[med-svn] [subread] 01/05: Imported Upstream version 1.5.1+dfsg
Alex Mestiashvili
malex-guest at moszumanska.debian.org
Sun Aug 28 07:09:00 UTC 2016
This is an automated email from the git hooks/post-receive script.
malex-guest pushed a commit to branch master
in repository subread.
commit e3249b5c67ca09c696b10421c5ea109aac772846
Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
Date: Sun Aug 28 08:30:43 2016 +0200
Imported Upstream version 1.5.1+dfsg
---
annotation/hg38_RefSeq_exon.txt | 261753 +++++++++++++++++++++++
doc/SubreadUsersGuide.tex | 143 +-
src/Makefile | 2 +-
src/Makefile.FreeBSD | 2 +-
src/Makefile.Linux | 2 +-
src/Makefile.MacOS | 2 +-
src/SNPCalling.c | 8 +-
src/core-indel.c | 38 +-
src/core-interface-aligner.c | 5 +
src/core-interface-subjunc.c | 6 +
src/core-junction.c | 2 +-
src/core.c | 86 +-
src/core.h | 5 +-
src/gene-value-index.c | 5 +-
src/input-files.c | 54 +-
src/input-files.h | 2 +
src/interval_merge.c | 24 +-
src/makefile.version | 2 +-
src/readSummary.c | 1166 +-
test/featureCounts/data/corner-MinOverlap.ora | 8 +-
test/featureCounts/data/corner-fractions.SAF | 5 +
test/featureCounts/data/corner-fractions.ora | 3 +
test/featureCounts/data/corner-fractions.sam | 7 +
test/featureCounts/data/test-fracOverlap.ora | 4 +
test/featureCounts/data/test-fracOverlap.sam | 4 +
test/featureCounts/test_corner_cases.sh | 8 +-
26 files changed, 262873 insertions(+), 473 deletions(-)
diff --git a/annotation/hg38_RefSeq_exon.txt b/annotation/hg38_RefSeq_exon.txt
new file mode 100644
index 0000000..4d5e5d6
--- /dev/null
+++ b/annotation/hg38_RefSeq_exon.txt
@@ -0,0 +1,261753 @@
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diff --git a/doc/SubreadUsersGuide.tex b/doc/SubreadUsersGuide.tex
index 0bb5644..01f3e3e 100644
--- a/doc/SubreadUsersGuide.tex
+++ b/doc/SubreadUsersGuide.tex
@@ -35,9 +35,9 @@
\begin{center}
{\Huge\bf Subread/Rsubread Users Guide}\\
\vspace{1 cm}
-{\centering\large Subread v1.5.0-p3/Rsubread v1.22.1\\}
+{\centering\large Subread v1.5.1/Rsubread v1.23.4\\}
\vspace{1 cm}
-\centering 27 May 2016\\
+\centering 25 August 2016\\
\vspace{5 cm}
\Large Wei Shi and Yang Liao\\
\vspace{1 cm}
@@ -306,19 +306,19 @@ An index must be built for the reference first and then the read mapping can be
{\noindent\bf Step 2: Align reads}\\
\noindent Map single-end reads from a gzipped file using 5 threads and save mapping results to a BAM file:\\
-\code{subread-align -T 5 -i my\_index -r reads.txt.gz -o subread\_results.bam}\\
+\code{subread-align -t 1 -T 5 -i my\_index -r reads.txt.gz -o subread\_results.bam}\\
\noindent Detect indels of up to 16bp:\\
-\code{subread-align -I 16 -i my\_index -r reads.txt -o subread\_results.sam}\\
+\code{subread-align -t 1 -I 16 -i my\_index -r reads.txt -o subread\_results.sam}\\
\noindent Report up to three best mapping locations:\\
-\code{subread-align -B 3 -i my\_index -r reads.txt -o subread\_results.sam}\\
+\code{subread-align -t 1 -B 3 -i my\_index -r reads.txt -o subread\_results.sam}\\
\noindent Report uniquely mapped reads only:\\
-\code{subread-align -u -i my\_index -r reads.txt -o subread\_results.sam}\\
+\code{subread-align -t 1 -u -i my\_index -r reads.txt -o subread\_results.sam}\\
\noindent Map paired-end reads:\\
-\code{subread-align -d 50 -D 600 -i my\_index -r reads1.txt -R reads2.txt \newline -o subread\_results.sam}\\
+\code{subread-align -t 1 -d 50 -D 600 -i my\_index -r reads1.txt -R reads2.txt \newline -o subread\_results.sam}\\
\section{A quick start for using Bioconductor {\Rsubread} package}
@@ -338,22 +338,22 @@ buildindex(basename="my_index",reference="genome.fa")
\noindent Map single-end reads using 5 threads:
\begin{Rcode}
-align(index="my_index",readfile1="reads.txt.gz",output_file="rsubread.bam",nthreads=5)
+align(index="my_index",readfile1="reads.txt.gz",type="dna",output_file="rsubread.bam",nthreads=5)
\end{Rcode}
\noindent Detect indels of up to 16bp:
\begin{Rcode}
-align(index="my_index",readfile1="reads.txt.gz",output_file="rsubread.bam",indels=16)
+align(index="my_index",readfile1="reads.txt.gz",type="dna",output_file="rsubread.bam",indels=16)
\end{Rcode}
\noindent Report up to three best mapping locations:
\begin{Rcode}
-align(index="my_index",readfile1="reads.txt.gz",output_file="rsubread.bam",nBestLocations=3)
+align(index="my_index",readfile1="reads.txt.gz",type="dna",output_file="rsubread.bam",nBestLocations=3)
\end{Rcode}
\noindent Map paired-end reads:
\begin{Rcode}
-align(index="my_index",readfile1="reads1.txt.gz",readfile2="reads2.txt.gz",
+align(index="my_index",readfile1="reads1.txt.gz",readfile2="reads2.txt.gz",type="dna",
output_file="rsubread.bam",minFragLength=50,maxFragLength=600)
\end{Rcode}
@@ -370,7 +370,7 @@ Table 1 describes the arguments used by the \code{subread-buildindex} program.
\newpage
\begin{table}[h]
-\raggedright{Table 1: Arguments used by the \code{subread-buildindex} program (\code{buildindex} function in \Rsubread).
+\raggedright{Table 1: Arguments used by the \code{subread-buildindex} program (\code{buildindex} function in \Rsubread) in alphabetical order.
Arguments in parenthesis in the first column are used by \code{buildindex}.\newline\\}
\begin{tabular}{|p{4cm}|p{12cm}|}
\hline
@@ -407,7 +407,7 @@ Arguments used in Bioconductor \code{Rsubread} package are included in parenthes
\begin{longtable}{|p{4cm}|p{12cm}|}
-\multicolumn{2}{p{16cm}}{Table 2: Arguments used by the \code{subread-align}/\code{subjunc} programs included in the SourceForge {\Subread} package.
+\multicolumn{2}{p{16cm}}{Table 2: Arguments used by the \code{subread-align}/\code{subjunc} programs included in the SourceForge {\Subread} package in alphabetical order.
Arguments in parenthesis in the first column are the equivalent arguments used in Bioconductor {\Rsubread} package.
Arguments used by \code{subread-align} only are marked with $^*$.
Arguments used by \code{subjunc} only are marked with $^{**}$.
@@ -447,7 +447,7 @@ Arguments & Description \\
\hline
-S $<ff:fr:rf>$ \newline (\code{PE\_orientation}) & Specify the orientation of the two reads from the same pair. It has three possible values including `fr', `ff' and `'rf. Letter `f' denotes the forward strand and letter `r' the reverse strand. `fr' by default (ie. the first read in the pair is on the forward strand and the second read on the reverse strand).\\
\hline
-$^*$ -t $<int>$ \newline (\code{type}) & Specify the type of input sequencing data. Possible values include \code{0}, denoting RNA-seq data, or \code{1}, denoting genomic DNA-seq data. Character values including `rna' and `dna' can also be used in the {\R} function. For genomic DNA-seq data, the aligner takes into account both the number of matched bases and the number of mis-matched bases to determine the the best mapping location after applying the `seed-and-vote' approach for read ma [...]
+$^*$ -t $<int>$ \newline (\code{type}) & Specify the type of input sequencing data. Possible values include \code{0}, denoting RNA-seq data, or \code{1}, denoting genomic DNA-seq data. User must specify the value. Character values including `rna' and `dna' can also be used in the {\R} function. For genomic DNA-seq data, the aligner takes into account both the number of matched bases and the number of mis-matched bases to determine the the best mapping location after applying the `seed-a [...]
\hline
-T $<int>$ \newline (\code{nthreads}) & Specify the number of threads/CPUs used for mapping. The value should be between 1 and 32. 1 by default.\\
\hline
@@ -489,23 +489,36 @@ $--$trim3 $<int>$ \newline (\code{nTrim3}) & Trim off $<int>$ number of bases fr
\section{Mapping quality scores}
-Both {\Subread} and {\Subjunc} aligners output a mapping quality score (MQS) for each mapped read,
-computed as
+{\Subread} and {\Subjunc} aligners assign a mapping quality score (MQS) to each mapped read to indicate the confidence of the mapping:\\
\[ MQS = \left\{
\begin{array}{l l}
-(\sum_{i \in b_m} ( 1 - p_i) - \sum_{i \in b_{mm}} (1 - p_i)) \times 60 / L & \quad \text{if uniquely mapped}\\
-& \quad \text{\scriptsize{[MQS is reset to 0 if less than 0]}}\\
+\frac{40}{(N_c + N_{mm})} & \quad \text{if only one best location found}\\
& \\
-0 & \quad \text{if mapped to $>1$ best location}\\
-\end{array} \right.\]
+& \\
+0 & \quad \text{if $>1$ equally best locations were found}\\
+\end{array} \right.\] \\
+
+\noindent where $N_c$ is the number of candidate locations that are considered for final full alignment (re-alignment step).
+Such locations must have a vote number within top three vote numbers counted from all locations considered in the subread-mapping step (first scan).
+Up to three candiate locations are considered for each read in the realignment step.
+$N_{mm}$ is the number of mismatches found in the alignment at each candidate location.
+
+
-where $L$ is the read length, $p_i$ is the base-calling $p$-value for the $i$th base in the read, $b_m$ is the set of locations of matched bases, and $b_{mm}$ is the set of locations of mismatched bases.
+% \[ MQS = \left\{
+% \begin{array}{l l}
+% (\sum_{i \in b_m} ( 1 - p_i) - \sum_{i \in b_{mm}} (1 - p_i)) \times 60 / L & \quad \text{if uniquely mapped}\\
+% & \quad \text{\scriptsize{[MQS is reset to 0 if less than 0]}}\\
+% & \\
+% 0 & \quad \text{if $>1$ equally best locations found}\\
+% \end{array} \right.\]
+% where $L$ is the read length, $p_i$ is the base-calling $p$-value for the $i$th base in the read, $b_m$ is the set of locations of matched bases, and $b_{mm}$ is the set of locations of mismatched bases.
+% Base-calling p values can be readily computed from the base quality scores.
+% Read bases of high sequencing quality have low base-calling p values.
+% Read bases that were found to be insertions are treated as matched bases in the MQS calculation.
+% The MQS is a read-length normalized value and it is in the range [0, 60).
-Base-calling p values can be readily computed from the base quality scores.
-Read bases of high sequencing quality have low base-calling p values.
-Read bases that were found to be insertions are treated as matched bases in the MQS calculation.
-The MQS is a read-length normalized value and it is in the range [0, 60).
\section{Mapping output}
@@ -542,7 +555,7 @@ You can provide a list of FASTA files or a single FASTA file including all the r
The commands used by {\Subread} to align RNA-seq reads are the same as those used to align gDNA-seq reads.
Below is an example of using {\Subread} to map single-end RNA-seq reads.\\
-\code{subread-align -i my\_index -r rnaseq-reads.txt -o subread\_results.sam}\\
+\code{subread-align -t 0 -i my\_index -r rnaseq-reads.txt -o subread\_results.sam}\\
\noindent Another RNA-seq aligner included in this package is the {\Subjunc} aligner.
{\Subjunc} not only performs read alignments but also detects exon-exon junctions.
@@ -652,10 +665,11 @@ We found that there was a significant decrease in the number of mapped reads whe
We therefore used a threshold of 4 consensus subreads to map this dataset.
However, what we observed might not be the case for other datasets that were generated from different cell types and different species.
-Below is an example of mapping 50bp long reads (adaptor sequences were included in the reads in addition to the miRNA sequences), with at least 4 consensus subreads required in the mapping:
+Below is an example of mapping 50bp long reads (adaptor sequences were included in the reads in addition to the miRNA sequences), with at least 4 consensus subreads required in the mapping.
+Note that `-t' option should have a value of 1 since miRNA-seq reads are more similar to gDNA-seq reads than mRNA-seq reads from the read mapping point of vew.
\code{\\
-subread-align -i mm10\_full\_index -n 35 -m 4 -M 3 -T 10 -I 0 -P 3 -B 10 \\
+subread-align -t 1 -i mm10\_full\_index -n 35 -m 4 -M 3 -T 10 -I 0 -P 3 -B 10 \\
-r miRNA\_reads.fastq -o result.sam\\
}
@@ -664,6 +678,8 @@ The multiple locations reported for the reads could be useful for investigating
The miRBase database (\url{http://www.mirbase.org/}) is a useful resource that includes annotations for miRNA genes in many species.
The {\featureCounts} program can be readily used for summarizing reads to miRNA genes.
+
+
\chapter{Read summarization}
\section{Introduction}
@@ -679,16 +695,16 @@ Here we describe the {\featureCounts} program, an efficient and accurate read qu
{\featureCounts} has the following features:
\begin{itemize}
\item It carries out precise and accurate read assignments by taking care of indels, junctions and structural variants in the reads.
-\item It takes only $\sim$1 minute to summarize 20 million read pairs of reads to 26 thousand RefSeq genes.
-\item It supports GTF/SAF format annotation and SAM/BAM read data.
-\item It supports strand-specific read summarization.
-\item It can perform read summarization at both feature level (eg. exon level) and meta-feature level (eg. gene level).
-\item It allows users to specify whether reads overlapping with more than one feature should be counted or not.
+\item It takes only half a minute to summarize 20 million reads.
+\item It supports GTF and SAF format annotation.
+\item It supports strand-specific read counting.
+\item It can count reads at feature (eg. exon) or meta-feature (eg. gene) level.
+\item Highly flexible in counting multi-mapping and multi-overlapping reads. Such reads can be excluded, fully counted or fractionally counted.
\item It gives users full control on the summarization of paired-end reads, including allowing them to check if both ends are mapped and/or if the fragment length falls within the specified range.
-\item It can discriminate the features that were overlapped by both ends of the fragment from the features that were overlapped by only one end of the same fragment to get more accurate read assignments.
+\item Reduce ambuiguity in assigning read pairs by searching features that overlap with both reads from the pair.
\item It allows users to specify whether chimeric fragments should be counted.
-\item It automatically detects the read input format (SAM or BAM).
-\item It automatically re-order paired-end reads if reads belonging to the same pair are not adjacent to each other in input read files.
+\item Automatically detect input format (SAM or BAM).
+\item Automatically sort paired-end reads. Users can provide either location-sorted or name-sorted bams files to featureCounts. Read sorting is implemented on the fly and it only incurs minimal time cost.
\end{itemize}
\section{featureCounts}
@@ -741,8 +757,8 @@ Chromosomal names included in the \code{Chr} column must match the chromosomal n
Reads may be paired or unpaired.
If paired reads are used, then each pair of reads defines a DNA or RNA fragment bookended by the two reads.
In this case, {\featureCounts} can be instructed to count fragments rather than reads.
-{\featureCounts} automatically sorts reads by name if paired reads are not in consecutive positions in the SAM or BAM file.
-Users do not need sort their paired reads before providing them to {\featureCounts}.
+{\featureCounts} automatically sorts reads by name if paired reads are not in consecutive positions in the SAM or BAM file, with minimal cost.
+Users do not need to sort their paired reads before providing them to {\featureCounts}.
\subsection{Features and meta-features}
@@ -753,12 +769,30 @@ We recommend to use unique gene identifiers, such as NCBI Entrez gene identifier
\subsection{Overlap of reads with features}
-{\featureCounts} preforms precise read assignment by comparing mapping location of every base in the read or fragment with the genomic region spanned by each feature. It takes account of any gaps (insertions, deletions, exon-exon junctions or structural variants) that are found in the read. It calls a hit if any overlap (1bp or more) is found between the read or fragment and a feature.
-A hit is called for a meta-feature if the read or fragment overlaps any component feature of the meta-feature.
+{\featureCounts} preforms precise read assignment by comparing mapping location of every base in the read or fragment with the genomic region spanned by each feature.
+It takes account of any gaps (insertions, deletions, exon-exon junctions or structural variants) that are found in the read.
+It calls a hit if any overlap is found between read and feature.
+
+Users may use `--minOverlap (\code{minOverlap} in \R)' and `--fracOverlap (\code{fracOverlap} in \R)' options to specify the minimum number of overlapping bases and minimum fraction of overlapping bases requried for assigning a read to a feature, respectively.
+The `--fracOverlap' option might be particularly useful for counting reads with variable lengths.
+% A hit is called for a meta-feature if the read or fragment overlaps any component feature of the meta-feature.
-\subsection{Multiple overlaps}
+\subsection{Multi-mapping reads}
-A multi-overlap read or fragment is one that overlaps more than one feature, or more than one meta-feature when summarizing at the meta-feature level. {\featureCounts} provides users with the option to either exclude multi-overlap reads or to count them for each feature that is overlapped. The decision whether or not to counting these reads is often determined by the experiment type. We recommend that reads or fragments overlapping more than one gene are not counted for RNA-seq experimen [...]
+A multi-mapping read is a read that can be equally best mapped to more than one location in the reference genome.
+Due to the mapping amguity, it is recommended that multi-mapping reads should be excluded from read counting (default behavior of {\featureCounts} program) to produce as accurate counts as possible.
+
+However we do provide users with different options to deal with the counting of such reads.
+Users can choose to discard multi-mapping reads, or fully count every alignment reported for a multi-mapping read (ie. each alignment carries 1 count) or count each alignment fractionally (ie. each alignment carries $1/n$ count where $n$ is the total number of alignments reported for the read).
+Relevent parameters for counting multi-mapping reads include `-M' (\code{countMultiMappingReads} in \R) and `--fraction' (\code{fraction} in \R).
+
+
+\subsection{Multi-overlap reads}
+
+A multi-overlap read or fragment is one that overlaps more than one feature, or more than one meta-feature when summarizing at the meta-feature level. {\featureCounts} provides users with the option to exclude multi-overlap reads, or fully count them for each overlapping feature (ie. each overlapping feature receives a count of 1 from the read) or assign a fractional count to each overlapping feature.
+Relevent parameters for counting multi-overlap reads include `-O' (\code{allowMultiOverlap} in \R) and `--fraction' (\code{fraction} in \R).
+
+The decision whether or not to counting these reads is often determined by the experiment type. We recommend that reads or fragments overlapping more than one gene are not counted for RNA-seq experiments, because any single fragment must originate from only one of the target genes but the identity of the true target gene cannot be confidently determined. On the other hand, we recommend that multi-overlap reads or fragments are counted for most ChIP-seq experiments because epigenetic modi [...]
Note that, when counting at the meta-feature level, reads that overlap multiple features of the same meta-feature are always counted exactly once for that meta-feature, provided there is no overlap with any other meta-feature. For example, an exon-spanning read will be counted only once for the corresponding gene even if it overlaps with more than one exon.
@@ -809,7 +843,7 @@ Table 3 describes the parameters used by the {\featureCounts} program.
\pagebreak
\begin{longtable}{|p{5cm}|p{11cm}|}
-\multicolumn{2}{p{16cm}}{Table 3: arguments used by the {\featureCounts} program included in the SourceForge {\Subread} package.
+\multicolumn{2}{p{16cm}}{Table 3: Arguments used by the {\featureCounts} program included in the SourceForge {\Subread} package in alphabetical order.
