From 75e1b59821cd95958bf6ce7e5021b028b9e9b1db Mon Sep 17 00:00:00 2001
From: sajvanderzeeuw <s.a.j.van_der_zeeuw@lumc.nl>
Date: Wed, 4 Nov 2015 15:03:40 +0100
Subject: [PATCH] num_reads_discarded changed into num_reads_discarded_total
---
.../gentrap/templates/pdf/lib_seqeval.tex | 24 ++-----------------
1 file changed, 2 insertions(+), 22 deletions(-)
diff --git a/public/gentrap/src/main/resources/nl/lumc/sasc/biopet/pipelines/gentrap/templates/pdf/lib_seqeval.tex b/public/gentrap/src/main/resources/nl/lumc/sasc/biopet/pipelines/gentrap/templates/pdf/lib_seqeval.tex
index ee2bc6a4f..472c22944 100644
--- a/public/gentrap/src/main/resources/nl/lumc/sasc/biopet/pipelines/gentrap/templates/pdf/lib_seqeval.tex
+++ b/public/gentrap/src/main/resources/nl/lumc/sasc/biopet/pipelines/gentrap/templates/pdf/lib_seqeval.tex
@@ -99,26 +99,6 @@ More information about clipping using cutadapt is available on the
\end{center}
\addtocounter{table}{-1}
-((* if lib.is_paired_end *))
-After clipping, all read pairs are then checked ('synced') for their
-completeness. Read pairs whose other half has been discarded during
-clipping, will also be discarded. The summary of this step is available in
-Table~\ref{tab:clipsync}.
-
-\begin{center}
- \captionof{table}{Summary of Post-Clipping Sync Step}
- \label{tab:clipsync}
- \begin{tabular}{ l r }
- \hline
- Parameter & Count\\ \hline \hline
- Discarded FASTQ records from read 1 & ((( lib.flexiprep.stats.fastq_sync.num_reads_discarded_R1|nice_int )))\\
- Discarded FASTQ records from read 2 & ((( lib.flexiprep.stats.fastq_sync.num_reads_discarded_R2|nice_int )))\\
- \hline
- Total kept FASTQ records & ((( lib.flexiprep.stats.fastq_sync.num_reads_kept|nice_int )))\\
- \hline
- \end{tabular}
-\end{center}
-((* endif *))
((* endif *))
\vspace{2mm}
@@ -141,8 +121,8 @@ Table~\ref{tab:clipsync}.
\begin{tabular}{ l r }
\hline
Parameter & Count\\ \hline \hline
- Discarded FASTQ records from read 1 & ((( lib.flexiprep.stats.trimming_R1.num_reads_discarded|nice_int )))\\
- Discarded FASTQ records from read 2 & ((( lib.flexiprep.stats.trimming_R2.num_reads_discarded|nice_int )))\\
+ Discarded FASTQ records from read 1 & ((( lib.flexiprep.stats.trimming_R1.num_reads_discarded_total|nice_int )))\\
+ Discarded FASTQ records from read 2 & ((( lib.flexiprep.stats.trimming_R2.num_reads_discarded_total|nice_int )))\\
\hline
\end{tabular}
\end{center}
--
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