate|float2nice_pct )))\% & ((( sample.aln_metrics.SECOND_OF_PAIR.pf_indel_rate|float2nice_pct )))\% \\
+ Chimeras & ((( sample.aln_metrics.PAIR.pct_chimeras|float2nice_pct )))\% & ((( sample.aln_metrics.FIRST_OF_PAIR.pct_chimeras|float2nice_pct )))\% & ((( sample.aln_metrics.SECOND_OF_PAIR.pct_chimeras|float2nice_pct )))\% \\
+ \hline
+ ((* else *))
+ \begin{tabular}{ l r }
+ \hline
+ \multirow{1}{*}{Parameter} & \multicolumn{1}{c}{Value} \\
+ \hline \hline
+ Total reads & ((( sample.aln_metrics.UNPAIRED.total_reads|nice_int ))) \\
+ Mean read length & ((( sample.aln_metrics.UNPAIRED.mean_read_length|nice_flt ))) \\
+ Strand balance & ((( sample.aln_metrics.UNPAIRED.strand_balance|nice_flt ))) \\
+ \% Mapped to reference & ((( sample.aln_metrics.UNPAIRED.pct_pf_reads_aligned|float2nice_pct )))\% \\
+ \% Mapped to reference (MAPQ >= 20) & ((( sample.aln_metrics.UNPAIRED.pct_pf_reads_aligned|float2nice_pct )))\% \\
+ Mismatch rate & ((( sample.aln_metrics.UNPAIRED.pf_mismatch_rate|float2nice_pct )))\% \\
+ Indel rate & ((( sample.aln_metrics.UNPAIRED.pf_indel_rate|float2nice_pct )))\% \\
+ \hline
+ ((* endif *))
+ \end{tabular}
+\end{center}
+
+((* if sample.is_paired_end *))
+% inferred insert size distribution
+\subsubsection{Insert size distribution}
+
+\IfFileExists{((( sample.inserts_metrics_files.output_histogram.path )))}
+{
+ \begin{figure}[h!]
+ \centering
+ \includegraphics[width=0.7\textwidth]{((( sample.inserts_metrics_files.output_histogram.path )))}
+ \caption{Distribution of insert size length of paired-end reads mapped to opposite strands.}
+ \end{figure}
+}
+((= TODO: strand-specific stats
+%{
+% \IfFileExists{((( vars['OUT_DIR'] )))/((( vars['SAMPLE'] ))).f.insertsizes.png}
+% {
+% \begin{figure}[h!]
+% \centering
+% \includegraphics[width=0.7\textwidth]{((( vars['OUT_DIR'] )))/((( vars['SAMPLE'] ))).f.insertsizes.png}
+% \caption{Distribution of insert size length of paired-end reads whose first read maps to the minus strand.}
+% \end{figure}
+% }{}
+% \IfFileExists{((( vars['OUT_DIR'] )))/((( vars['SAMPLE'] ))).r.insertsizes.png}
+% {
+% \begin{figure}[h!]
+% \centering
+% \includegraphics[width=0.7\textwidth]{((( vars['OUT_DIR'] )))/((( vars['SAMPLE'] ))).r.insertsizes.png}
+% \caption{Distribution of insert size length of paired-end reads whose first read maps to the plus strand.}
+% \end{figure}
+% }{}
+%}
+=))
+((* endif *))
+
\subsection{RNA-specific metrics}