Arguments included in parenthesis are the equivalent parameters used by {\featureCounts} function in Bioconductor {\Rsubread} package.}
\endfirsthead
\hline
@@ -819,7 +853,7 @@ input\_files \newline (\code{files}) & Give the names of input read files that i
\hline
-a $<input> \newline (\code{annot.ext, annot.inbuilt}) $ & Give the name of an annotation file. \\
\hline
--A \newline (\code{chrAliases}) & Give the name of a file that contains aliases of chromosome names. The file should be a comma delimited text file that includes two columns. The first column gives the chromosome names used in the annotation and the second column gives the chromosome names used by reads. This file should not contain header lines. Names included in this file are case sensitive.\\
+-A \newline (\code{chrAliases}) & Provide a chromosome name alias file to match chr names in annotation with those in the reads. This should be a two-column comma-delimited text file. Its first column should include chr names in the annotation and its second column should include chr names in the reads. Chr names are case sensitive. No column header should be included in the file.\\
\hline
-B \newline (\code{requireBothEndsMapped}) & If specified, only fragments that have both ends successfully aligned will be considered for summarization. This option should be used together with \code{-p} (or \code{isPairedEnd} in {\Rsubread} {\featureCounts}).\\
\hline
@@ -835,7 +869,8 @@ input\_files \newline (\code{files}) & Give the names of input read files that i
\hline
-g $<input>$ \newline (\code{GTF.attrType}) & Specify the attribute type used to group features (eg. exons) into meta-features (eg. genes) when GTF annotation is provided. `gene\_id' by default. This attribute type is usually the gene identifier. This argument is useful for the meta-feature level summarization.\\
\hline
--G $<input>$ \newline (\code{genome}) & Provide the name of a FASTA-format file that includes the reference genome sequences. The reference genome provided here should be the same as the one used in read mapping.\\
+-G $<input>$ \newline (\code{genome}) & Provide the name of a FASTA-format file that contains the reference sequences used in
+read mapping that produced the provided SAM/BAM files. This optional argument can be used with '-J' option to improve read counting for junctions.\\
\hline
-J \newline (\code{juncCounts}) & Count the number of reads supporting each exon-exon junction. Junctions are identified from those exon-spanning reads (containing `N' in CIGAR string) in input data. For each junction, the reported data include number of supporting reads, genes that the junction belongs to, chromosomal coordinates of splice sites etc.\\
\hline
@@ -851,9 +886,9 @@ input\_files \newline (\code{files}) & Give the names of input read files that i
\hline
-Q $<int>$ \newline (\code{minMQS}) & The minimum mapping quality score a read must satisfy in order to be counted. For paired-end reads, at least one end should satisfy this criteria. 0 by default.\\
\hline
--R & Output read assignment results for each read (or fragment if paired end). They are saved to a tab-delimited file that contains four columns including read name, status(assigned or the reason if not assigned), name of target feature/meta-feature and number of hits if the read/fragment is counted multiple times. Name of the file is the input file name added with a suffix `.featureCounts'.\\
+-R \newline (\code{reportReads}) & Output detailed read assignment results for each read (or fragment if paired end). They are saved to a tab-delimited file that contains four columns including read name, status(assigned or the reason if not assigned), name of target feature/meta-feature and total number of hits if the read/fragment is counted multiple times. Names of output files are the same as input file names except a suffix string `.featureCounts' is added.\\
\hline
--s $<int>$ \newline (\code{isStrandSpecific}) & Indicate if strand-specific read counting should be performed. It has three possible values: 0 (unstranded), 1 (stranded) and 2 (reversely stranded). 0 by default. For paired-end reads, strand of the first read is taken as the strand of the whole fragment and FLAG field of the current read is used to tell if it is the first read in the fragment.\\
+-s $<int>$ \newline (\code{isStrandSpecific}) & Indicate if strand-specific read counting should be performed. Acceptable values: 0 (unstranded), 1 (stranded) and 2 (reversely stranded). 0 by default. For paired-end reads, strand of the first read is taken as the strand of the whole fragment and FLAG field of the current read is used to tell if it is the first read in the fragment.\\
\hline
-t $<input>$ \newline (\code{GTF.featureType}) & Specify the feature type. Only rows which have the matched feature type in the provided GTF annotation file will be included for read counting. `exon' by default.\\
\hline
@@ -861,13 +896,15 @@ input\_files \newline (\code{files}) & Give the names of input read files that i
\hline
-v & Output version of the program. \\
\hline
-$--$countSplitAlignmentsOnly \newline (\code{splitOnly}) & If specified, only split alignments (CIGAR strings contain letter `N') will be counted. All the other alignments will be ignored. An example of split alignments is the exon-spanning reads in RNA-seq data. If exon-spanning reads need to be assigned to all their overlapping exons, `-f' and `-O' options should be provided as well.\\
+$--$countSplit \newline AlignmentsOnly \newline (\code{splitOnly}) & If specified, only split alignments (CIGAR strings contain letter `N') will be counted. All the other alignments will be ignored. An example of split alignments is the exon-spanning reads in RNA-seq data. If exon-spanning reads need to be assigned to all their overlapping exons, `-f' and `-O' options should be provided as well.\\
\hline
-$--$countNonSplitAlignmentsOnly \newline (\code{nonSplitOnly}) & If specified, only non-split alignments (CIGAR strings do not contain letter `N') will be counted. All the other alignments will be ignored.\\
+$--$countNonSplit \newline AlignmentsOnly \newline (\code{nonSplitOnly}) & If specified, only non-split alignments (CIGAR strings do not contain letter `N') will be counted. All the other alignments will be ignored.\\
\hline
$--$donotsort \newline (\code{autosort}) & If specified, paired end reads will not be re-ordered even if reads from the same pair were found not to be next to each other in the input.\\
\hline
-$--$fraction \newline (\code{fraction}) & If specified, a fractional count 1/n will be generated for each multi-mapping read, where n is the number of alignments (indicated by `NH' tag) reported for the read. This option must be used together with the `-M' option.\\
+$--$fraction \newline (\code{fraction}) & Assign fractional counts to features. This option must be used together with '-M' or '-O' or both. When '-M' is specified, each reported alignment from a multi-mapping read (identified via `NH' tag) will carry a fractional count of 1/x, instead of 1 (one), where x is the total number of alignments reported for the same read. When '-O' is specified, each overlapping feature will receive a fractional count of 1/y, where y is the total number of fea [...]
+\hline
+$--$fracOverlap $<value>$ \newline (\code{fracOverlap}) & Minimum fraction of overlapping bases in a read that is required for read assignment. Value should be within range [0,1]. 0 by default. If paired end, number of overlapping bases is counted from both reads. Soft-clipped bases are counted when calculating total read length (but ignored when counting overlapping bases). Both this option and `--minOverlap' option need to be satisfied for read assignment. \\
\hline
$--$ignoreDup \newline (\code{ignoreDup}) & If specified, reads that were marked as duplicates will be ignored. Bit Ox400 in FLAG field of SAM/BAM file is used for identifying duplicate reads. In paired end data, the entire read pair will be ignored if at least one end is found to be a duplicate read.\\
\hline
@@ -875,7 +912,7 @@ $--$largestOverlap \newline (\code{largestOverlap}) & If specified, reads (or fr
\hline
$--$maxMOp $<int>$ \newline (\code{maxMOp}) & Specify the maximum number of `M' operations (matches or mis-matches) allowed in a CIGAR string. 10 by default. Both `X' and `=' operations are treated as `M' and adjacent `M' operations are merged in the CIGAR string. When the number of `M' operations exceeds the limit, only the first `maxMOp' number of `M' operations will be used in read assignment.\\
\hline
-$--$minOverlap $<int>$ \newline (\code{minOverlap}) & Specify the minimum required number of overlapping bases between a read (or a fragment) and an overlapping feature. 1 by default. If a negative value is provided, the read will be extended from both ends.\\
+$--$minOverlap $<int>$ \newline (\code{minOverlap}) & Minimum number of overlapping bases in a read that is required for read assignment. 1 by default. If a negative value is provided, then a gap of up to specified size will be allowed between read and the feature that the read is assigned to. For assignment of read pairs (fragments), number of overlapping bases from each read from the same pair will be summed. \\
\hline
$--$primary \newline (\code{primaryOnly}) & If specified, only primary alignments will be counted. Primary and secondary alignments are identified using bit 0x100 in the Flag field of SAM/BAM files. All primary alignments in a dataset will be counted no matter they are from multi-mapping reads or not (ie. `-M' is ignored).\\
\hline
@@ -885,6 +922,8 @@ $--$readExtension5 $<int>$ \newline (\code{readExtension5}) & Reads are extended
\hline
$--$readExtension3 $<int>$ \newline (\code{readExtension3}) & Reads are extended downstream by $<int>$ bases from their 3' end. 0 by default.\\
\hline
+$--$tmpDir $<string>$ \newline (\code{tmpDir}) & Directory under which intermediate files are saved (later removed). By default, intermediate files will be saved to the directory specified in `-o' argument (In \R, intermediate files are saved to the current working directory by default).\\
+\hline
\end{longtable}
\pagebreak
@@ -1026,7 +1065,7 @@ The complete list of parameters used by \code{exactSNP} can be found in Table 4.
\begin{longtable}{|p{4.5cm}|p{11cm}|}
-\multicolumn{2}{p{16cm}}{Table 4: arguments used by the \code{exactSNP} program included in the SourceForge {\Subread} package.
+\multicolumn{2}{p{16cm}}{Table 4: Arguments used by the \code{exactSNP} program included in the SourceForge {\Subread} package in alphabetical order.
Arguments included in parenthesis are the equivalent parameters used by \code{exactSNP} function in Bioconductor {\Rsubread} package.}
\endfirsthead
\hline
diff --git a/src/Makefile b/src/Makefile
index 41e8d9f..b43113e 100644
--- a/src/Makefile
+++ b/src/Makefile
@@ -1,7 +1,7 @@
all:
@echo
- @echo " Subread currently supports Linux, Mac OS X, FreeBSD and Solaris. Please choose the correct Makefile to build Subread."
+ @echo " Subread currently supports Linux, Mac OS X and FreeBSD. Please choose the correct Makefile to build Subread."
@echo
@echo " For building subread in Linux, please run ' make -f Makefile.Linux '."
@echo " For building subread in Mac OS X, please run ' make -f Makefile.MacOS '."
diff --git a/src/Makefile.FreeBSD b/src/Makefile.FreeBSD
index 47689cc..f588afc 100644
--- a/src/Makefile.FreeBSD
+++ b/src/Makefile.FreeBSD
@@ -21,7 +21,7 @@ all: featureCounts removeDup exactSNP subread-buildindex subindel subread-align
@echo
@echo "###########################################################"
@echo "# #"
- @echo "# Installation finished. #"
+ @echo "# Installation complete. #"
@echo "# #"
@echo "# Generated executables were copied to directory ../bin/ #"
@echo "# #"
diff --git a/src/Makefile.Linux b/src/Makefile.Linux
index 87ec810..fced4fc 100644
--- a/src/Makefile.Linux
+++ b/src/Makefile.Linux
@@ -20,7 +20,7 @@ all: repair featureCounts removeDup exactSNP subread-buildindex subindel subrea
@echo
@echo "###########################################################"
@echo "# #"
- @echo "# Installation finished. #"
+ @echo "# Installation complete. #"
@echo "# #"
@echo "# Generated executables were copied to directory ../bin/ #"
@echo "# #"
diff --git a/src/Makefile.MacOS b/src/Makefile.MacOS
index 39a61c9..7c8e2bf 100644
--- a/src/Makefile.MacOS
+++ b/src/Makefile.MacOS
@@ -18,7 +18,7 @@ all: repair featureCounts removeDup exactSNP subread-buildindex subindel subrea
@echo
@echo "###########################################################"
@echo "# #"
- @echo "# Installation finished. #"
+ @echo "# Installation complete. #"
@echo "# #"
@echo "# Generated executables were copied to directory ../bin/ #"
@echo "# #"
diff --git a/src/SNPCalling.c b/src/SNPCalling.c
index e34184f..b1feeb9 100644
--- a/src/SNPCalling.c
+++ b/src/SNPCalling.c
@@ -156,7 +156,8 @@ double fisher_exact_test(int a, int b, int c, int d)
if(1){
double ret = fast_fisher_test_one_side(a,b,c,d, precalculated_factorial, PRECALCULATE_FACTORIAL);
- //SUBREADprintf("FISHER_RES %d %d %d %d %.9f %.9f\n", a,b,c,d, ret, log(ret));
+ //#warning ">>>>>> FOR ACCURACY MEASUREMENT ONLY <<<<<<<<"
+ //SUBREADprintf("FISHER_RES %d %d %d %d %.19G %.19G\n", a,b,c,d, ret, log(ret));
return ret;
}else{
int AA=a, BB=b, CC=c, DD=d;
@@ -1735,6 +1736,11 @@ int main_snp_calling_test(int argc,char ** argv)
}
}
+ if(argc > optind){
+ SUBREADprintf("Invalid parameter '%s'\n", argv[optind]);
+ return -1;
+ }
+
if(out_BED_file[0]==0 || in_FASTA_file[0]==0 || (parameters.pile_file_name [0] == 0 && in_SAM_file[0]==0))
{
SUBREADprintf("The names of the input file, the output file and the reference sequence file must be specified using -i, -o and -g options.\n");
diff --git a/src/core-indel.c b/src/core-indel.c
index 31d4bfe..09c2979 100644
--- a/src/core-indel.c
+++ b/src/core-indel.c
@@ -1447,10 +1447,11 @@ int find_new_indels(global_context_t * global_context, thread_context_t * thread
if(first_correct_base < last_correct_base || first_correct_base > last_correct_base + 3000)
SUBREADprintf("WRONG ORDER: F=%u, L=%d\n", first_correct_base , last_correct_base);
- //int last_second_part_base = find_subread_end(read_len, global_context->config.total_subreads , next_correct_subread_last) ;
- if(0 && FIXLENstrcmp("DB7DT8Q1:236:C2NGTACXX:2:1213:17842:64278", read_name) == 0)
+
+ //#warning ">>>>>>> COMMENT NEXT BLOCK IN RELEASE <<<<<<<<"
+ if(0 && FIXLENstrcmp("D00491:277:C89FUANXX:7:1110:20418:31541", read_name) == 0)
//if(current_result->selected_position > 433897 - 100 && current_result->selected_position < 433897)
- SUBREADprintf("INDEL_P03: I=%d; INDELS=%d; POS=%u; COVER=%d -- %d\n", i, indels, current_result->selected_position, last_correct_subread, next_correct_subread);
+ SUBREADprintf("INDEL_P03: I=%d; INDELS=%d; POS=%u; COVER=%d -- %d (vote_no : %d - %d)\n", i, indels, current_result->selected_position, last_correct_base, first_correct_base, last_correct_subread, next_correct_subread);
if(global_context -> config.use_dynamic_programming_indel || read_len > EXON_LONG_READ_LENGTH)
{
@@ -1467,7 +1468,8 @@ int find_new_indels(global_context_t * global_context, thread_context_t * thread
movement_buffer[dyna_steps]=0;
- if(0 && FIXLENstrcmp("DB7DT8Q1:236:C2NGTACXX:2:1213:17842:64278", read_name) == 0)
+ //#warning ">>>>>>> COMMENT NEXT BLOCK IN RELEASE <<<<<<<<"
+ if(0 && FIXLENstrcmp("D00491:277:C89FUANXX:7:1110:20418:31541", read_name) == 0)
{
SUBREADprintf("IR= %d %d~%d\n", dyna_steps, last_correct_base, first_correct_base);
@@ -1518,20 +1520,26 @@ int find_new_indels(global_context_t * global_context, thread_context_t * thread
// let's test if it is ambiguous:
gene_value_index_t * current_value_index = thread_context?thread_context->current_value_index:global_context->current_value_index;
- int ambiguous_i, ambiguous_count=0;
- int best_matched_bases = match_chro(read_text + cursor_on_read - 6, current_value_index, indel_left_boundary - 6, 6, 0, global_context->config.space_type) +
- match_chro(read_text + cursor_on_read - min(current_indel_len,0), current_value_index, indel_left_boundary + max(0, current_indel_len), 6, 0, global_context->config.space_type);
- for(ambiguous_i=-5; ambiguous_i<=5; ambiguous_i++)
- {
- int left_match = match_chro(read_text + cursor_on_read - 6, current_value_index, indel_left_boundary - 6, 6+ambiguous_i, 0, global_context->config.space_type);
- int right_match = match_chro(read_text + cursor_on_read + ambiguous_i - min(current_indel_len,0), current_value_index, indel_left_boundary + ambiguous_i + max(0, current_indel_len), 6-ambiguous_i, 0,global_context->config.space_type);
- if(left_match+right_match == best_matched_bases) ambiguous_count ++;
+
+ //#warning ">>>>>>> COMMENT NEXT BLOCK IN RELEASE <<<<<<<<"
+ if(0 && FIXLENstrcmp("D00491:277:C89FUANXX:7:1110:20418:31541",read_name ) == 0){
+ SUBREADprintf("INDEL_DDADD: abs(I=%d); INDELS=%d; PN=%d; LOC=%ul READ_CUR=%d\n",i, current_indel_len, pair_number, indel_left_boundary-1, cursor_on_read);
}
- //#warning "=========== COMMENT THIS LINE ==============="
- if(0 && FIXLENstrcmp("DB7DT8Q1:236:C2NGTACXX:2:1213:17842:64278", read_name) == 0)
- SUBREADprintf("INDEL_DDADD: abs(I=%d); INDELS=%d; PN=%d; LOC=%u\n",i, current_indel_len, pair_number, indel_left_boundary-1);
+ int ambiguous_count=0;
+ //#warning " >>>>>>>> MAKE SURE DISABLING THE NEXT BLOCK IS HARMLESS <<<<<<<<< "
+ if(0){
+ int ambiguous_i, best_matched_bases = match_chro(read_text + cursor_on_read - 6, current_value_index, indel_left_boundary - 6, 6, 0, global_context->config.space_type) +
+ match_chro(read_text + cursor_on_read - min(current_indel_len,0), current_value_index, indel_left_boundary + max(0, current_indel_len), 6, 0, global_context->config.space_type);
+ for(ambiguous_i=-5; ambiguous_i<=5; ambiguous_i++)
+ {
+ int left_match = match_chro(read_text + cursor_on_read - 6, current_value_index, indel_left_boundary - 6, 6+ambiguous_i, 0, global_context->config.space_type);
+ int right_match = match_chro(read_text + cursor_on_read + ambiguous_i - min(current_indel_len,0), current_value_index, indel_left_boundary + ambiguous_i + max(0, current_indel_len), 6-ambiguous_i, 0,global_context->config.space_type);
+ if(left_match+right_match == best_matched_bases) ambiguous_count ++;
+ }
+ }
+
if(abs(current_indel_len)<=global_context -> config.max_indel_length)
{
chromosome_event_t * new_event = local_add_indel_event(global_context, thread_context, event_table, read_text + cursor_on_read + min(0,current_indel_len), indel_left_boundary - 1, current_indel_len, 1, ambiguous_count, 0);
diff --git a/src/core-interface-aligner.c b/src/core-interface-aligner.c
index e870452..5145414 100644
--- a/src/core-interface-aligner.c
+++ b/src/core-interface-aligner.c
@@ -499,6 +499,11 @@ int parse_opts_aligner(int argc , char ** argv, global_context_t * global_contex
}
}
+ if(argc > optind){
+ SUBREADprintf("Invalid parameter '%s'\n", argv[optind]);
+ return -1;
+ }
+
global_context->config.more_accurate_fusions = global_context->config.more_accurate_fusions && global_context->config.do_fusion_detection;
if(global_context->config.more_accurate_fusions)
{
diff --git a/src/core-interface-subjunc.c b/src/core-interface-subjunc.c
index a9d43ef..f89330c 100644
--- a/src/core-interface-subjunc.c
+++ b/src/core-interface-subjunc.c
@@ -538,6 +538,12 @@ int parse_opts_subjunc(int argc , char ** argv, global_context_t * global_contex
}
}
+ if(argc > optind){
+ SUBREADprintf("Invalid parameter '%s'\n", argv[optind]);
+ return -1;
+ }
+
+
if(global_context->config.is_SAM_file_input) global_context->config.phred_score_format = FASTQ_PHRED33;
global_context->config.more_accurate_fusions = global_context->config.more_accurate_fusions && global_context->config.do_fusion_detection;
diff --git a/src/core-junction.c b/src/core-junction.c
index 3e94dbc..d2fb9a4 100644
--- a/src/core-junction.c
+++ b/src/core-junction.c
@@ -2012,7 +2012,7 @@ int find_donor_receptor(global_context_t * global_context, thread_context_t * th
char out1pos[100];
absoffset_to_posstr(global_context, search_in_chro_start, out1pos);
- if(1 || FIXLENstrcmp("chr14:105",out1pos)==0){
+ if(0 && FIXLENstrcmp("chr14:105",out1pos)==0){
SUBREADprintf("POS=%s\t\tINS=%d\t\t%s\n", out1pos, best_insertion_in_between, rname);
SUBREADprintf("R= %s\nS1=%s%s\nS2=%s%s\n %s|%s|\n\n", rtext, sp1s, chro_bases_startside, sp1s, chro_bases_endside, spE, spBB);
}
diff --git a/src/core.c b/src/core.c
index 3e47262..591802a 100644
--- a/src/core.c
+++ b/src/core.c
@@ -63,6 +63,25 @@ void core_version_number(char * program)
SUBREADprintf("\n%s v%s\n\n" , program, SUBREAD_VERSION);
}
+int is_valid_float(char * optarg, char * optname){
+ int xk1=0;
+ while(1){
+ int nch = optarg[xk1++];
+ if(!nch){
+ if(xk1 == 1){
+ SUBREADprintf("Value for argumant %s-%s is missing.\n", optname[1]?"-":"", optname);
+ return 0;
+ }
+ break;
+ }
+ if(( nch!='-' || xk1 > 1 ) && nch != '.' && !isdigit(nch)){
+ SUBREADprintf("Value for argumant %s-%s is not a valid number: '%s'\n", optname[1]?"-":"", optname, optarg);
+ return 0;
+ }
+ }
+ return 1;
+}
+
int is_valid_digit(char * optarg, char * optname){
int xk1=0;
while(1){
@@ -1187,10 +1206,6 @@ int convert_read_to_tmp(global_context_t * global_context , subread_output_conte
is_r_OK = (current_result -> mapping_result -> result_flags & CORE_IS_FULLY_EXPLAINED) > 0;
- if(is_r_OK)
- if((current_result -> mapping_result -> result_flags & CORE_IS_BREAKEVEN) && !global_context -> config.report_multi_mapping_reads)
- is_r_OK = 0;
-
if(0 && FIXLENstrcmp("V0112_0155:7:1101:5279:29143#ATCACG", read_name) == 0)
SUBREADprintf("%s R_%d CPOINT1 : is_OK=%d\n", read_name , is_second_read + 1 , is_r_OK);
@@ -1205,9 +1220,13 @@ int convert_read_to_tmp(global_context_t * global_context , subread_output_conte
r->is_first_section_jumpped = is_first_section_jumped;
r->linear_position = current_result -> first_base_position;
- r->mapping_quality = current_result -> final_quality;
- if(current_result -> mapping_result -> result_flags & CORE_IS_BREAKEVEN)
- r ->mapping_quality = 0;
+ //r->mapping_quality = current_result -> final_quality;
+ r->mapping_quality = 40; // changed on 10-JUN-2016
+ if(current_result -> realign_flags & CORE_IS_BREAKEVEN)
+ r -> mapping_quality = 0;
+ else
+ r -> mapping_quality /= current_result->MAPQ_adjustment;
+ //SUBREADprintf("REP=%d\n", current_result->MAPQ_adjustment);
strcpy(r->cigar, r -> current_cigar_decompress);
r->strand = (current_result -> mapping_result -> result_flags & CORE_IS_NEGATIVE_STRAND)?1:0;
@@ -1219,7 +1238,7 @@ int convert_read_to_tmp(global_context_t * global_context , subread_output_conte
if(global_context -> config.do_fusion_detection)
{
- chimeric_sections = chimeric_cigar_parts(global_context, r->linear_position, is_first_section_jumped ^ current_strand, is_first_section_jumped, r->current_cigar_decompress, r->out_poses, output_context->out_cigar_buffer, r->out_strands, read_len, r->out_lens);
+ chimeric_sections = chimeric_cigar_parts(global_context, r->linear_position, is_first_section_jumped ^ current_strand, is_first_section_jumped, r->current_cigar_decompress, r->out_poses, output_context->out_cigar_buffer, r->out_strands, read_len, r->out_lens, read_name);
if(chimeric_sections > 0){
int xk1;
@@ -2543,6 +2562,7 @@ int do_iteration_two(global_context_t * global_context, thread_context_t * threa
//memset(final_MATCH_buffer, 0, sizeof(int) * 2 * global_context -> config.multi_best_reads);
//memset(final_MISMATCH_buffer, 0, sizeof(int) * 2 * global_context -> config.multi_best_reads);
int r1_candidate_locations = 0, r2_candidate_locations = 0;
+ int r1_step2_locations = 0, r2_step2_locations = 0;
clear_repeated_buffer(global_context, repeated_buffer_pos, repeated_buffer_cigars, &repeated_count);
for (is_second_read = 0; is_second_read < 1 + global_context -> input_reads.is_paired_end_reads; is_second_read ++)
@@ -2594,6 +2614,14 @@ int do_iteration_two(global_context_t * global_context, thread_context_t * threa
current_result -> result_flags &= ~CORE_IS_FULLY_EXPLAINED;
+
+ if(is_second_read) r2_step2_locations = best_read_id + 1;
+ else r1_step2_locations = best_read_id + 1;
+
+ if(0 && FIXLENstrcmp("V0112_0155:7:1101:7921:2517#ACTTGA", read_name_1)==0){
+ SUBREADprintf("R1 N2=%d, R2 N2=%d, R%d : pos=%u\n", r1_step2_locations, r2_step2_locations, is_second_read+1, current_result->selected_position);
+ }
+
unsigned int final_alignments = explain_read(global_context, thread_context , final_realignments + (is_second_read + 2 * best_read_id) * MAX_ALIGNMENT_PER_ANCHOR,
current_read_number, current_rlen, current_read_name, current_read, current_qual, is_second_read, best_read_id, is_negative_strand);
@@ -2641,9 +2669,9 @@ int do_iteration_two(global_context_t * global_context, thread_context_t * threa
unsigned int scores_array [global_context -> config.multi_best_reads * MAX_ALIGNMENT_PER_ANCHOR];
for(read_record_i = 0; read_record_i < current_candidate_locations; read_record_i++){
- realignment_result_t * current_realignment_result = final_realignments + current_realignment_index[read_record_i];
- mapping_result_t *current_result = current_realignment_result -> mapping_result;
- assert(current_result -> result_flags & CORE_IS_FULLY_EXPLAINED);
+ //realignment_result_t * current_realignment_result = final_realignments + current_realignment_index[read_record_i];
+ //mapping_result_t *current_result = current_realignment_result -> mapping_result;
+ //assert(current_result -> result_flags & CORE_IS_FULLY_EXPLAINED);
unsigned int this_MATCH = current_MATCH_buffer[read_record_i];
unsigned int this_MISMATCH = current_MISMATCH_buffer[read_record_i];
@@ -2682,6 +2710,8 @@ int do_iteration_two(global_context_t * global_context, thread_context_t * threa
}
if(highest_score_occurence<2 || global_context -> config.report_multi_mapping_reads){
+ int is_break_even = 0;
+ if(highest_score_occurence>1) is_break_even = 1;
highest_score_occurence = min(highest_score_occurence, global_context -> config.reported_multi_best_reads);
for(read_record_i = 0; read_record_i < current_candidate_locations ; read_record_i++){
@@ -2694,6 +2724,8 @@ int do_iteration_two(global_context_t * global_context, thread_context_t * threa
strcpy(qual_text_1, raw_qual_text_1);
strcpy(qual_text_2, raw_qual_text_2);
+ if(is_break_even) current_realignment_result -> realign_flags |= CORE_IS_BREAKEVEN;
+ current_realignment_result -> MAPQ_adjustment = current_MISMATCH_buffer [read_record_i] + ( is_second_read?(r2_step2_locations): (r1_step2_locations));
//if(161430 <= current_read_number) SUBREADprintf("ALL_SE=%d, THIS_HIT=%d\n", highest_score_occurence, output_cursor);
//if(161436 == current_read_number)SUBREADprintf("DOUBLE_ADD_SE for %d (%p): %u %d/%d, BEST=%d\n", scores_array[read_record_i] , current_realignment_result, current_read_number, output_cursor , highest_score_occurence, best_score_highest);
@@ -2793,6 +2825,10 @@ int do_iteration_two(global_context_t * global_context, thread_context_t * threa
//SUBREADprintf("Highest score = %llu, Occurance = %d\n", highest_score , highest_score_occurence);
// Then, copy the (R1, R2) that have the highest score into the align_res buffer.
if(highest_score_occurence <= 1 || global_context -> config.report_multi_mapping_reads){
+
+ int is_break_even = 0;
+ if(highest_score_occurence>1)is_break_even = 1;
+
highest_score_occurence = min(highest_score_occurence, global_context -> config.reported_multi_best_reads);
for(r1_best_id = 0; r1_best_id < r1_candidate_locations; r1_best_id ++)
{
@@ -2814,7 +2850,15 @@ int do_iteration_two(global_context_t * global_context, thread_context_t * threa
strcpy(qual_text_1, raw_qual_text_1);
strcpy(qual_text_2, raw_qual_text_2);
- //if(161436 == current_read_number)SUBREADprintf("DOUBLE_ADD_PE: %u %d/%d\n", current_read_number, output_cursor , highest_score_occurence);
+ if(is_break_even){
+ r1_realign -> realign_flags |= CORE_IS_BREAKEVEN;
+ r2_realign -> realign_flags |= CORE_IS_BREAKEVEN;
+ }
+
+ r1_realign -> MAPQ_adjustment = r1_step2_locations + final_MISMATCH_buffer1[r1_best_id];
+ r2_realign -> MAPQ_adjustment = r2_step2_locations + final_MISMATCH_buffer2[r2_best_id];
+
+ //SUBREADprintf("R1R2_Rep = %d,%d\n", r1_step2_locations,r2_step2_locations);
write_realignments_for_fragment(global_context, thread_context, &out_context, current_read_number, r1_realign, r2_realign, read_name_1, read_name_2, read_text_1, read_text_2, qual_text_1, qual_text_2, read_len_1, read_len_2, highest_score_occurence, output_cursor, non_informative_subreads_r1, non_informative_subreads_r2);
output_cursor ++;
}
@@ -3068,7 +3112,8 @@ int do_voting(global_context_t * global_context, thread_context_t * thread_conte
{
//SUBREADprintf("P%d %llu %s\n", is_reversed, current_read_number, read_name_1);
- if(0 && FIXLENstrcmp("R003577537", read_name_1) ==0 ) {
+ //#warning ">>>>>>> DISABLE THE FOLLOING BLOCK <<<<<<"
+ if(0 && FIXLENstrcmp("V0112_0155:7:1101:7921:2517#ACTTGA", read_name_1) ==0 ) {
SUBREADprintf(">>>%llu<<<\n%s [%d] %s\n%s [%d] %s\n", current_read_number, read_name_1, read_len_1, read_text_1, read_name_2, read_len_2, read_text_2);
SUBREADprintf(" ======= PAIR %s = %llu ; NON_INFORMATIVE = %d, %d =======\n", read_name_1, current_read_number, vote_1 -> noninformative_subreads, vote_2 -> noninformative_subreads);
print_votes(vote_1, global_context -> config.index_prefix);
@@ -4134,11 +4179,11 @@ void absoffset_to_posstr(global_context_t * global_context, unsigned int pos, ch
sprintf(res, "%s:%u", ch, off);
}
-int chimeric_cigar_parts(global_context_t * global_context, unsigned int sel_pos, int is_first_section_negative_strand, int is_first_section_reversed, char * in_cigar, unsigned int * out_poses, char ** out_cigars, char * out_strands, int read_len, short * perfect_lens)
+int chimeric_cigar_parts(global_context_t * global_context, unsigned int sel_pos, int is_first_section_negative_strand, int is_first_section_reversed, char * in_cigar, unsigned int * out_poses, char ** out_cigars, char * out_strands, int read_len, short * perfect_lens, char * read_name)
{
unsigned int current_perfect_map_start = sel_pos;
int current_perfect_section_no = 0;
- int current_perfect_cursor = sel_pos;
+ unsigned int current_perfect_cursor = sel_pos;
int is_reversed = is_first_section_reversed;
int is_negative = is_first_section_negative_strand;
int read_cursor = 0;
@@ -4204,15 +4249,22 @@ int chimeric_cigar_parts(global_context_t * global_context, unsigned int sel_pos
assert(new_chr);
is_chro_jump = (curr_chr != new_chr);
- long long int dist = current_perfect_cursor;
- dist -= jummped_location;
+ long long int dist = (long long int)current_perfect_cursor;
+ dist -= (long long int)jummped_location;
if(abs(dist) >= global_context -> config.maximum_intron_length)
is_long_jump = 1;
+
+ //#warning ">>>>>> COMMENT WHEN RELEASE <<<<<<"
+ if(0 && FIXLENstrcmp("R000000007", read_name)==0)
+ SUBREADprintf("dist=%lld, abs=%lld, %u, %u\n",dist,abs(dist), current_perfect_cursor, jummped_location);
// A long jump is the jump longer than 2^27.
// Picard does not like it!!
}
// is_long_jump is true only if the two sections are on different chromosomes.
+ //#warning ">>>>>> COMMENT WHEN RELEASE <<<<<<"
+ if(0 && FIXLENstrcmp("R000000007", read_name)==0)
+ SUBREADprintf("CHR_JMP=%d, NCCH=%c, LONG_JMP=%d\n", is_chro_jump, ncch, is_long_jump);
if(is_chro_jump || islower(ncch) || ncch == 'B' || is_long_jump)
{
current_perfect_cursor = jummped_location;
diff --git a/src/core.h b/src/core.h
index e521226..90cfa2b 100644
--- a/src/core.h
+++ b/src/core.h
@@ -372,7 +372,7 @@ typedef struct{
short realign_flags;
short final_quality;
short chromosomal_length;
-
+ short MAPQ_adjustment;
} realignment_result_t;
#define BUCKETED_TABLE_INIT_ITEMS 3
@@ -619,7 +619,7 @@ unsigned short * _global_retrieve_big_margin_ptr(global_context_t * global_conte
// The first base in the read actually has a larger coordinate than Pos.
unsigned int reverse_cigar(unsigned int pos, char * cigar, char * new_cigar);
-int chimeric_cigar_parts(global_context_t * global_context , unsigned int sel_pos, int is_first_section_negative_strand, int is_first_section_reversed, char * in_cigar, unsigned int * out_poses, char ** out_cigars, char * out_strands, int read_len, short * out_read_lens);
+int chimeric_cigar_parts(global_context_t * global_context , unsigned int sel_pos, int is_first_section_negative_strand, int is_first_section_reversed, char * in_cigar, unsigned int * out_poses, char ** out_cigars, char * out_strands, int read_len, short * out_read_lens, char * read_name);
void warning_file_limit();
void quick_sort(void * arr,int arr_size, int compare (void * arr, int l, int r), void exchange(void * arr, int l, int r));
@@ -637,5 +637,6 @@ int FIXLENstrcmp(char * fixed_len, char * rname);
int is_valid_digit(char * optarg, char * optname);
int is_valid_digit_range(char * optarg, char * optname, int min, int max_inc);
+int is_valid_float(char * optarg, char * optname);
int exec_cmd(char * cmd, char * outstr, int out_limit);
#endif
diff --git a/src/gene-value-index.c b/src/gene-value-index.c
index 810ed04..d14a64c 100644
--- a/src/gene-value-index.c
+++ b/src/gene-value-index.c
@@ -888,9 +888,12 @@ int match_chro(char * read, gene_value_index_t * index, unsigned int pos, int te
case 'C':
ret += tt==2;
break;
+ case 0:
+ //SUBREADprintf("NON-ATGC-CHAR:%d\n", tv);
+ //assert(0);
+ break;
default:
ret += tt==3;
- break;
}
offset_bit+=2;
diff --git a/src/input-files.c b/src/input-files.c
index 7e6f8f4..2839eac 100644
--- a/src/input-files.c
+++ b/src/input-files.c
@@ -61,6 +61,20 @@ void fastq_64_to_33(char * qs)
qs[i++] -= 31;
}
+void * delay_run(void * ptr){
+ usleep(100000);
+ free(ptr);
+ return NULL;
+}
+
+void * delay_realloc(void * old_pntr, size_t old_size, size_t new_size){
+ pthread_t thread;
+ void * new_ret = malloc(new_size);
+ memcpy(new_ret, old_pntr, old_size);
+ pthread_create(&thread, NULL, delay_run, old_pntr);
+ return new_ret;
+}
+
double guess_reads_density(char * fname, int is_sam)
{
return guess_reads_density_format(fname, is_sam, NULL, NULL, NULL);
@@ -1268,7 +1282,7 @@ void fix_cigar_SAM14(char * cig){
}
//This function returns 0 if the line is a mapped read; -1 if the line is in a wrong format and 1 if the read is unmapped.
-int parse_SAM_line(char * sam_line, char * read_name, int * flags, char * chro, unsigned int * pos, char * cigar, int * mapping_quality, unsigned int * pair_dist, char * sequence , char * quality_string, int * rl, int * repeated)
+int parse_SAM_line(char * sam_line, char * read_name, int * flags, char * chro, unsigned int * pos, char * cigar, int * mapping_quality, unsigned int * pair_dist, char * sequence, char * quality_string, int * rl, int * repeated)
{
char cc;
int ci = 0, k=0, field=0, ret_quality = 0, ret_flag = 0, ret_pairdist=0;
@@ -1822,7 +1836,7 @@ int break_SAM_file(char * in_SAM_file, int is_BAM_file, char * temp_file_prefix,
//SUBREADprintf("ARRI_0=%p ; OFFS=%p ; EVT=%p\n%s\n",array_index, offsets, event_table, line_buffer);
- int line_parse_result = parse_SAM_line(line_buffer, read_name, &flags, chro, &pos, cigar, & mapping_quality, &pairdist, sequence , quality_string, &rl, &repeated);
+ int line_parse_result = parse_SAM_line(line_buffer, read_name, &flags, chro, &pos, cigar, & mapping_quality, &pairdist, sequence, quality_string, &rl, &repeated);
//SUBREADprintf("ARRI_2=%p ; OFFS=%p ; EVT=%p\n",array_index, offsets, event_table);
if(strlen(quality_string)<2)
@@ -1910,7 +1924,7 @@ int break_SAM_file(char * in_SAM_file, int is_BAM_file, char * temp_file_prefix,
}
// printf("INST: RL=%d; INSL=%d; READ_CUR=%d; IGNORE=%d\n", rl, insert_length, read_cursor , base_ignored_head_tail);
- if(need_write && insert_length >= 5)
+ if(need_write && insert_length >= 5 && sequence[0]!='*')
{
sprintf(temp_file_name, "%s%s", temp_file_prefix , temp_file_suffix);
temp_fp = get_temp_file_pointer(temp_file_name, fp_table, &close_now);
@@ -1947,7 +1961,7 @@ int break_SAM_file(char * in_SAM_file, int is_BAM_file, char * temp_file_prefix,
// the left edge ( last WANTED base ) is chromosome_cursor-1
// the indel length is -tmpv;
// now we add this into the event table.
- if(event_table)
+ if(event_table && sequence[0]!='*')
add_cigar_indel_event(event_table, chro, chromosome_cursor-1, -tmpv, sequence + read_cursor);
read_cursor += tmpv;
tmpv = 0;
@@ -2161,6 +2175,8 @@ void delete_with_prefix(char * prefix){
strcpy(del_suffix , prefix);
}
+ //#warning ">>>>>>>> COMMENT THIS OUT <<<<<<<<<<<<<<<<<<<<<"
+ //SUBREADprintf("SCANDEL: %s, PREFIX %s, SUFFIX %s\n", del2, prefix, del_suffix);
if(strlen(del_suffix)>8)
{
DIR *d;
@@ -2173,11 +2189,13 @@ void delete_with_prefix(char * prefix){
{
if(strstr(dir->d_name, del_suffix))
{
- //SUBREADprintf("DEL:%s\n", dir->d_name);
strcpy(del_name, del2);
strcat(del_name, "/");
strcat(del_name, dir->d_name);
unlink(del_name);
+
+ // #warning ">>>>>>>> COMMENT THIS OUT <<<<<<<<<<<<<<<<<<<<<"
+ // SUBREADprintf("DEL: %s\n", del_name);
//test fix
}
}
@@ -2371,7 +2389,7 @@ int SAM_pairer_create(SAM_pairer_context_t * pairer, int all_threads, int bin_bu
pairer -> input_fp = f_subr_open(in_file, "rb");
if(NULL == pairer -> input_fp) return 1;
- SAM_pairer_warning_file_open_limit(pairer);
+ SAM_pairer_warning_file_open_limit();
pairer -> input_is_BAM = BAM_input;
pairer -> tiny_mode = is_Tiny_Mode;
@@ -2392,11 +2410,11 @@ int SAM_pairer_create(SAM_pairer_context_t * pairer, int all_threads, int bin_bu
pairer -> appendix1 = appendix1;
- _REPAIRER_delete_temp_prefix = tmp_path;
old_sig_TERM = signal (SIGTERM, REPAIR_SIGINT_hook);
old_sig_INT = signal (SIGINT, REPAIR_SIGINT_hook);
strcpy(pairer -> tmp_file_prefix, tmp_path);
+ _REPAIRER_delete_temp_prefix = pairer -> tmp_file_prefix;
pairer -> threads = malloc(all_threads * sizeof(SAM_pairer_thread_t));
memset(pairer -> threads, 0, all_threads * sizeof(SAM_pairer_thread_t));
@@ -2481,7 +2499,9 @@ int SAM_pairer_read_BAM_block(FILE * fp, int max_read_len, char * inbuff) {
unsigned char gz_header_12 [12];
//SUBREADprintf("STAT GZ POS=%llu\n", ftello(fp));
int read_len = fread(gz_header_12, 1, 12, fp );
- if(read_len < 12) return -1;
+ if(read_len < 12){
+ return -1;
+ }
if(gz_header_12[0]!=31 || gz_header_12[1]!=139){
SUBREADprintf("Unrecognized Gzip headers: %u, %u\nPlease make sure if the input file is in the BAM format.\n", gz_header_12[0], gz_header_12[1]);
return -1;
@@ -2569,26 +2589,31 @@ void SAM_pairer_fill_BIN_buff(SAM_pairer_context_t * pairer , SAM_pairer_thread
// For SAM files: must be the full lines.
int current_buffer_used = 0;
int current_blocks = 0;
+ int last_read_len = -1, this_size;
if(pairer -> input_is_BAM){
while(1){
- if(feof(pairer -> input_fp)){
+ if( feof(pairer -> input_fp)){
*is_finished = 1;
break;
}
if(pairer -> input_buff_SBAM_size - current_buffer_used < MIN_BAM_BLOCK_SIZE) {
break;
}
- int this_size = 0;
-
this_size = SAM_pairer_read_BAM_block( pairer -> input_fp , pairer -> input_buff_SBAM_size - current_buffer_used , thread_context -> input_buff_SBAM + current_buffer_used);
current_blocks ++;
if(this_size >= 0) {
current_buffer_used += this_size;
} else {
+ if(feof(pairer -> input_fp) && last_read_len != -1 ){
+ pairer -> is_bad_format |= (last_read_len > 2);
+ pairer -> is_incomplete_BAM |= (last_read_len > 2);
+ //SUBREADprintf("BAM-FINISHED, CORRECT=%d (%d)\n", !pairer -> is_bad_format, last_read_len);
+ }
*is_finished = 1;
break;
}
+ last_read_len = this_size;
}
}else{
current_buffer_used = SAM_pairer_read_SAM_MB(pairer -> input_fp , pairer -> input_buff_SBAM_size , thread_context -> input_buff_SBAM);
@@ -2908,8 +2933,9 @@ int online_register_contig(SAM_pairer_context_t * pairer , SAM_pairer_thread_t *
if(refId < 0){
refId = pairer->sam_contig_number_table->numOfElements;
pairer -> output_header(pairer, thread_context -> thread_id, 0, 1 , header_sec , 8+reflen);
- char * mem_ref = malloc(reflen);
+ char * mem_ref = malloc(reflen+1);
memcpy(mem_ref, ref, reflen);
+ mem_ref[reflen]=0;
HashTablePut(pairer->sam_contig_number_table, mem_ref, NULL + refId + 1);
}
subread_lock_release(&pairer -> output_header_lock);
@@ -4932,7 +4958,7 @@ int SAM_pairer_run( SAM_pairer_context_t * pairer){
}else for(corrected_run = 0; corrected_run < 2 ; corrected_run ++){
SAM_pairer_run_once(pairer);
- if(pairer -> is_bad_format && pairer->input_is_BAM){
+ if(pairer -> is_bad_format && pairer->input_is_BAM && ! pairer -> is_incomplete_BAM){
//#warning ">>>>>> REMOVE '+ 1' FROM NEXT LINE IN RELEASE <<<<<<"
assert(1 != corrected_run);
//#warning ">>>>>> COMMENT NEXT LINE IN RELEASE <<<<<<"
@@ -4946,7 +4972,7 @@ int SAM_pairer_run( SAM_pairer_context_t * pairer){
}else break;
}
- return 0;
+ return pairer -> is_bad_format;
}
int sort_SAM_create(SAM_sort_writer * writer, char * output_file, char * tmp_path)
diff --git a/src/input-files.h b/src/input-files.h
index d7a96c3..8e8de89 100644
--- a/src/input-files.h
+++ b/src/input-files.h
@@ -145,6 +145,7 @@ typedef struct {
unsigned int BAM_l_text;
unsigned int BAM_n_ref;
int is_unsorted_notified;
+ int is_incomplete_BAM;
void (* reset_output_function) (void * pairer);
int (* output_function) (void * pairer, int thread_no, char * rname, char * bin1, char * bin2);
@@ -307,4 +308,5 @@ int SAM_pairer_writer_create( SAM_pairer_writer_main_t * bam_main , int all_thre
void SAM_pairer_writer_destroy( SAM_pairer_writer_main_t * bam_main ) ;
int SAM_pairer_iterate_int_tags(unsigned char * bin, int bin_len, char * tag_name, int * saved_value);
int SAM_pairer_warning_file_open_limit();
+void *delay_realloc(void * old_pntr, size_t old_size, size_t new_size);
#endif
diff --git a/src/interval_merge.c b/src/interval_merge.c
index 4f687ff..82f3810 100644
--- a/src/interval_merge.c
+++ b/src/interval_merge.c
@@ -62,26 +62,26 @@ int mergeIntervals(unsigned int * intervals, unsigned int * result_ints, int nin
stack_buffer_mem[stock_pointer*2+1] = intervals[1];
stock_pointer++;
- for (ii = 1 ; ii < nints; ii++)
- {
+ for (ii = 1 ; ii < nints; ii++)
+ {
//int top_start = stack_buffer_mem[stock_pointer*2-2];
int top_stop = stack_buffer_mem[stock_pointer*2-1];
- if (top_stop < intervals[ii*2])
- {
+ if (top_stop < intervals[ii*2])
+ {
stack_buffer_mem[stock_pointer * 2] = intervals[ii*2];
stack_buffer_mem[stock_pointer * 2+1] = intervals[ii*2+1];
stock_pointer++;
- }
- else if (top_stop < intervals[ii*2+1])
- {
- top_stop = intervals[ii*2+1];
+ }
+ else if (top_stop < intervals[ii*2+1])
+ {
+ top_stop = intervals[ii*2+1];
stack_buffer_mem[stock_pointer*2-1] = top_stop;
- }
+ }
// Otherwise the ii-th interval is useless because it is enclosed in the top item
- }
+ }
- return stock_pointer;
+ return stock_pointer;
}
#ifdef MAKE_TEST_INTERVL_MERGE
@@ -126,6 +126,6 @@ int main()
gaps = mergeIntervals(inbuff, outbuff, 6);
print_gaps(outbuff, gaps);
- return 0;
+ return 0;
}
#endif
diff --git a/src/makefile.version b/src/makefile.version
index 3266789..f0e22ca 100644
--- a/src/makefile.version
+++ b/src/makefile.version
@@ -1,4 +1,4 @@
-SUBREAD_VERSION_BASE=1.5.0-p3
+SUBREAD_VERSION_BASE=1.5.1
SUBREAD_VERSION_DATE=$(SUBREAD_VERSION_BASE)-$(shell date +"%d%b%Y")
SUBREAD_VERSION="$(SUBREAD_VERSION_DATE)"
SUBREAD_VERSION="$(SUBREAD_VERSION_BASE)"
diff --git a/src/readSummary.c b/src/readSummary.c
index 8457f9c..c759674 100644
--- a/src/readSummary.c
+++ b/src/readSummary.c
@@ -122,22 +122,26 @@ typedef struct {
unsigned int chunk_read_ptr;
pthread_t thread_object;
- unsigned short hits_read_start_base1[MAX_HIT_NUMBER];
- unsigned short hits_read_start_base2[MAX_HIT_NUMBER];
+ unsigned int hits_start_pos1[MAX_HIT_NUMBER];
+ unsigned int hits_start_pos2[MAX_HIT_NUMBER];
- short hits_read_len1[MAX_HIT_NUMBER];
- short hits_read_len2[MAX_HIT_NUMBER];
+ unsigned short hits_length1[MAX_HIT_NUMBER];
+ unsigned short hits_length2[MAX_HIT_NUMBER];
+
+ char * hits_chro1[MAX_HIT_NUMBER];
+ char * hits_chro2[MAX_HIT_NUMBER];
long hits_indices1 [MAX_HIT_NUMBER];
long hits_indices2 [MAX_HIT_NUMBER];
- long decision_table_ids [MAX_HIT_NUMBER];
- unsigned short decision_table_votes [MAX_HIT_NUMBER];
- long decision_table_exon_ids [MAX_HIT_NUMBER];
- char decision_table_read1_used[MAX_HIT_NUMBER];
- char decision_table_read2_used[MAX_HIT_NUMBER];
- long uniq_gene_exonid_table [MAX_HIT_NUMBER];
- long uniq_gene_table [MAX_HIT_NUMBER];
- char * read_coverage_bits;
+
+ char ** scoring_buff_gap_chros;
+ unsigned int * scoring_buff_gap_starts;
+ unsigned short * scoring_buff_gap_lengths;
+
+ unsigned int scoring_buff_numbers[MAX_HIT_NUMBER * 2];
+ unsigned int scoring_buff_flags[MAX_HIT_NUMBER * 2];
+ unsigned short scoring_buff_overlappings[MAX_HIT_NUMBER * 2];
+ long scoring_buff_exon_ids[MAX_HIT_NUMBER * 2];
char * chro_name_buff;
z_stream * strm_buffer;
@@ -193,6 +197,9 @@ typedef struct {
int use_fraction_multi_mapping;
int do_junction_counting;
+ int need_calculate_overlap_len;
+ int need_calculate_fragment_len;
+
int min_mapping_quality_score;
int min_paired_end_distance;
int max_paired_end_distance;
@@ -204,7 +211,7 @@ typedef struct {
int five_end_extension;
int three_end_extension;
int fragment_minimum_overlapping;
- int calculate_overlapping_lengths;
+ float fractional_minimum_overlapping;
int use_overlapping_break_tie;
unsigned long long int all_reads;
@@ -213,6 +220,7 @@ typedef struct {
fc_thread_thread_context_t * thread_contexts;
int is_all_finished;
int sambam_chro_table_items;
+ int is_input_bad_format;
SamBam_Reference_Info * sambam_chro_table;
pthread_spinlock_t sambam_chro_table_lock;
@@ -234,6 +242,7 @@ typedef struct {
char raw_input_file_name[300];
char output_file_name[300];
char output_file_path[300];
+ char temp_file_dir[300];
unsigned char ** gene_name_array; // gene_internal_number -> gene_name
int input_file_unique;
@@ -532,21 +541,23 @@ unsigned int unistr_cpy(fc_thread_global_context_t * global_context, char * str,
return ret;
}
-void print_FC_configuration(fc_thread_global_context_t * global_context, char * annot, char * sam, char * out, int is_sam, int is_GTF, int *n_input_files, int isReadSummaryReport)
+int print_FC_configuration(fc_thread_global_context_t * global_context, char * annot, char * sam, char * out, int is_sam, int is_GTF, int *n_input_files, int isReadSummaryReport)
{
- char * tmp_ptr1 = NULL , * next_fn, *sam_used = malloc(strlen(sam)+1), sam_ntxt[30],bam_ntxt[30], next_ntxt[50];
+ char * tmp_ptr1 = NULL , * next_fn, *sam_used = malloc(strlen(sam)+300), sam_ntxt[30],bam_ntxt[30], next_ntxt[50];
int nfiles=1, nBAMfiles = 0, nNonExistFiles = 0;
- strcpy(sam_used, sam);
+ sprintf(sam_used, "%s/featureCounts_test_file_writable.tmp", global_context -> temp_file_dir);
+ FILE * fp = fopen(sam_used,"w");
+ if(fp){
+ fclose(fp);
+ unlink(sam_used);
+ }else{
+ SUBREADprintf("\nERROR: temporary directory is not writable: '%s'\n\n", global_context -> temp_file_dir);
+ return 1;
+ }
- SUBREADputs("");
- print_subread_logo();
- SUBREADputs("");
- print_in_box(80,1,1,"featureCounts setting");
- print_in_box(80,0,0,"");
-
+ strcpy(sam_used, sam);
nfiles = 0;
-
while(1)
{
next_fn = strtok_r(nfiles==0?sam_used:NULL, ";", &tmp_ptr1);
@@ -557,10 +568,20 @@ void print_FC_configuration(fc_thread_global_context_t * global_context, char *
int file_probe = is_certainly_bam_file(next_fn, NULL, &BAM_header_size);
//SUBREADprintf(" >>> %s : header=%lld , BSIZE=%lld\n", next_fn,BAM_header_size, global_context -> max_BAM_header_size );
if(BAM_header_size>0) global_context -> max_BAM_header_size = max( global_context -> max_BAM_header_size , BAM_header_size + 180000);
- if(file_probe==-1) nNonExistFiles++;
+ if(file_probe==-1){
+ nNonExistFiles++;
+ SUBREADprintf("\nERROR: invalid parameter: '%s'\n\n", next_fn);
+ return 1;
+ }
if(file_probe == 1) nBAMfiles++;
}
+ SUBREADputs("");
+ print_subread_logo();
+ SUBREADputs("");
+ print_in_box(80,1,1,"featureCounts setting");
+ print_in_box(80,0,0,"");
+
sam_ntxt[0]=0;
bam_ntxt[0]=0;
next_ntxt[0]=0;
@@ -598,13 +619,17 @@ void print_FC_configuration(fc_thread_global_context_t * global_context, char *
print_in_box(80,0,0," Output file : %s", out);
print_in_box(80,0,0," Summary : %s.summary", out);
print_in_box(80,0,0," Annotation : %s (%s)", annot, is_GTF?"GTF":"SAF");
- if(isReadSummaryReport)
+ if(isReadSummaryReport){
print_in_box(80,0,0," Assignment details : <input_file>.featureCounts");
+ print_in_box(80,0,0," (Note that files are saved to the output directory)");
+ print_in_box(80,0,0,"");
+ }
if(global_context -> do_junction_counting)
print_in_box(80,0,0," Junction Counting : <output_file>.jcounts");
if(global_context -> alias_file_name[0])
print_in_box(80,0,0," Chromosome alias file : %s", global_context -> alias_file_name);
+ print_in_box(80,0,0," Dir for temp files : %s", global_context->temp_file_dir);
print_in_box(80,0,0,"");
print_in_box(80,0,0," Threads : %d", global_context->thread_number);
@@ -629,6 +654,8 @@ void print_FC_configuration(fc_thread_global_context_t * global_context, char *
print_in_box(80,0,0," Split alignments : %s", (1 == global_context -> is_split_or_exonic_only)?"only split alignments":"only exonic alignments");
if(global_context -> fragment_minimum_overlapping !=1)
print_in_box(80,0,0," Overlapping bases : %d", global_context -> fragment_minimum_overlapping);
+ if(global_context -> fractional_minimum_overlapping !=1)
+ print_in_box(81,0,0," Overlapping bases : %0.1f%%%%", global_context -> fractional_minimum_overlapping*100);
if(global_context -> five_end_extension || global_context -> three_end_extension)
print_in_box(80,0,0," Read extensions : %d on 5' and %d on 3' ends", global_context -> five_end_extension , global_context -> three_end_extension);
if(global_context -> reduce_5_3_ends_to_one)
@@ -658,6 +685,7 @@ void print_FC_configuration(fc_thread_global_context_t * global_context, char *
print_in_box(80,0,0,"%ld chromosome name aliases are loaded.", global_context -> annot_chro_name_alias_table ->numOfElements);
free(sam_used);
+ return 0;
}
void print_FC_results(fc_thread_global_context_t * global_context)
@@ -1414,6 +1442,11 @@ int strcmp_slash(char * s1, char * s2)
#define NH_FRACTION_INT 65536
+unsigned int calculate_multi_overlap_fraction(fc_thread_global_context_t * global_context, unsigned int fixed_fractional_count, int maximum_total_count){
+ if(global_context -> use_fraction_multi_mapping) return fixed_fractional_count / maximum_total_count;
+ else return fixed_fractional_count;
+}
+
unsigned int calc_fixed_fraction(int nh){
if(nh==1) return NH_FRACTION_INT;
else if(nh == 2) return NH_FRACTION_INT>>1;
@@ -1483,11 +1516,6 @@ void print_read_wrapping(char * rl, int is_second){
}
-void vote_and_add_count(fc_thread_global_context_t * global_context, fc_thread_thread_context_t * thread_context,
- long * hits_indices1, unsigned short * hits_read_start_base1, short * hits_read_len1, int nhits1, unsigned short rl1,
- long * hits_indices2, unsigned short * hits_read_start_base2, short * hits_read_len2, int nhits2, unsigned short rl2,
- int fixed_fractional_count, char * read_name);
-
void process_pairer_reset(void * pairer_vp){
SAM_pairer_context_t * pairer = (SAM_pairer_context_t *) pairer_vp;
@@ -1540,7 +1568,7 @@ int process_pairer_header (void * pairer_vp, int thread_no, int is_text, unsigne
if( !is_text ){
if(global_context -> sambam_chro_table)
- global_context -> sambam_chro_table = realloc(global_context -> sambam_chro_table, (items + global_context -> sambam_chro_table_items) * sizeof(SamBam_Reference_Info));
+ global_context -> sambam_chro_table = delay_realloc(global_context -> sambam_chro_table, global_context -> sambam_chro_table_items * sizeof(SamBam_Reference_Info), (items + global_context -> sambam_chro_table_items) * sizeof(SamBam_Reference_Info));
else global_context -> sambam_chro_table = malloc(items * sizeof(SamBam_Reference_Info));
int x1, bin_ptr = 0;
@@ -1726,8 +1754,276 @@ int reverse_flag(int mf){
return ret;
}
-void parse_bin(SamBam_Reference_Info * sambam_chro_table, char * bin, char * bin2, char ** read_name, int * flag, char ** chro, long * pos, int * mapq, char ** mate_chro, long * mate_pos, long * tlen, int * is_junction_read, int * cigar_sect, unsigned int * Starting_Chro_Points, unsigned short * Starting_Read_Points, unsigned short * Section_Read_Lengths, char ** ChroNames, char * Event_After_Section, int * NH_value, int max_M){
- int x1;
+#define MAXIMUM_INSERTION_IN_SECTION 8
+
+typedef struct {
+ char * chro;
+ unsigned int start_pos;
+ unsigned int chromosomal_length;
+ short insertions;
+ unsigned int insertion_start_pos[ MAXIMUM_INSERTION_IN_SECTION ];
+ unsigned short insertion_lengths[ MAXIMUM_INSERTION_IN_SECTION ];
+} CIGAR_interval_t;
+
+
+int calc_total_frag_one_len(CIGAR_interval_t * intvs, int intvn){
+ int ret = 0, x1;
+ for(x1 = 0; x1 < intvn; x1++){
+ int x2;
+ for(x2 = 0; x2 < intvs[x1].insertions; x2++) ret += intvs[x1].insertion_lengths[x2];
+ ret += intvs[x1].chromosomal_length;
+ }
+ return ret;
+}
+
+int calc_total_has_overlap(unsigned int r1_start, unsigned int r1_end, unsigned int r2_start, unsigned int r2_end, unsigned int * overlap_start, unsigned int * overlap_end){
+ if((r1_start <= r2_start && r1_end > r2_start) || (r2_start <= r1_start && r2_end > r1_start) ){
+ (*overlap_start) = max( r1_start, r2_start );
+ (*overlap_end) = min( r1_end, r2_end );
+ return 1;
+ }
+ return 0;
+}
+
+int calc_total_frag_len( fc_thread_global_context_t * global_context, fc_thread_thread_context_t * thread_context, CIGAR_interval_t * CIGAR_intervals_R1, int CIGAR_intervals_R1_sections, CIGAR_interval_t * CIGAR_intervals_R2, int CIGAR_intervals_R2_sections, char * read_name){
+ if ( CIGAR_intervals_R1_sections == 0 && CIGAR_intervals_R2_sections > 0) return calc_total_frag_one_len( CIGAR_intervals_R2,CIGAR_intervals_R2_sections );
+ else if( CIGAR_intervals_R1_sections > 0 && CIGAR_intervals_R2_sections== 0) return calc_total_frag_one_len( CIGAR_intervals_R1,CIGAR_intervals_R1_sections );
+ else if( CIGAR_intervals_R1_sections == 0 && CIGAR_intervals_R2_sections== 0) return 0;
+
+ if(CIGAR_intervals_R1_sections > 0 && CIGAR_intervals_R2_sections > 0 && strcmp(CIGAR_intervals_R1[0].chro, CIGAR_intervals_R2[0].chro )!=0 )
+ // two reads are from different chromosomes
+ return calc_total_frag_one_len( CIGAR_intervals_R2,CIGAR_intervals_R2_sections ) + calc_total_frag_one_len( CIGAR_intervals_R1,CIGAR_intervals_R1_sections );
+
+
+ unsigned int merged_section_count = 0;
+ unsigned int merged_section_start_positions[ MAXIMUM_INSERTION_IN_SECTION * 3 ];
+ unsigned short merged_section_lengths[ MAXIMUM_INSERTION_IN_SECTION * 3 ];
+ unsigned char merged_section_belong_R1[ MAXIMUM_INSERTION_IN_SECTION * 3 ];
+ unsigned char merged_section_belong_R2[ MAXIMUM_INSERTION_IN_SECTION * 3 ];
+ unsigned int merged_section_indel_counts[ MAXIMUM_INSERTION_IN_SECTION * 3 ];
+ unsigned int merged_section_indel_positions[ MAXIMUM_INSERTION_IN_SECTION * 3 ][ MAXIMUM_INSERTION_IN_SECTION ];
+ unsigned short merged_section_indel_lengths[ MAXIMUM_INSERTION_IN_SECTION * 3 ][ MAXIMUM_INSERTION_IN_SECTION ];
+
+ int R1_i = 0 , R2_i = 0;
+ while (1){
+ //SUBREADprintf("FRAGDEBUG %s : %d < %d & %d < %d; MC=%d; INS1=%d INS2=%d\n", read_name, R1_i,CIGAR_intervals_R1_sections,R2_i,CIGAR_intervals_R2_sections, merged_section_count, CIGAR_intervals_R1[R1_i].insertions, CIGAR_intervals_R2[R2_i].insertions);
+ if( R1_i >= CIGAR_intervals_R1_sections && R2_i >= CIGAR_intervals_R2_sections ) break;
+
+ if( R1_i < CIGAR_intervals_R1_sections && R2_i < CIGAR_intervals_R2_sections){
+ // see if R1 and R2 overlap
+ // if not: add R2 to specific sction; R2_i ++
+ // elif overlap: add the R1 first_half and/or R2 first_half or zero to specific section, and add overlapping part to overlapping section; DO NOT add the second specific half!
+ // if R1_end > R2_end: R1_section_start = overlapping_end; R2_i ++
+ // elif R2_end > R1_end: R2_section_start = overlapping_end; R1_i ++
+ // elif R2_end == R1_end: R1_i++; R2_i++
+
+ unsigned int overlapping_start= 0 , overlapping_end = 0;
+
+ int is_r1r2_overlap = 0;
+
+ is_r1r2_overlap = calc_total_has_overlap( CIGAR_intervals_R1[R1_i].start_pos, CIGAR_intervals_R1[R1_i].start_pos + CIGAR_intervals_R1[R1_i].chromosomal_length , CIGAR_intervals_R2[R2_i].start_pos, CIGAR_intervals_R2[R2_i].start_pos + CIGAR_intervals_R2[R2_i].chromosomal_length , & overlapping_start , & overlapping_end);
+
+ if( is_r1r2_overlap ){
+ if (CIGAR_intervals_R1[R1_i].start_pos > CIGAR_intervals_R2[R2_i].start_pos ){
+ //first half_R2 add special
+ merged_section_start_positions[merged_section_count] = CIGAR_intervals_R2[R2_i].start_pos;
+ merged_section_lengths[merged_section_count] = overlapping_start - CIGAR_intervals_R2[R2_i].start_pos;
+ merged_section_belong_R1[merged_section_count]=0;
+ merged_section_belong_R2[merged_section_count]=1;
+
+ int indel_i;
+ for(indel_i = 0; indel_i < CIGAR_intervals_R2[R2_i].insertions; indel_i++){
+ if( CIGAR_intervals_R2[R2_i].insertion_start_pos[indel_i] >= overlapping_start ){
+ if(indel_i>0){
+ int insmov_i, ins_dist_i = 0;
+ for(insmov_i = indel_i ; insmov_i < CIGAR_intervals_R2[R2_i].insertions; insmov_i++){
+ CIGAR_intervals_R2[R2_i].insertion_start_pos[ins_dist_i] = CIGAR_intervals_R2[R2_i].insertion_start_pos[insmov_i];
+ CIGAR_intervals_R2[R2_i].insertion_lengths[ins_dist_i] = CIGAR_intervals_R2[R2_i].insertion_lengths[insmov_i];
+ ins_dist_i++;
+ }
+ CIGAR_intervals_R2[R2_i].insertions = ins_dist_i;
+ }
+ break;
+ }
+ merged_section_indel_positions[merged_section_count][indel_i] = CIGAR_intervals_R2[R2_i].insertion_start_pos[indel_i];
+ merged_section_indel_lengths[merged_section_count][indel_i] = CIGAR_intervals_R2[R2_i].insertion_lengths[indel_i];
+ }
+ merged_section_indel_counts[merged_section_count] = indel_i;
+
+ merged_section_count ++;
+
+ }else if( CIGAR_intervals_R1[R1_i].start_pos < CIGAR_intervals_R2[R2_i].start_pos ){
+ //first half_R1 add special
+ merged_section_start_positions[merged_section_count] = CIGAR_intervals_R1[R1_i].start_pos;
+ merged_section_lengths[merged_section_count] = overlapping_start - CIGAR_intervals_R1[R1_i].start_pos;
+ merged_section_belong_R1[merged_section_count]=1;
+ merged_section_belong_R2[merged_section_count]=0;
+
+ int indel_i;
+ for(indel_i = 0; indel_i < CIGAR_intervals_R1[R1_i].insertions; indel_i++){
+ if( CIGAR_intervals_R1[R1_i].insertion_start_pos[indel_i] >= overlapping_start ){
+ if(indel_i>0){
+ int insmov_i, ins_dist_i = 0;
+ for(insmov_i = indel_i ; insmov_i < CIGAR_intervals_R1[R1_i].insertions; insmov_i++){
+ CIGAR_intervals_R1[R1_i].insertion_start_pos[ins_dist_i] = CIGAR_intervals_R1[R1_i].insertion_start_pos[insmov_i];
+ CIGAR_intervals_R1[R1_i].insertion_lengths[ins_dist_i] = CIGAR_intervals_R1[R1_i].insertion_lengths[insmov_i];
+ ins_dist_i++;
+ }
+ CIGAR_intervals_R1[R1_i].insertions = ins_dist_i;
+ }
+ break;
+ }
+
+ merged_section_indel_positions[merged_section_count][indel_i] = CIGAR_intervals_R1[R1_i].insertion_start_pos[indel_i];
+ merged_section_indel_lengths[merged_section_count][indel_i] = CIGAR_intervals_R1[R1_i].insertion_lengths[indel_i];
+ }
+ merged_section_indel_counts[merged_section_count] = indel_i;
+
+ merged_section_count ++;
+ }
+
+ merged_section_start_positions[merged_section_count] = overlapping_start;
+ merged_section_lengths[merged_section_count] = overlapping_end - overlapping_start;
+ merged_section_belong_R1[merged_section_count]=1;
+ merged_section_belong_R2[merged_section_count]=1;
+ merged_section_indel_counts[merged_section_count] = 0;
+
+
+ int indel_i_R1 = 0, indel_i_R2 = 0;
+ while(1){
+ //SUBREADprintf("FRAGDEBUG: CC[%d] = %d ; II1=%d < %d; II2=%d < %d\n", merged_section_count, merged_section_indel_counts[merged_section_count], indel_i_R1, CIGAR_intervals_R1[R1_i].insertions , indel_i_R2, CIGAR_intervals_R2[R2_i].insertions);
+
+ if( indel_i_R1 >= CIGAR_intervals_R1[R1_i].insertions || indel_i_R2 >= CIGAR_intervals_R2[R2_i].insertions ){
+ if(indel_i_R1 > 0){
+ int insmov_i, ins_dist_i = 0;
+ for(insmov_i = indel_i_R1 ; insmov_i < CIGAR_intervals_R1[R1_i].insertions; insmov_i++){
+ CIGAR_intervals_R1[R1_i].insertion_start_pos[ins_dist_i] = CIGAR_intervals_R1[R1_i].insertion_start_pos[insmov_i];
+ CIGAR_intervals_R1[R1_i].insertion_lengths[ins_dist_i] = CIGAR_intervals_R1[R1_i].insertion_lengths[insmov_i];
+ ins_dist_i++;
+ }
+ CIGAR_intervals_R1[R1_i].insertions = ins_dist_i;
+ }
+ if(indel_i_R2 > 0){
+ int insmov_i, ins_dist_i = 0;
+ for(insmov_i = indel_i_R2 ; insmov_i < CIGAR_intervals_R2[R2_i].insertions; insmov_i++){
+ CIGAR_intervals_R2[R2_i].insertion_start_pos[ins_dist_i] = CIGAR_intervals_R2[R2_i].insertion_start_pos[insmov_i];
+ CIGAR_intervals_R2[R2_i].insertion_lengths[ins_dist_i] = CIGAR_intervals_R2[R2_i].insertion_lengths[insmov_i];
+ ins_dist_i++;
+ }
+ CIGAR_intervals_R2[R2_i].insertions = ins_dist_i;
+ }
+ break;
+ }
+
+ if( CIGAR_intervals_R1[R1_i].insertion_start_pos[indel_i_R1] > CIGAR_intervals_R2[R2_i].insertion_start_pos[indel_i_R2] ) indel_i_R2 ++;
+ else if( CIGAR_intervals_R1[R1_i].insertion_start_pos[indel_i_R1] < CIGAR_intervals_R2[R2_i].insertion_start_pos[indel_i_R2] ) indel_i_R1 ++;
+ else{
+ if( CIGAR_intervals_R1[R1_i].insertion_lengths[ indel_i_R1 ] == CIGAR_intervals_R2[R2_i].insertion_lengths[ indel_i_R2 ] ){
+ merged_section_indel_positions[merged_section_count][ merged_section_indel_counts[merged_section_count] ] = CIGAR_intervals_R1[R1_i].insertion_start_pos[indel_i_R1];
+ merged_section_indel_lengths[merged_section_count][ merged_section_indel_counts[merged_section_count] ] = CIGAR_intervals_R1[R1_i].insertion_lengths[indel_i_R1];
+ merged_section_indel_counts[merged_section_count] ++;
+ }
+ indel_i_R2++;
+ indel_i_R1++;
+ }
+ }
+
+ merged_section_count ++;
+
+ // add common
+
+ if(CIGAR_intervals_R1[R1_i].start_pos + CIGAR_intervals_R1[R1_i].chromosomal_length > CIGAR_intervals_R2[R2_i].start_pos + CIGAR_intervals_R2[R2_i].chromosomal_length){
+ CIGAR_intervals_R1[R1_i].chromosomal_length -= ( overlapping_end - CIGAR_intervals_R1[R1_i].start_pos );
+ CIGAR_intervals_R1[R1_i].start_pos = overlapping_end;
+ R2_i ++;
+ }else if(CIGAR_intervals_R1[R1_i].start_pos + CIGAR_intervals_R1[R1_i].chromosomal_length < CIGAR_intervals_R2[R2_i].start_pos + CIGAR_intervals_R2[R2_i].chromosomal_length){
+ CIGAR_intervals_R2[R2_i].chromosomal_length -= ( overlapping_end - CIGAR_intervals_R2[R2_i].start_pos );
+ CIGAR_intervals_R2[R2_i].start_pos = overlapping_end;
+ R1_i ++;
+ }else{
+ R1_i ++;
+ R2_i ++;
+ }
+
+ }else if(CIGAR_intervals_R1[R1_i].start_pos > CIGAR_intervals_R2[R2_i].start_pos){
+ merged_section_start_positions[merged_section_count] = CIGAR_intervals_R2[R2_i].start_pos;
+ merged_section_lengths[merged_section_count] = CIGAR_intervals_R2[R2_i].chromosomal_length;
+ merged_section_belong_R1[merged_section_count]=0;
+ merged_section_belong_R2[merged_section_count]=1;
+
+ int indel_i;
+ for(indel_i = 0; indel_i < CIGAR_intervals_R2[R2_i].insertions; indel_i++){
+ merged_section_indel_positions[merged_section_count][indel_i] = CIGAR_intervals_R2[R2_i].insertion_start_pos[indel_i];
+ merged_section_indel_lengths[merged_section_count][indel_i] = CIGAR_intervals_R2[R2_i].insertion_lengths[indel_i];
+ }
+ merged_section_indel_counts[merged_section_count] = CIGAR_intervals_R2[R2_i].insertions;
+
+ merged_section_count ++;
+ R2_i ++;
+ }else{
+ merged_section_start_positions[merged_section_count] = CIGAR_intervals_R1[R1_i].start_pos;
+ merged_section_lengths[merged_section_count] = CIGAR_intervals_R1[R1_i].chromosomal_length;
+ merged_section_belong_R1[merged_section_count]=1;
+ merged_section_belong_R2[merged_section_count]=0;
+
+ int indel_i;
+ for(indel_i = 0; indel_i < CIGAR_intervals_R1[R1_i].insertions; indel_i++){
+ merged_section_indel_positions[merged_section_count][indel_i] = CIGAR_intervals_R1[R1_i].insertion_start_pos[indel_i];
+ merged_section_indel_lengths[merged_section_count][indel_i] = CIGAR_intervals_R1[R1_i].insertion_lengths[indel_i];
+ }
+ merged_section_indel_counts[merged_section_count] = CIGAR_intervals_R1[R1_i].insertions;
+
+ merged_section_count ++;
+ R1_i ++;
+ }
+ }else if(R1_i < CIGAR_intervals_R1_sections){
+ // add R1 section to specific section
+ // R1_i ++
+ merged_section_start_positions[merged_section_count] = CIGAR_intervals_R1[R1_i].start_pos;
+ merged_section_lengths[merged_section_count] = CIGAR_intervals_R1[R1_i].chromosomal_length;
+ merged_section_belong_R1[merged_section_count]=1;
+ merged_section_belong_R2[merged_section_count]=0;
+
+ int indel_i;
+ for(indel_i = 0; indel_i < CIGAR_intervals_R1[R1_i].insertions; indel_i++){
+ merged_section_indel_positions[merged_section_count][indel_i] = CIGAR_intervals_R1[R1_i].insertion_start_pos[indel_i];
+ merged_section_indel_lengths[merged_section_count][indel_i] = CIGAR_intervals_R1[R1_i].insertion_lengths[indel_i];
+ }
+ merged_section_indel_counts[merged_section_count] = CIGAR_intervals_R1[R1_i].insertions;
+
+ merged_section_count ++;
+ R1_i ++;
+ }else if(R2_i < CIGAR_intervals_R2_sections){
+ merged_section_start_positions[merged_section_count] = CIGAR_intervals_R2[R2_i].start_pos;
+ merged_section_lengths[merged_section_count] = CIGAR_intervals_R2[R2_i].chromosomal_length;
+ merged_section_belong_R1[merged_section_count]=0;
+ merged_section_belong_R2[merged_section_count]=1;
+
+ int indel_i;
+ for(indel_i = 0; indel_i < CIGAR_intervals_R2[R2_i].insertions; indel_i++){
+ merged_section_indel_positions[merged_section_count][indel_i] = CIGAR_intervals_R2[R2_i].insertion_start_pos[indel_i];
+ merged_section_indel_lengths[merged_section_count][indel_i] = CIGAR_intervals_R2[R2_i].insertion_lengths[indel_i];
+ }
+ merged_section_indel_counts[merged_section_count] = CIGAR_intervals_R2[R2_i].insertions;
+
+ merged_section_count ++;
+ R2_i ++;
+ }
+ }
+
+ int ret = 0, x1, x2;
+ for(x1 = 0; x1 < merged_section_count ; x1++){
+ ret += merged_section_lengths[x1];
+ for(x2 = 0; x2 < merged_section_indel_counts[x1]; x2++)
+ ret += merged_section_indel_lengths[x1][x2];
+// SUBREADprintf("FRAGDEBUG %s [%d] : len = %d , indels = %d\n" , read_name, x1, merged_section_lengths[x1] , merged_section_indel_counts[x1]);
+ }
+
+ return ret;
+}
+
+void parse_bin(SamBam_Reference_Info * sambam_chro_table, char * bin, char * bin2, char ** read_name, int * flag, char ** chro, long * pos, int * mapq, char ** mate_chro, long * mate_pos, long * tlen, int * is_junction_read, int * cigar_sect, unsigned int * Starting_Chro_Points, unsigned short * Starting_Read_Points, unsigned short * Section_Read_Lengths, char ** ChroNames, char * Event_After_Section, int * NH_value, int max_M, CIGAR_interval_t * intervals_buffer, int * intervals_i){
+ int x1, len_of_S1 = 0;
*cigar_sect = 0;
*NH_value = 1;
*flag = 0;
@@ -1778,6 +2074,12 @@ void parse_bin(SamBam_Reference_Info * sambam_chro_table, char * bin, char * bin
int * cigar_opt_ints = (int *)(bin + 36 + l_read_name);
unsigned int chro_cursor = (*pos), section_start_chro = (*pos);
unsigned short read_cursor = 0, this_section_length = 0, section_start_read = 0;
+
+ if(intervals_buffer){
+ intervals_buffer[ *intervals_i ].start_pos = chro_cursor;
+ intervals_buffer[ *intervals_i ].chro = *chro;
+ }
+
for(x1 = 0 ; x1 < cigar_opts; x1++){
int optype = cigar_opt_ints[x1]&0xf;
int optval = (cigar_opt_ints[x1]>>4)& 0xfffffff;
@@ -1795,7 +2097,14 @@ void parse_bin(SamBam_Reference_Info * sambam_chro_table, char * bin, char * bin
char event_char=0;
if(optype == 3) event_char = 'N';
if(optype == 2) event_char = 'D';
- else if(optype == 1) event_char = 'I';
+ else if(optype == 1){
+ if(intervals_buffer && intervals_buffer[ *intervals_i ].insertions < MAXIMUM_INSERTION_IN_SECTION){
+ intervals_buffer[ *intervals_i ].insertion_start_pos[ intervals_buffer[ *intervals_i ].insertions ] = chro_cursor;
+ intervals_buffer[ *intervals_i ].insertion_lengths[ intervals_buffer[ *intervals_i ].insertions ] = optval;
+ intervals_buffer[ *intervals_i ].insertions ++;
+ }
+ event_char = 'I';
+ }
if( (*cigar_sect) < max_M){
Event_After_Section[*cigar_sect] = event_char;
@@ -1804,26 +2113,46 @@ void parse_bin(SamBam_Reference_Info * sambam_chro_table, char * bin, char * bin
Section_Read_Lengths[*cigar_sect] = this_section_length;
ChroNames[*cigar_sect] = (*chro);
(*cigar_sect)++;
+
+ if(intervals_buffer){
+ intervals_buffer[ *intervals_i ].chromosomal_length = chro_cursor - intervals_buffer[ *intervals_i ].start_pos;
+ (*intervals_i) ++;
+ }
}
- if(optype == 2 || optype == 3)
+ if(optype == 2 || optype == 3)// N or D
chro_cursor += optval;
- else read_cursor += optval;
+ else
+ read_cursor += optval;
+
+ if(intervals_buffer && (*cigar_sect) < max_M){
+ intervals_buffer[ *intervals_i ].start_pos = chro_cursor;
+ intervals_buffer[ *intervals_i ].chro = *chro;
+ }
section_start_chro = chro_cursor;
- this_section_length = 0;
section_start_read = read_cursor;
+ this_section_length = 0;
}else if(optype == 4){ // 'S'
if(read_cursor==0)
{
read_cursor += optval;
section_start_read = read_cursor;
- }
+
+ if(intervals_buffer){
+ if(intervals_buffer[ *intervals_i ].start_pos > optval) intervals_buffer[ *intervals_i ].start_pos -= optval;
+ else intervals_buffer[ *intervals_i ].start_pos = 0;
+ }
+ }else len_of_S1 = optval;
} // H and P do not have effect on cigar parsing.
}
if(this_section_length>0){
// add new section
if( (*cigar_sect) < max_M){
+ if(intervals_buffer){
+ intervals_buffer[ *intervals_i ].chromosomal_length = chro_cursor - intervals_buffer[ *intervals_i ].start_pos + len_of_S1;
+ (*intervals_i)++;
+ }
Starting_Chro_Points[*cigar_sect] = section_start_chro;
Starting_Read_Points[*cigar_sect] = section_start_read;
Section_Read_Lengths[*cigar_sect] = this_section_length ;
@@ -1913,7 +2242,7 @@ void process_line_junctions(fc_thread_global_context_t * global_context, fc_thre
char Event_After_Section[global_context -> max_M];
if(is_second_read && !global_context -> is_paired_end_mode_assign) break;
- parse_bin(global_context -> sambam_chro_table, is_second_read?bin2:bin1, is_second_read?bin1:bin2 , &read_name, &alignment_masks , &read_chr, &read_pos, &mapping_qual, &mate_chr, &mate_pos, &fragment_length, &is_junction_read, &cigar_sections, Starting_Chro_Points, Starting_Read_Points, Section_Read_Lengths, ChroNames, Event_After_Section, &NH_value, global_context -> max_M);
+ parse_bin(global_context -> sambam_chro_table, is_second_read?bin2:bin1, is_second_read?bin1:bin2 , &read_name, &alignment_masks , &read_chr, &read_pos, &mapping_qual, &mate_chr, &mate_pos, &fragment_length, &is_junction_read, &cigar_sections, Starting_Chro_Points, Starting_Read_Points, Section_Read_Lengths, ChroNames, Event_After_Section, &NH_value, global_context -> max_M, NULL, NULL);
assert(cigar_sections <= global_context -> max_M);
int * njunc_current = is_second_read?&njunc2:&njunc1;
@@ -1948,6 +2277,11 @@ int process_pairer_output(void * pairer_vp, int thread_no, char * rname, char *
return 0;
}
+void sort_bucket_table(fc_thread_global_context_t * global_context);
+void vote_and_add_count(fc_thread_global_context_t * global_context, fc_thread_thread_context_t * thread_context,
+ long * hits_indices1, int nhits1, long * hits_indices2, int nhits2, unsigned int total_frag_len,
+ char ** hits_chro1, char ** hits_chro2, unsigned int * hits_start_pos1, unsigned int * hits_start_pos2, unsigned short * hits_length1, unsigned short * hits_length2,
+ int fixed_fractional_count, char * read_name);
void process_line_buffer(fc_thread_global_context_t * global_context, fc_thread_thread_context_t * thread_context, char * bin1, char * bin2)
{
@@ -1957,9 +2291,10 @@ void process_line_buffer(fc_thread_global_context_t * global_context, fc_thread_
unsigned int search_start = 0, search_end;
int nhits1 = 0, nhits2 = 0, alignment_masks, search_block_id, search_item_id, mapping_qual;
long * hits_indices1 = thread_context -> hits_indices1, * hits_indices2 = thread_context -> hits_indices2;
- unsigned short * hits_read_start_base1 = thread_context -> hits_read_start_base1 , * hits_read_start_base2 = thread_context -> hits_read_start_base2;
- short * hits_read_len1 = thread_context -> hits_read_len1, * hits_read_len2 = thread_context -> hits_read_len2;
- unsigned short cigar_read_len1 = 0, cigar_read_len2 = 0;
+ unsigned int * hits_start_pos1 = thread_context -> hits_start_pos1 , * hits_start_pos2 = thread_context -> hits_start_pos2;
+ unsigned short * hits_length1 = thread_context -> hits_length1 , * hits_length2 = thread_context -> hits_length2;
+ char ** hits_chro1 = thread_context -> hits_chro1 , **hits_chro2 = thread_context -> hits_chro2;
+ unsigned int total_frag_len =0;
int cigar_sections, is_junction_read;
unsigned int Starting_Chro_Points[global_context -> max_M];
@@ -1971,18 +2306,30 @@ void process_line_buffer(fc_thread_global_context_t * global_context, fc_thread_
int is_second_read;
int maximum_NH_value = 1, NH_value;
int skipped_for_exonic = 0;
- int first_read_quality_score = 0;
+ int first_read_quality_score = 0, CIGAR_intervals_R1_sections = 0, CIGAR_intervals_R2_sections = 0;
+
+ CIGAR_interval_t CIGAR_intervals_R1 [ global_context -> max_M ];
+ CIGAR_interval_t CIGAR_intervals_R2 [ global_context -> max_M ];
+
+ if(global_context -> need_calculate_overlap_len ){
+ memset( CIGAR_intervals_R1, 0, sizeof(CIGAR_interval_t) * global_context -> max_M );
+ memset( CIGAR_intervals_R2, 0, sizeof(CIGAR_interval_t) * global_context -> max_M );
+ }
thread_context->all_reads++;
//if(thread_context->all_reads>1000000) printf("TA=%llu\n%s\n",thread_context->all_reads, thread_context -> line_buffer1);
+
for(is_second_read = 0 ; is_second_read < 2; is_second_read++)
{
if(is_second_read && !global_context -> is_paired_end_mode_assign) break;
- parse_bin(global_context -> sambam_chro_table, is_second_read?bin2:bin1, is_second_read?bin1:bin2 , &read_name, &alignment_masks , &read_chr, &read_pos, &mapping_qual, &mate_chr, &mate_pos, &fragment_length, &is_junction_read, &cigar_sections, Starting_Chro_Points, Starting_Read_Points, Section_Read_Lengths, ChroNames, Event_After_Section, &NH_value, global_context -> max_M);
+ parse_bin(global_context -> sambam_chro_table, is_second_read?bin2:bin1, is_second_read?bin1:bin2 , &read_name, &alignment_masks , &read_chr, &read_pos, &mapping_qual, &mate_chr, &mate_pos, &fragment_length, &is_junction_read, &cigar_sections, Starting_Chro_Points, Starting_Read_Points, Section_Read_Lengths, ChroNames, Event_After_Section, &NH_value, global_context -> max_M , global_context -> need_calculate_overlap_len?(is_second_read?CIGAR_intervals_R2:CIGAR_intervals_R1):NULL, is_s [...]
// SUBREADprintf(" RNAME=%s\n", read_name);
+ //#warning "==================== REMOVE WHEN RELEASE ========================"
+ //if(global_context -> SAM_output_fp)
+ // fprintf(global_context -> SAM_output_fp, "SAMDEBUG: %s\t\t%s, %ld\n", read_name, read_chr, read_pos);
if(is_second_read == 0)
{
//skip the read if unmapped (its mate will be skipped as well if paired-end)
@@ -2120,12 +2467,9 @@ void process_line_buffer(fc_thread_global_context_t * global_context, fc_thread_
int cigar_section_id;
long * hits_indices = (is_second_read?hits_indices2:hits_indices1);
- unsigned short * hits_read_start_base = is_second_read?hits_read_start_base2:hits_read_start_base1;
- short * hits_read_len = is_second_read?hits_read_len2:hits_read_len1;
- unsigned short * cigar_read_len = is_second_read?&cigar_read_len2:&cigar_read_len1;
-
- (*cigar_read_len) = Starting_Read_Points[cigar_sections-1] + Section_Read_Lengths[cigar_sections-1];
-
+ unsigned int * hits_start_pos = is_second_read?hits_start_pos2:hits_start_pos1;
+ unsigned short * hits_length = is_second_read?hits_length2:hits_length1;
+ char ** hits_chro = is_second_read?hits_chro2:hits_chro1;
if(global_context->is_split_or_exonic_only == 1 && !is_junction_read) {
skipped_for_exonic ++;
@@ -2292,12 +2636,12 @@ void process_line_buffer(fc_thread_global_context_t * global_context, fc_thread_
{
hits_indices[nhits] = search_item_id;
- if(global_context -> calculate_overlapping_lengths)
- {
- int section_overlapped = min(global_context -> exontable_stop[search_item_id] , section_end_pos)
- - max(global_context -> exontable_start[search_item_id] , section_begin_pos) + 1;
- hits_read_len[nhits] = (short)section_overlapped;
- hits_read_start_base[nhits] = (section_begin_pos > global_context -> exontable_start[search_item_id]?(Starting_Read_Points[cigar_section_id]):(Starting_Read_Points[cigar_section_id] + (global_context -> exontable_start[search_item_id] - section_begin_pos)));
+ if(global_context -> need_calculate_overlap_len) {
+ hits_start_pos[nhits] = max(Starting_Chro_Points[cigar_section_id], global_context -> exontable_start[search_item_id]);
+ hits_length[nhits] = min(global_context -> exontable_stop[search_item_id] , section_end_pos)+1 - hits_start_pos[nhits] ;
+ hits_chro[nhits] = ChroNames[cigar_section_id];
+ if(0 && FIXLENstrcmp("V0112_0155:7:1101:10214:3701", read_name)==0)
+ SUBREADprintf("QNAME: [%d] %s %d ~ %d\n", nhits, hits_chro[nhits], hits_start_pos[nhits], hits_start_pos[nhits]+hits_length[nhits]);
}
nhits++;
@@ -2317,14 +2661,19 @@ void process_line_buffer(fc_thread_global_context_t * global_context, fc_thread_
} // loop for is_second_read
+ if(global_context -> need_calculate_fragment_len )
+ total_frag_len = calc_total_frag_len( global_context, thread_context, CIGAR_intervals_R1, CIGAR_intervals_R1_sections, CIGAR_intervals_R2, CIGAR_intervals_R2_sections , read_name);
+
+ //SUBREADprintf("FRAGLEN: %s %d\n", read_name, total_frag_len);
+
int fixed_fractional_count = global_context -> use_fraction_multi_mapping ?calc_fixed_fraction(maximum_NH_value): NH_FRACTION_INT;
// we have hits_indices1 and hits_indices2 and nhits1 and nhits2 here
// we also have fixed_fractional_count which is the value to add
vote_and_add_count(global_context, thread_context,
- hits_indices1, hits_read_start_base1, hits_read_len1, nhits1, cigar_read_len1,
- hits_indices2, hits_read_start_base2, hits_read_len2, nhits2, cigar_read_len2,
+ hits_indices1, nhits1, hits_indices2, nhits2, total_frag_len,
+ hits_chro1, hits_chro2, hits_start_pos1, hits_start_pos2, hits_length1, hits_length2,
fixed_fractional_count, read_name);
return;
}
@@ -2404,13 +2753,63 @@ void add_fragment_supported_junction( fc_thread_global_context_t * global_contex
}
}
+int overlap_compare(void * arr, int L, int R){
+ unsigned int * pos = (unsigned int *)arr;
+ return pos[ L*2 ] - pos[R*2];
+}
+
+void overlap_exchange(void * arr, int L, int R){
+ unsigned int * pos = (unsigned int *)arr, tt;
+ tt=pos[L*2];
+ pos[L*2] = pos[R*2];
+ pos[R*2] = tt;
+
+ tt=pos[L*2+1];
+ pos[L*2+1] = pos[R*2+1];
+ pos[R*2+1] = tt;
+}
+
+unsigned short calc_score_overlaps(fc_thread_global_context_t * global_context, fc_thread_thread_context_t * thread_context, char ** chros, unsigned int * start_poses, unsigned short * lens, int sections){
+ unsigned int in_intervals[ 2*sections ];
+ unsigned int out_intervals[ 2*sections ], x1;
+ char used_interval[ sections ];
+
+ memset(used_interval, 0 , sections);
+ unsigned int ret = 0;
+
+ for(x1 = 0 ; x1 < sections ; x1++){
+ if( used_interval [x1] )continue;
+
+ in_intervals[x1*2] = start_poses[x1];
+ in_intervals[x1*2 + 1] = start_poses[x1] + lens[x1];
+ used_interval[x1]=1;
+
+ int x2, this_sections = 1;
+ for(x2 = x1 + 1; x2 < sections; x2++){
+ if(strcmp( chros[x2], chros[x1] ) == 0){
+ in_intervals[this_sections*2] = start_poses[x2];
+ in_intervals[this_sections*2 + 1] = start_poses[x2] + lens[x2];
+ used_interval[x2]=1;
+ this_sections++;
+ }
+ }
+
+ basic_sort( in_intervals, this_sections, overlap_compare, overlap_exchange );
+
+ int merged_secs = mergeIntervals( in_intervals, out_intervals, this_sections );
+ for(x2 = 0; x2 < merged_secs; x2++){
+ ret += ( out_intervals[x2*2+1] - out_intervals[x2*2] );
+ }
+ }
+ return ret;
+}
+
+
void vote_and_add_count(fc_thread_global_context_t * global_context, fc_thread_thread_context_t * thread_context,
- long * hits_indices1, unsigned short * hits_read_start_base1, short * hits_read_len1, int nhits1, unsigned short rl1,
- long * hits_indices2, unsigned short * hits_read_start_base2, short * hits_read_len2, int nhits2, unsigned short rl2,
+ long * hits_indices1, int nhits1, long * hits_indices2, int nhits2, unsigned int total_frag_len,
+ char ** hits_chro1, char ** hits_chro2, unsigned int * hits_start_pos1, unsigned int * hits_start_pos2, unsigned short * hits_length1, unsigned short * hits_length2,
int fixed_fractional_count, char * read_name){
-//char * read_name, fc_junction_info_t * supported_junctions1, int njunc1, fc_junction_info_t * supported_junctions2, int njunc2)
- if(global_context -> calculate_overlapping_lengths == 0 && nhits2+nhits1==1)
- {
+ if(global_context -> need_calculate_overlap_len == 0 && nhits2+nhits1==1) {
long hit_exon_id = nhits2?hits_indices2[0]:hits_indices1[0];
thread_context->count_table[hit_exon_id] += fixed_fractional_count;
thread_context->nreads_mapped_to_exon++;
@@ -2418,12 +2817,10 @@ void vote_and_add_count(fc_thread_global_context_t * global_context, fc_thread_t
{
int final_gene_number = global_context -> exontable_geneid[hit_exon_id];
unsigned char * final_feture_name = global_context -> gene_name_array[final_gene_number];
- fprintf(global_context -> SAM_output_fp,"%s\tAssigned\t%s\t*\n", read_name, final_feture_name);
+ fprintf(global_context -> SAM_output_fp,"%s\tAssigned\t%s\tTotal=1\n", read_name, final_feture_name);
}
thread_context->read_counters.assigned_reads ++;
- }
- else if(global_context -> calculate_overlapping_lengths == 0 && nhits2 == 1 && nhits1 == 1 && hits_indices2[0]==hits_indices1[0])
- {
+ } else if(global_context -> need_calculate_overlap_len == 0 && nhits2 == 1 && nhits1 == 1 && hits_indices2[0]==hits_indices1[0]) {
long hit_exon_id = hits_indices1[0];
thread_context->count_table[hit_exon_id] += fixed_fractional_count;
thread_context->nreads_mapped_to_exon++;
@@ -2431,13 +2828,10 @@ void vote_and_add_count(fc_thread_global_context_t * global_context, fc_thread_t
{
int final_gene_number = global_context -> exontable_geneid[hit_exon_id];
unsigned char * final_feture_name = global_context -> gene_name_array[final_gene_number];
- fprintf(global_context -> SAM_output_fp,"%s\tAssigned\t%s\t*\n", read_name, final_feture_name);
+ fprintf(global_context -> SAM_output_fp,"%s\tAssigned\t%s\tTotal=1\n", read_name, final_feture_name);
}
thread_context->read_counters.assigned_reads ++;
- }
- else
- {
- int ends;
+ } else {
// Build a voting table.
// The voting table should be:
// total_length [nhit_final] = total_length_overlapping
@@ -2454,176 +2848,159 @@ void vote_and_add_count(fc_thread_global_context_t * global_context, fc_thread_t
//
// two ends in a fragment is considered individually; the overlapping bases are not added up.
//
- char * read_coverage_bits = thread_context -> read_coverage_bits;
- for(ends = 0; ends < global_context -> is_paired_end_mode_assign + 1; ends++)
- {
- long * hits_indices = ends?hits_indices2:hits_indices1;
- unsigned short * hits_read_start_base = ends?hits_read_start_base2:hits_read_start_base1;
- short * hits_read_len = ends?hits_read_len2:hits_read_len1;
- int nhits = ends?nhits2:nhits1;
- int x1;
+
+ unsigned int * scoring_numbers = thread_context -> scoring_buff_numbers; // size is : MAX_HIT_NUMBER *2
+ unsigned int * scoring_flags = thread_context -> scoring_buff_flags; // size is : MAX_HIT_NUMBER *2
+ unsigned short * scoring_overlappings = thread_context -> scoring_buff_overlappings; // size is : MAX_HIT_NUMBER *2
+ long * scoring_exon_ids = thread_context -> scoring_buff_exon_ids; // size is : MAX_HIT_NUMBER *2
+ int scoring_count = 0, score_x1;
- if(read_coverage_bits)
- {
- int covergae_bitmap_size = max(rl1,rl2)/8+2;
- for(x1 = 0; x1 < nhits; x1++)
- memset(read_coverage_bits + x1 * (MAX_FC_READ_LENGTH / 8 + 1), 0, covergae_bitmap_size);
- }
- // calculating the summed lengths of overlapping exons
- for(x1=0; x1<nhits;x1++)
- {
- long exon_no = hits_indices[x1];
- if(exon_no>=0x7fffffff) continue; //already removed
+ if( global_context -> need_calculate_overlap_len ){
- char * x1_bitmap = read_coverage_bits + (MAX_FC_READ_LENGTH /8 +1) * x1;
+ char ** scoring_gap_chros = thread_context -> scoring_buff_gap_chros;
+ unsigned int * scoring_gap_starts = thread_context -> scoring_buff_gap_starts; // size is : MAX_HIT_NUMBER *2;
+ unsigned short * scoring_gap_lengths = thread_context -> scoring_buff_gap_lengths; // size is : MAX_HIT_NUMBER *2* global_context -> max_M*2
- //if(0 && FIXLENstrcmp("R0002957", read_name)==0)
- // SUBREADprintf("CREATE bitmap: for x1 = %d, on read %d len = %d \n", x1, hits_read_start_base[x1], hits_read_len[x1]);
+ int end1, end2, hit_x1, hit_x2;
+ char used_hit1 [nhits1];
+ char used_hit2 [nhits2];
+ memset(used_hit1 , 0 , nhits1);
+ memset(used_hit2 , 0 , nhits2);
- if(read_coverage_bits)
- add_bitmap_overlapping(x1_bitmap, hits_read_start_base[x1], hits_read_len[x1]);
+ for(end1 = 0; end1 < global_context -> is_paired_end_mode_assign + 1 ; end1++){
+ long * hits_indices_X1 = end1?hits_indices2:hits_indices1;
+ char * used_hit_X1 = end1?used_hit2:used_hit1;
+ int nhit_X1 = end1?nhits2:nhits1;
- // if(FIXLENstrcmp("V0112_0155:7:1306:9527:74733", read_name)==0)
- // SUBREADprintf("CREATE bitmap: for x1 = %d, on read %d len = %d \n", x1, hits_read_start_base[x1], hits_read_len[x1]);
- long merge_key = global_context -> is_gene_level? global_context -> exontable_geneid[exon_no] : exon_no;
- int x2;
- for(x2=x1+1; x2<nhits; x2++)
- {
- long tomerge_exon_no = hits_indices[x2];
- if(tomerge_exon_no >=0x7fffffff) continue;
+ for( hit_x1 = 0 ; hit_x1 < nhit_X1; hit_x1 ++ ){
+ if(used_hit_X1[hit_x1])continue;
- long tomerge_key = global_context -> is_gene_level? global_context -> exontable_geneid[tomerge_exon_no] : tomerge_exon_no;
- if(tomerge_key==merge_key)
- {
- if(read_coverage_bits)
- add_bitmap_overlapping(x1_bitmap, hits_read_start_base[x2], hits_read_len[x2]);
-
- // if(0 && FIXLENstrcmp("R0002957", read_name)==0)
- // SUBREADprintf("APPEND bitmap: for x1 = %d, on read %d len = %d \n", x1, hits_read_start_base[x2], hits_read_len[x2]);
- //TODO: change this part to uniquely-overlapping length. Not simply adding.
- //hits_read_start_base[x1]+=hits_read_start_base[x2];
- hits_indices[x2]=0x7fffffff;
-
- }
- }
- }
+ int gaps = 0;
+ long tmp_exon_id = hits_indices_X1[hit_x1];
+ long score_merge_key;
+ if (global_context -> is_gene_level )
+ score_merge_key = global_context -> exontable_geneid[tmp_exon_id];
+ else score_merge_key = tmp_exon_id;
- // remove the exons in the hits table when it is marked as removed (0x7fffffff)
- int new_hits=0;
- for(x1 = 0; x1< nhits; x1++)
- {
- if(hits_indices[x1]>=0x7fffffff) continue;
- if(new_hits != x1)
- hits_indices[new_hits]=hits_indices[x1];
-
- if(global_context -> calculate_overlapping_lengths)
- {
- char * x1_bitmap = read_coverage_bits + (MAX_FC_READ_LENGTH /8 +1) * x1;
- hits_read_len[new_hits]=count_bitmap_overlapping(x1_bitmap, ends?rl2:rl1);
- //if(0 && FIXLENstrcmp("R0002957", read_name)==0)
- // SUBREADprintf("COUNT BITMAP FOR gene#%d LEN=%d\n", x1, hits_read_len[new_hits]);
- }
+ scoring_gap_chros[0 ] = (end1?hits_chro2:hits_chro1)[hit_x1];
+ scoring_gap_starts[0 ] = (end1?hits_start_pos2:hits_start_pos1)[hit_x1];
+ scoring_gap_lengths[0 ] = (end1?hits_length2:hits_length1)[hit_x1];
- new_hits++;
- }
- if(ends) nhits2 = new_hits;
- else nhits1 = new_hits;
- }
+ gaps=1;
- unsigned short * decision_total_lengths = thread_context ->decision_table_votes;
- int decision_number = 0, decision_table_no;
- long * decision_table_exon_ids = thread_context -> decision_table_exon_ids;
- long * decision_table_keys = thread_context -> decision_table_ids;
- char * read1_used = thread_context -> decision_table_read1_used;
- char * read2_used = thread_context -> decision_table_read2_used;
-
- for(ends =0 ; ends < global_context -> is_paired_end_mode_assign + 1 ; ends++){
- int nhits = ends?nhits2:nhits1;
- short * hits_read_len = ends?hits_read_len2:hits_read_len1;
- long * hits_indices = ends?hits_indices2:hits_indices1;
- int hit_x1;
- for(hit_x1 = 0; hit_x1 < nhits ; hit_x1++){
- int decision_i;
- long decision_key; // gene_id if is_gene_level, or exon_id.
- long decision_exon_id;
- if (global_context -> is_gene_level ){
- decision_exon_id = hits_indices[hit_x1];
- decision_key = global_context -> exontable_geneid[decision_exon_id];
- }else
- decision_exon_id = decision_key = hits_indices[hit_x1];
-
- // get decision_table_no from decision_key
- // add into decision_tables if decision_key is unfound.
- decision_table_no = -1;
- for(decision_i = 0; decision_i < decision_number ; decision_i ++){
- if(decision_key == decision_table_keys[decision_i])
- {
- decision_table_no = decision_i;
- break;
- }
- }
+ scoring_flags[scoring_count] = end1?2:1;
+ scoring_numbers[scoring_count] =1;
+ scoring_exon_ids[scoring_count] = tmp_exon_id;
- if(decision_table_no<0){
- decision_table_exon_ids[decision_number] = decision_exon_id;
- decision_table_keys[decision_number] = decision_key;
- decision_total_lengths[decision_number] = 0;
- read1_used[decision_number]=0;
- read2_used[decision_number]=0;
+ used_hit_X1[ hit_x1 ]=1;
- decision_table_no = decision_number;
- decision_number ++;
- }
+ for(end2 = 0; end2 < global_context -> is_paired_end_mode_assign + 1 ; end2++){
+ long * hits_indices_X2 = end2?hits_indices2:hits_indices1;
+ char * used_hit_X2 = end2?used_hit2:used_hit1;
+ int nhit_X2 = end2?nhits2:nhits1;
- if(ends)read2_used[decision_table_no] = 1;
- else read1_used[decision_table_no] = 1;
+ for( hit_x2 = 0 ; hit_x2 < nhit_X2; hit_x2 ++ ){
+ if(used_hit_X2[hit_x2])continue;
- assert(read2_used[decision_table_no]<2);
- assert(read1_used[decision_table_no]<2);
+ long X2_merge_key;
+ if (global_context -> is_gene_level )
+ X2_merge_key = global_context -> exontable_geneid[ hits_indices_X2[hit_x2] ];
+ else X2_merge_key = hits_indices_X2[hit_x2];
- if(global_context -> calculate_overlapping_lengths){
+ if( X2_merge_key == score_merge_key ){
+ used_hit_X2[ hit_x2 ]=1;
+ scoring_gap_chros[ gaps ] = (end2?hits_chro2:hits_chro1)[hit_x2];
+ scoring_gap_starts[ gaps ] = (end2?hits_start_pos2:hits_start_pos1)[hit_x2];
+ scoring_gap_lengths[ gaps ] = (end2?hits_length2:hits_length1)[hit_x2];
- // if(0 && FIXLENstrcmp("R0002957", read_name)==0)
- // SUBREADprintf("READ DECIDE LEN=%d, += %d for %s\n", decision_total_lengths[decision_table_no], hits_read_len[hit_x1] , read_name);
+ if((scoring_flags[scoring_count] & (end2?2:1))== 0 ){
+ scoring_flags[scoring_count] |= end2?2:1;
+ scoring_numbers[scoring_count] ++;
+ }
+ gaps ++;
+ }
+ }
+ }
- decision_total_lengths[decision_table_no] += hits_read_len[hit_x1];
+ scoring_overlappings [scoring_count] = calc_score_overlaps(global_context, thread_context, scoring_gap_chros, scoring_gap_starts, scoring_gap_lengths, gaps);
+ if( global_context -> use_overlapping_break_tie )
+ scoring_numbers[scoring_count] = scoring_overlappings [scoring_count];
+ scoring_count++;
}
+ }
+ }else{
+ int ends;
+ for(ends =0 ; ends < global_context -> is_paired_end_mode_assign + 1 ; ends++){
+ int nhits = ends?nhits2:nhits1;
+ long * hits_indices = ends?hits_indices2:hits_indices1;
+
+ int hit_x1;
+ for(hit_x1 = 0; hit_x1 < nhits; hit_x1++){
+ long tmp_exon_id = hits_indices[hit_x1], score_merge_key;
+ int found = 0;
+ if (global_context -> is_gene_level )
+ score_merge_key = global_context -> exontable_geneid[tmp_exon_id];
+ else score_merge_key = tmp_exon_id;
+
+ for(score_x1 = 0; score_x1 < scoring_count; score_x1 ++){
+ long score_x1_key ;
+ if (global_context -> is_gene_level )
+ score_x1_key = global_context -> exontable_geneid[ scoring_exon_ids[score_x1] ];
+ else score_x1_key = scoring_exon_ids[score_x1] ;
+
+ //fprintf(stderr, "Q222KEY: exon=%ld, gene=%ld\n", scoring_exon_ids[score_x1] , score_x1_key );
+ if( score_x1_key == score_merge_key ){
+ if((scoring_flags[score_x1] & ( ends?2:1 )) == 0) {
+ scoring_flags[score_x1] |= (ends?2:1);
+ scoring_numbers[score_x1] ++;
+ }
+
+ found = 1;
+ break;
+ }
+ }
+
+ if(0 == found){
+ scoring_exon_ids[scoring_count] = tmp_exon_id;
+ scoring_flags[scoring_count] = ends?2:1;
+ scoring_numbers[scoring_count] = 1;
+ scoring_count++;
+ }
+ }
}
}
- int maximum_decision_score = 0;
+
+ int maximum_score = 0;
int maximum_total_count = 0;
- int maximum_decision_no = 0;
- for(decision_table_no = 0; decision_table_no < decision_number; decision_table_no++)
- {
- //if(0 && FIXLENstrcmp("R0002957", read_name)==0)
- // SUBREADprintf("READ DECIDE LEN=%d for %s\n", decision_total_lengths[decision_table_no] , read_name);
- if(global_context -> fragment_minimum_overlapping == 1 || decision_total_lengths[decision_table_no] >= global_context -> fragment_minimum_overlapping)
- {
- int this_decision_score;
- if(global_context -> use_overlapping_break_tie) {
- this_decision_score = decision_total_lengths[decision_table_no];
- } else {
- if(global_context -> restricted_no_multi_overlap) {
- this_decision_score = (read1_used[decision_table_no] || read2_used[decision_table_no])?1:0;
- } else {
- this_decision_score = read1_used[decision_table_no] + read2_used[decision_table_no];
- }
- }
+ int maximum_score_x1 = 0;
+ int applied_fragment_minimum_overlapping = 1;
- // if(0 && FIXLENstrcmp("R0002957", read_name)==0)
- // SUBREADprintf("%s LEN[%d] = %d , score=%d <? %d # %d\n", read_name, decision_table_no , decision_total_lengths[decision_table_no], this_decision_score, maximum_decision_score , maximum_total_count);
+ if( global_context -> fragment_minimum_overlapping > 1 || global_context -> need_calculate_fragment_len){
+ applied_fragment_minimum_overlapping = max( global_context -> fragment_minimum_overlapping, global_context -> fractional_minimum_overlapping * ( total_frag_len) );
+ }
- if(maximum_decision_score < this_decision_score){
- maximum_total_count = 1;
- maximum_decision_no = decision_table_no;
- maximum_decision_score = this_decision_score;
- }else if(maximum_decision_score == this_decision_score)
- maximum_total_count ++;
- }
+
+ for(score_x1 = 0; score_x1 < scoring_count ; score_x1++){
+
+ if(0 && FIXLENstrcmp("V0112_0155:7:1101:5387:6362", read_name)==0) SUBREADprintf("Scoring Overlap %s = %d >=%d, score=%d, exonid=%ld\n", read_name, scoring_overlappings[score_x1], applied_fragment_minimum_overlapping, scoring_numbers[score_x1], scoring_exon_ids[score_x1]);
+ //SUBREADprintf("RLTEST: %s %d\n", read_name, scoring_overlappings[score_x1]);
+ if( applied_fragment_minimum_overlapping > 1 )
+ if( applied_fragment_minimum_overlapping > scoring_overlappings[score_x1] ){
+ scoring_numbers[score_x1] = 0;
+ continue;
+ }
+
+ if( maximum_score < scoring_numbers[score_x1] ){
+ maximum_total_count = 1;
+ maximum_score = scoring_numbers[score_x1];
+ maximum_score_x1 = score_x1;
+ }else if( maximum_score == scoring_numbers[score_x1] )
+ maximum_total_count++;
}
if(maximum_total_count == 0){
@@ -2636,42 +3013,31 @@ void vote_and_add_count(fc_thread_global_context_t * global_context, fc_thread_t
// final adding votes.
if(1 == maximum_total_count && !global_context -> is_multi_overlap_allowed) {
// simple add to the exon ( EXON_ID = decision_table_exon_ids[maximum_decision_no])
- long max_exon_id = decision_table_exon_ids[maximum_decision_no];
+ long max_exon_id = scoring_exon_ids[maximum_score_x1];
thread_context->count_table[max_exon_id] += fixed_fractional_count;
thread_context->nreads_mapped_to_exon++;
if(global_context -> SAM_output_fp)
{
int final_gene_number = global_context -> exontable_geneid[max_exon_id];
unsigned char * final_feture_name = global_context -> gene_name_array[final_gene_number];
- if(decision_number>1)
- fprintf(global_context -> SAM_output_fp,"%s\tAssigned\t%s\t%s/Targets=%d/%d\n", read_name, final_feture_name, global_context -> use_overlapping_break_tie? "MaximumOverlapping":"Votes", maximum_decision_score, decision_number);
+ if(scoring_count>1)
+ fprintf(global_context -> SAM_output_fp,"%s\tAssigned\t%s\tTotal=1;%s/Targets=%d/%d\n", read_name, final_feture_name, global_context -> use_overlapping_break_tie? "MaximumOverlapping":"Votes", maximum_score, scoring_count);
else
- fprintf(global_context -> SAM_output_fp,"%s\tAssigned\t%s\t*\n", read_name, final_feture_name);
+ fprintf(global_context -> SAM_output_fp,"%s\tAssigned\t%s\tTotal=1\n", read_name, final_feture_name);
}
thread_context->read_counters.assigned_reads ++;
}else if(global_context -> is_multi_overlap_allowed) {
char final_feture_names[1000];
int assigned_no = 0, xk1;
final_feture_names[0]=0;
- for(xk1 = 0; xk1 < decision_number; xk1++)
+ for(xk1 = 0; xk1 < scoring_count; xk1++)
{
- int this_decision_score;
- if(global_context -> use_overlapping_break_tie) {
- this_decision_score = decision_total_lengths[xk1];
- } else {
- if(global_context -> restricted_no_multi_overlap) {
- this_decision_score = (read1_used[xk1] || read2_used[xk1])?1:0;
- } else {
- this_decision_score = read1_used[xk1] + read2_used[xk1];
- }
- }
-
// This change was made on 31/MAR/2016
- if( this_decision_score < maximum_decision_score ) continue ;
+ if( scoring_numbers[xk1] < maximum_score ) continue ;
- long tmp_voter_id = decision_table_exon_ids[xk1];
- thread_context->count_table[tmp_voter_id] += fixed_fractional_count;
+ long tmp_voter_id = scoring_exon_ids[xk1];
+ thread_context->count_table[tmp_voter_id] += calculate_multi_overlap_fraction(global_context, fixed_fractional_count, maximum_total_count);
if(global_context -> SAM_output_fp)
{
@@ -2838,12 +3204,23 @@ HashTable * load_alias_table(char * fname)
HashTablePut(ret, sam_chr_buf, anno_chr_buf);
}
+ fclose(fp);
free(fl);
return ret;
}
-void fc_thread_init_global_context(fc_thread_global_context_t * global_context, unsigned int buffer_size, unsigned short threads, int line_length , int is_PE_data, int min_pe_dist, int max_pe_dist, int is_gene_level, int is_overlap_allowed, int is_strand_checked, char * output_fname, int is_sam_out, int is_both_end_required, int is_chimertc_disallowed, int is_PE_distance_checked, char *feature_name_column, char * gene_id_column, int min_map_qual_score, int is_multi_mapping_allowed, int i [...]
+void get_temp_dir_from_out(char * tmp, char * out){
+ char * slash = strrchr(out,'/');
+ if(NULL == slash){
+ strcpy(tmp, "./");
+ }else{
+ memcpy(tmp, out, slash - out);
+ tmp[slash - out]=0;
+ }
+}
+
+void fc_thread_init_global_context(fc_thread_global_context_t * global_context, unsigned int buffer_size, unsigned short threads, int line_length , int is_PE_data, int min_pe_dist, int max_pe_dist, int is_gene_level, int is_overlap_allowed, int is_strand_checked, char * output_fname, int is_sam_out, int is_both_end_required, int is_chimertc_disallowed, int is_PE_distance_checked, char *feature_name_column, char * gene_id_column, int min_map_qual_score, int is_multi_mapping_allowed, int i [...]
{
int x1;
@@ -2853,7 +3230,6 @@ void fc_thread_init_global_context(fc_thread_global_context_t * global_context,
global_context -> redo = 0;
global_context -> SAM_output_fp = NULL;
-
global_context -> isCVersion = isCVersion;
global_context -> is_read_details_out = is_sam_out;
global_context -> is_multi_overlap_allowed = is_overlap_allowed;
@@ -2887,8 +3263,10 @@ void fc_thread_init_global_context(fc_thread_global_context_t * global_context,
global_context -> five_end_extension = fiveEndExtension;
global_context -> three_end_extension = threeEndExtension;
global_context -> fragment_minimum_overlapping = minFragmentOverlap;
+ global_context -> fractional_minimum_overlapping = fracOverlap;
global_context -> use_overlapping_break_tie = useOverlappingBreakTie;
- global_context -> calculate_overlapping_lengths = (global_context -> fragment_minimum_overlapping > 1) || global_context -> use_overlapping_break_tie;
+ global_context -> need_calculate_fragment_len = ( global_context -> fractional_minimum_overlapping > 1E-10 );
+ global_context -> need_calculate_overlap_len = global_context -> fractional_minimum_overlapping > 1E-10 || (global_context -> fragment_minimum_overlapping > 1) || global_context -> use_overlapping_break_tie;
global_context -> debug_command = debug_command;
global_context -> max_M = max_M;
global_context -> max_BAM_header_size = buffer_size;
@@ -2927,14 +3305,14 @@ void fc_thread_init_global_context(fc_thread_global_context_t * global_context,
strcpy(global_context -> output_file_path, ".");
}
+ if(temp_dir == NULL)get_temp_dir_from_out(global_context -> temp_file_dir, output_fname);
+ else strcpy(global_context -> temp_file_dir, temp_dir);
//SUBREADprintf("OFPP:%s, OFNN:%s\n", global_context -> output_file_path, global_context -> output_file_name);
global_context -> min_paired_end_distance = min_pe_dist;
global_context -> max_paired_end_distance = max_pe_dist;
global_context -> thread_number = threads;
global_context -> line_length = line_length;
-
-
}
@@ -2958,7 +3336,6 @@ int fc_thread_start_threads(fc_thread_global_context_t * global_context, int et_
global_context -> is_unpaired_warning_shown = 0;
global_context -> is_stake_warning_shown = 0;
-
if(global_context -> is_read_details_out)
{
char tmp_fname[350], *modified_fname;
@@ -3018,9 +3395,6 @@ int fc_thread_start_threads(fc_thread_global_context_t * global_context, int et_
global_context -> thread_contexts[xk1].all_reads = 0;
global_context -> thread_contexts[xk1].chro_name_buff = malloc(CHROMOSOME_NAME_LENGTH);
global_context -> thread_contexts[xk1].strm_buffer = malloc(sizeof(z_stream));
- if(global_context -> calculate_overlapping_lengths)
- global_context -> thread_contexts[xk1].read_coverage_bits = malloc((MAX_FC_READ_LENGTH / 8 + 1)*MAX_HIT_NUMBER);
- else global_context -> thread_contexts[xk1].read_coverage_bits = NULL;
global_context -> thread_contexts[xk1].unpaired_fragment_no = 0;
global_context -> thread_contexts[xk1].read_counters.assigned_reads = 0;
@@ -3035,6 +3409,12 @@ int fc_thread_start_threads(fc_thread_global_context_t * global_context, int et_
global_context -> thread_contexts[xk1].read_counters.unassigned_junction_condition = 0;
global_context -> thread_contexts[xk1].read_counters.unassigned_duplicate = 0;
+ if(global_context -> need_calculate_overlap_len){
+ global_context -> thread_contexts[xk1].scoring_buff_gap_chros = malloc( sizeof(char *) * MAX_HIT_NUMBER * 2 * global_context -> max_M *2);
+ global_context -> thread_contexts[xk1].scoring_buff_gap_starts = malloc( sizeof(unsigned int ) * MAX_HIT_NUMBER * 2 * global_context -> max_M *2);
+ global_context -> thread_contexts[xk1].scoring_buff_gap_lengths = malloc( sizeof(unsigned short) * MAX_HIT_NUMBER * 2 * global_context -> max_M *2);
+ } else global_context -> thread_contexts[xk1].scoring_buff_gap_chros = NULL;
+
if(global_context -> do_junction_counting)
{
global_context -> thread_contexts[xk1].junction_counting_table = HashTableCreate(131317);
@@ -3054,10 +3434,10 @@ int fc_thread_start_threads(fc_thread_global_context_t * global_context, int et_
thread_args[1] = & global_context -> thread_contexts[xk1];
}
- char rand_prefix[200];
+ char rand_prefix[500];
char MAC_or_random[13];
mac_or_rand_str(MAC_or_random);
- sprintf(rand_prefix, "./temp-core-%06u-%s.sam", getpid(), MAC_or_random);
+ sprintf(rand_prefix, "%s/temp-core-%06u-%s.sam", global_context -> temp_file_dir, getpid(), MAC_or_random);
//#warning "REMOVE ' * 2 ' FROM NEXT LINE !!!!!!"
SAM_pairer_create(&global_context -> read_pairer, global_context -> thread_number , global_context -> max_BAM_header_size/1024/1024+2, !global_context-> is_SAM_file, 1, !global_context -> is_paired_end_mode_assign, global_context ->is_paired_end_mode_assign && global_context -> do_not_sort ,0, global_context -> input_file_name, process_pairer_reset, process_pairer_header, process_pairer_output, rand_prefix, global_context);
@@ -3078,11 +3458,14 @@ void fc_thread_destroy_thread_context(fc_thread_global_context_t * global_contex
for(xk1=0; xk1<global_context-> thread_number; xk1++)
{
//printf("CHRR_FREE\n");
- if(global_context -> thread_contexts[xk1].read_coverage_bits)
- free(global_context -> thread_contexts[xk1].read_coverage_bits);
free(global_context -> thread_contexts[xk1].count_table);
free(global_context -> thread_contexts[xk1].chro_name_buff);
free(global_context -> thread_contexts[xk1].strm_buffer);
+ if(global_context -> thread_contexts[xk1].scoring_buff_gap_chros){
+ free(global_context -> thread_contexts[xk1].scoring_buff_gap_chros);
+ free(global_context -> thread_contexts[xk1].scoring_buff_gap_starts);
+ free(global_context -> thread_contexts[xk1].scoring_buff_gap_lengths);
+ }
if(global_context -> do_junction_counting){
HashTableDestroy(global_context -> thread_contexts[xk1].junction_counting_table);
HashTableDestroy(global_context -> thread_contexts[xk1].splicing_point_table);
@@ -3094,7 +3477,7 @@ void fc_thread_destroy_thread_context(fc_thread_global_context_t * global_contex
}
void fc_thread_wait_threads(fc_thread_global_context_t * global_context)
{
- SAM_pairer_run(&global_context -> read_pairer);
+ global_context -> is_input_bad_format |= SAM_pairer_run(&global_context -> read_pairer);
}
void BUFstrcat(char * targ, char * src, char ** buf){
@@ -3243,21 +3626,22 @@ void fc_write_final_gene_results(fc_thread_global_context_t * global_context, in
{
int merged_gaps = mergeIntervals(input_start_stop_list, output_start_stop_list, gap_merge_ptr);
- for(xk3=0; xk3<merged_gaps; xk3++)
+ for(xk3=0; xk3<gap_merge_ptr; xk3++)
{
char numbbuf[12];
BUFstrcat(out_chr_list, matched_chr, &tmp_chr_list);
BUFstrcat(out_chr_list, ";", &tmp_chr_list);
- sprintf(numbbuf,"%u;", output_start_stop_list[xk3 * 2]);
+ sprintf(numbbuf,"%u;", input_start_stop_list[xk3 * 2]);
BUFstrcat(out_start_list, numbbuf, &tmp_start_list);
- sprintf(numbbuf,"%u;", output_start_stop_list[xk3 * 2 + 1] - 1);
+ sprintf(numbbuf,"%u;", input_start_stop_list[xk3 * 2 + 1] - 1);
BUFstrcat(out_end_list, numbbuf, &tmp_end_list);
sprintf(numbbuf,"%c;", matched_strand?'-':'+');
BUFstrcat(out_strand_list, numbbuf, &tmp_strand_list);
- gene_nonoverlap_len += output_start_stop_list[xk3 * 2 + 1] - output_start_stop_list[xk3 * 2];
}
+ for(xk3=0; xk3<merged_gaps; xk3++)
+ gene_nonoverlap_len += output_start_stop_list[xk3 * 2 + 1] - output_start_stop_list[xk3 * 2];
}
}
}
@@ -3274,18 +3658,20 @@ void fc_write_final_gene_results(fc_thread_global_context_t * global_context, in
fprintf(fp_out, "%s\t%s\t%s\t%s\t%s\t%d" , gene_symbol, out_chr_list, out_start_list, out_end_list, out_strand_list, gene_nonoverlap_len);
// all exons: gene_exons_number[xk1] : gene_exons_pointer[xk1]
- for(i_files=0; i_files< non_empty_files; i_files++)
+ int non_empty_file_index = 0;
+ for(i_files=0; i_files< n_input_files; i_files++)
{
if(column_numbers[i_files])
{
read_count_type_t longlong_res = 0;
double double_res = 0;
- int is_double_number = calc_float_fraction(gene_columns[i_files+non_empty_files*xk1], &longlong_res, &double_res);
+ int is_double_number = calc_float_fraction(gene_columns[non_empty_file_index+non_empty_files*xk1], &longlong_res, &double_res);
if(is_double_number){
fprintf(fp_out,"\t%.2f", double_res);
}else{
fprintf(fp_out,"\t%llu", longlong_res);
}
+ non_empty_file_index ++;
}
}
fprintf(fp_out,"\n");
@@ -3421,8 +3807,9 @@ static struct option long_options[] =
{"readExtension3", required_argument, 0, 0},
{"read2pos", required_argument, 0, 0},
{"minOverlap", required_argument, 0, 0},
- {"countSplitAlignmentsOnly", no_argument, 0, 0},
- {"countNonSplitAlignmentsOnly", no_argument, 0, 0},
+ {"fracOverlap", required_argument, 0, 0},
+ {"splitOnly", no_argument, 0, 0},
+ {"nonSplitOnly", no_argument, 0, 0},
{"debugCommand", required_argument, 0, 0},
{"ignoreDup", no_argument, 0, 0},
{"donotsort", no_argument, 0, 0},
@@ -3431,6 +3818,7 @@ static struct option long_options[] =
{"order", required_argument, 0, 'S'},
{"genome", required_argument, 0, 'G'},
{"maxMOp", required_argument, 0, 0},
+ {"tmpDir", required_argument, 0, 0},
{"largestOverlap", no_argument, 0,0},
{0, 0, 0, 0}
};
@@ -3440,24 +3828,19 @@ void print_usage()
SUBREADprintf("\nVersion %s\n\n", SUBREAD_VERSION);
SUBREADputs("Usage: featureCounts [options] -a <annotation_file> -o <output_file> input_file1 [input_file2] ... \n");
- SUBREADputs("Required arguments:");
+ SUBREADputs("## Required arguments:");
SUBREADputs("");
SUBREADputs(" -a <string> Name of an annotation file. GTF/GFF format by default.");
SUBREADputs(" See -F option for more formats.");
SUBREADputs("");
- SUBREADputs(" -o <string> Name of the output file including read counts. A separate ");
- SUBREADputs(" file including summary statistics of counting results is ");
+ SUBREADputs(" -o <string> Name of the output file including read counts. A separate");
+ SUBREADputs(" file including summary statistics of counting results is");
SUBREADputs(" also included in the output (`<string>.summary')");
SUBREADputs("");
- SUBREADputs(" input_files List of input files in BAM or SAM format. Users do not ");
- SUBREADputs(" need to specify it is BAM or SAM.");
- SUBREADputs("");
- SUBREADputs("Optional arguments:");
+ SUBREADputs(" input_file1 [input_file2] ... A list of SAM or BAM format files.");
SUBREADputs("");
- SUBREADputs(" -A <string> Name of a comma delimited file including chromosome alias ");
- SUBREADputs(" names used to match chromosome names used in annotation ");
- SUBREADputs(" with those used in BAM/SAM input, if they are different. ");
- SUBREADputs(" See Users Guide for file format.");
+ SUBREADputs("## Options:");
+ SUBREADputs("# Annotation");
SUBREADputs("");
SUBREADputs(" -F <string> Specify format of provided annotation file. Acceptable");
SUBREADputs(" formats include `GTF/GFF' and `SAF'. `GTF/GFF' by default.");
@@ -3471,65 +3854,90 @@ void print_usage()
SUBREADputs(" default. Meta-features used for read counting will be ");
SUBREADputs(" extracted from annotation using the provided value.");
SUBREADputs("");
+ SUBREADputs(" -A <string> Provide a chromosome name alias file to match chr names in");
+ SUBREADputs(" annotation with those in the reads. This should be a two-");
+ SUBREADputs(" column comma-delimited text file. Its first column should");
+ SUBREADputs(" include chr names in the annotation and its second column");
+ SUBREADputs(" should include chr names in the reads. Chr names are case");
+ SUBREADputs(" sensitive. No column header should be included in the");
+ SUBREADputs(" file.");
+ SUBREADputs("");
+
+ SUBREADputs("# Level of summarization");
+ SUBREADputs("");
SUBREADputs(" -f Perform read counting at feature level (eg. counting ");
SUBREADputs(" reads for exons rather than genes).");
SUBREADputs("");
+
+ SUBREADputs("# Overlap between reads and features");
+ SUBREADputs("");
SUBREADputs(" -O Assign reads to all their overlapping meta-features (or ");
SUBREADputs(" features if -f is specified).");
SUBREADputs("");
- SUBREADputs(" -s <int> Perform strand-specific read counting. Possible values: ");
- SUBREADputs(" 0 (unstranded), 1 (stranded) and 2 (reversely stranded). ");
- SUBREADputs(" 0 by default.");
+ SUBREADputs(" --minOverlap <int> Minimum number of overlapping bases in a read that is");
+ SUBREADputs(" required for read assignment. 1 by default. Number of");
+ SUBREADputs(" overlapping bases is counted from both reads if paired");
+ SUBREADputs(" end. If a negative value is provided, then a gap of up");
+ SUBREADputs(" to specified size will be allowed between read and the");
+ SUBREADputs(" feature that the read is assigned to.");
+ SUBREADputs("");
+ SUBREADputs(" --fracOverlap <value> Minimum fraction of overlapping bases in a read that is");
+ SUBREADputs(" required for read assignment. Value should be within range");
+ SUBREADputs(" [0,1]. 0 by default. Number of overlapping bases is");
+ SUBREADputs(" counted from both reads if paired end. Both this option");
+ SUBREADputs(" and '--minOverlap' option need to be satisfied for read");
+ SUBREADputs(" assignment.");
SUBREADputs("");
- SUBREADputs(" -M Multi-mapping reads will also be counted. For a multi-");
- SUBREADputs(" mapping read, all its reported alignments will be ");
- SUBREADputs(" counted. The `NH' tag in BAM/SAM input is used to detect ");
- SUBREADputs(" multi-mapping reads.");
+ SUBREADputs(" --largestOverlap Assign reads to a meta-feature/feature that has the ");
+ SUBREADputs(" largest number of overlapping bases.");
SUBREADputs("");
- SUBREADputs(" -Q <int> The minimum mapping quality score a read must satisfy in");
- SUBREADputs(" order to be counted. For paired-end reads, at least one");
- SUBREADputs(" end should satisfy this criteria. 0 by default.");
+ SUBREADputs(" --readExtension5 <int> Reads are extended upstream by <int> bases from their");
+ SUBREADputs(" 5' end.");
SUBREADputs("");
- SUBREADputs(" -T <int> Number of the threads. 1 by default.");
+ SUBREADputs(" --readExtension3 <int> Reads are extended upstream by <int> bases from their");
+ SUBREADputs(" 3' end.");
SUBREADputs("");
- SUBREADputs(" -v Output version of the program.");
+ SUBREADputs(" --read2pos <5:3> Reduce reads to their 5' most base or 3' most base. Read");
+ SUBREADputs(" counting is then performed based on the single base the ");
+ SUBREADputs(" read is reduced to.");
SUBREADputs("");
- SUBREADputs(" -J Count number of reads supporting each exon-exon junction.");
- SUBREADputs(" Junctions were identified from those exon-spanning reads");
- SUBREADputs(" in the input (containing 'N' in CIGAR string). Counting");
- SUBREADputs(" results are saved to a file named '<output_file>.jcounts'");
+
+ SUBREADputs("# Multi-mapping reads");
SUBREADputs("");
- SUBREADputs(" -G <string> The Fasta file containing the reference genome used in");
- SUBREADputs(" generating the input SAM or BAM files. This argument is");
- SUBREADputs(" only needed when doing junction counting.");
+ SUBREADputs(" -M Multi-mapping reads will also be counted. For a multi-");
+ SUBREADputs(" mapping read, all its reported alignments will be ");
+ SUBREADputs(" counted. The `NH' tag in BAM/SAM input is used to detect ");
+ SUBREADputs(" multi-mapping reads.");
SUBREADputs("");
- SUBREADputs(" -R Output detailed assignment result for each read. A text ");
- SUBREADputs(" file will be generated for each input file, including ");
- SUBREADputs(" names of reads and meta-features/features reads were ");
- SUBREADputs(" assigned to. See Users Guide for more details.");
+ SUBREADputs("# Fractional counting");
SUBREADputs("");
- SUBREADputs(" --largestOverlap Assign reads to a meta-feature/feature that has the ");
- SUBREADputs(" largest number of overlapping bases.");
+ SUBREADputs(" --fraction Assign fractional counts to features. This option must");
+ SUBREADputs(" be used together with '-M' or '-O' or both. When '-M' is");
+ SUBREADputs(" specified, each reported alignment from a multi-mapping");
+ SUBREADputs(" read (identified via 'NH' tag) will carry a fractional");
+ SUBREADputs(" count of 1/x, instead of 1 (one), where x is the total");
+ SUBREADputs(" number of alignments reported for the same read. When '-O'");
+ SUBREADputs(" is specified, each overlapping feature will receive a");
+ SUBREADputs(" fractional count of 1/y, where y is the total number of");
+ SUBREADputs(" features overlapping with the read. When both '-M' and");
+ SUBREADputs(" '-O' are specified, each alignment will carry a fraction");
+ SUBREADputs(" count of 1/(x*y).");
SUBREADputs("");
- SUBREADputs(" --minOverlap <int> Specify minimum number of overlapping bases requried ");
- SUBREADputs(" between a read and a meta-feature/feature that the read ");
- SUBREADputs(" is assigned to. 1 by default.");
+
+
+ SUBREADputs("# Read filtering");
SUBREADputs("");
- SUBREADputs(" --read2pos <5:3> Reduce reads to their 5' most base or 3' most base. Read");
- SUBREADputs(" counting is then performed based on the single base the ");
- SUBREADputs(" read is reduced to.");
+ SUBREADputs(" -Q <int> The minimum mapping quality score a read must satisfy in");
+ SUBREADputs(" order to be counted. For paired-end reads, at least one");
+ SUBREADputs(" end should satisfy this criteria. 0 by default.");
SUBREADputs("");
- SUBREADputs(" --readExtension5 <int> Reads are extended upstream by <int> bases from their");
- SUBREADputs(" 5' end.");
- SUBREADputs("");
- SUBREADputs(" --readExtension3 <int> Reads are extended upstream by <int> bases from their");
- SUBREADputs(" 3' end.");
- SUBREADputs("");
- SUBREADputs(" --fraction Use a fractional count 1/n, instead of 1 (one) count, for ");
- SUBREADputs(" each reported alignment of a multi-mapping read in read ");
- SUBREADputs(" counting. n is total number of alignments reported for ");
- SUBREADputs(" the multi-mapping read. This option must be used together ");
- SUBREADputs(" with '-M' option.");
+ SUBREADputs(" --splitOnly Count split alignments only (ie. alignments with CIGAR");
+ SUBREADputs(" string containing 'N'). An example of split alignments is");
+ SUBREADputs(" exon-spanning reads in RNA-seq data.");
+ SUBREADputs("");
+ SUBREADputs(" --nonSplitOnly If specified, only non-split alignments (CIGAR strings do");
+ SUBREADputs(" not contain letter 'N') will be counted. All the other");
+ SUBREADputs(" alignments will be ignored.");
SUBREADputs("");
SUBREADputs(" --primary Count primary alignments only. Primary alignments are ");
SUBREADputs(" identified using bit 0x100 in SAM/BAM FLAG field.");
@@ -3539,23 +3947,42 @@ void print_usage()
SUBREADputs(" whole read pair is ignored if one of the reads is a ");
SUBREADputs(" duplicate read for paired end data.");
SUBREADputs("");
- SUBREADputs(" --countSplitAlignmentsOnly Count split alignments only (ie. alignments with ");
- SUBREADputs(" CIGAR string containing `N'). An example of split ");
- SUBREADputs(" alignments is exon-spanning reads in RNA-seq data.");
+
+ SUBREADputs("# Strandness");
+ SUBREADputs("");
+ SUBREADputs(" -s <int> Perform strand-specific read counting. Acceptable values:");
+ SUBREADputs(" 0 (unstranded), 1 (stranded) and 2 (reversely stranded).");
+ SUBREADputs(" 0 by default.");
+ SUBREADputs("");
+
+ SUBREADputs("# Exon-exon junctions");
+ SUBREADputs("");
+ SUBREADputs(" -J Count number of reads supporting each exon-exon junction.");
+ SUBREADputs(" Junctions were identified from those exon-spanning reads");
+ SUBREADputs(" in the input (containing 'N' in CIGAR string). Counting");
+ SUBREADputs(" results are saved to a file named '<output_file>.jcounts'");
+ SUBREADputs("");
+ SUBREADputs(" -G <string> Provide the name of a FASTA-format file that contains the");
+ SUBREADputs(" reference sequences used in read mapping that produced the");
+ SUBREADputs(" provided SAM/BAM files. This optional argument can be used");
+ SUBREADputs(" with '-J' option to improve read counting for junctions.");
+ SUBREADputs("");
+
+ SUBREADputs("# Parameters specific to paired end reads");
SUBREADputs("");
SUBREADputs(" -p If specified, fragments (or templates) will be counted");
SUBREADputs(" instead of reads. This option is only applicable for");
SUBREADputs(" paired-end reads.");
SUBREADputs("");
+ SUBREADputs(" -B Count read pairs that have both ends successfully aligned ");
+ SUBREADputs(" only.");
+ SUBREADputs("");
SUBREADputs(" -P Check validity of paired-end distance when counting read ");
SUBREADputs(" pairs. Use -d and -D to set thresholds.");
SUBREADputs("");
- SUBREADputs(" -d <int> Minimum fragment/template length, 50 by default.");
- SUBREADputs("");
- SUBREADputs(" -D <int> Maximum fragment/template length, 600 by default.");
+ SUBREADputs(" -d <int> Minimum fragment/template length, 50 by default.");
SUBREADputs("");
- SUBREADputs(" -B Count read pairs that have both ends successfully aligned ");
- SUBREADputs(" only.");
+ SUBREADputs(" -D <int> Maximum fragment/template length, 600 by default.");
SUBREADputs("");
SUBREADputs(" -C Do not count read pairs that have their two ends mapping ");
SUBREADputs(" to different chromosomes or mapping to same chromosome ");
@@ -3565,10 +3992,30 @@ void print_usage()
SUBREADputs(" the same pair are required to be located next to each ");
SUBREADputs(" other in the input.");
SUBREADputs("");
- SUBREADputs(" --maxMOp <int> Maximum number of 'M' operations allowed in a CIGAR string");
- SUBREADputs(" . 10 by default. Both 'X' and '=' are treated as 'M' and");
- SUBREADputs(" adjacent 'M' operations are merged in the CIGAR string.");
+
+ SUBREADputs("# Number of CPU threads");
+ SUBREADputs("");
+ SUBREADputs(" -T <int> Number of the threads. 1 by default.");
+ SUBREADputs("");
+ SUBREADputs("# Miscellaneous");
+ SUBREADputs("");
+ SUBREADputs(" -R Output detailed assignment result for each read. A text ");
+ SUBREADputs(" file will be generated for each input file, including ");
+ SUBREADputs(" names of reads and meta-features/features reads were ");
+ SUBREADputs(" assigned to. See Users Guide for more details.");
SUBREADputs("");
+ SUBREADputs(" --tmpDir <string> Directory under which intermediate files are saved (later");
+ SUBREADputs(" removed). By default, intermediate files will be saved to");
+ SUBREADputs(" the directory specified in '-o' argument.");
+ SUBREADputs("");
+ SUBREADputs(" --maxMOp <int> Maximum number of 'M' operations allowed in a CIGAR");
+ SUBREADputs(" string. 10 by default. Both 'X' and '=' are treated as 'M'");
+ SUBREADputs(" and adjacent 'M' operations are merged in the CIGAR");
+ SUBREADputs(" string.");
+ SUBREADputs("");
+ SUBREADputs(" -v Output version of the program.");
+ SUBREADputs("");
+
}
int junckey_sort_compare(void * inptr, int i, int j){
@@ -3925,7 +4372,6 @@ char * get_short_fname(char * lname){
return ret;
}
-void sort_bucket_table(fc_thread_global_context_t * global_context);
int readSummary_single_file(fc_thread_global_context_t * global_context, read_count_type_t * column_numbers, int nexons, int * geneid, char ** chr, long * start, long * stop, unsigned char * sorted_strand, char * anno_chr_2ch, char ** anno_chrs, long * anno_chr_head, long * block_end_index, long * block_min_start , long * block_max_end, fc_read_counters * my_read_counter, HashTable * junc_glob_tab, HashTable * splicing_glob_tab);
int readSummary(int argc,char *argv[]){
@@ -3976,14 +4422,17 @@ int readSummary(int argc,char *argv[]){
37: file name of genome fasta (for determine the strandness of junctions by looking for GT/AG or CT/AC).
38: as.numeric(max_M_Ops) # maximum "M" sections allowed in the CIGAR string. This parameter is needed in parse_BIN()
39: as.numeric(is_Restrictly_No_Overlapping) # when "1", disable the voting-based tie breaking (e.g., when the reads are paired-end and one gene receives two votes but the other gene only has one.). "0" by default.
+ 40: as.numeric(min_Fractional_Overlap) # A fractioal number. 0.00 : at least 1 bp overlapping
+ 41: temp_directory # the directory to put temp files. "<use output directory>" by default, namely find it from the output file dir.
*/
int isStrandChecked, isCVersion, isChimericDisallowed, isPEDistChecked, minMappingQualityScore=0, isInputFileResortNeeded, feature_block_size = 20, reduce_5_3_ends_to_one;
+ float fracOverlap;
char **chr;
long *start, *stop;
int *geneid;
- char *nameFeatureTypeColumn, *nameGeneIDColumn,*debug_command, *pair_orientations="fr";
+ char *nameFeatureTypeColumn, *nameGeneIDColumn,*debug_command, *pair_orientations="fr", *temp_dir;
long nexons;
@@ -4143,27 +4592,38 @@ int readSummary(int argc,char *argv[]){
if(argc>39)
isRestrictlyNoOvelrapping = atoi(argv[39]);
else isRestrictlyNoOvelrapping = 0;
+
+ if(argc>40)
+ fracOverlap = atof(argv[40]);
+ else fracOverlap= 0.0;
+ if(argc>41){
+ if(strcmp("<use output directory>", argv[41])!=0)temp_dir = argv[41];
+ else temp_dir = NULL;
+ }
+ else temp_dir = NULL;// get_temp_dir_from_out(temp_dir, (char *)argv[3]);
+
if(SAM_pairer_warning_file_open_limit()) return -1;
fc_thread_global_context_t global_context;
- fc_thread_init_global_context(& global_context, FEATURECOUNTS_BUFFER_SIZE, thread_number, MAX_LINE_LENGTH, isPE, minPEDistance, maxPEDistance,isGeneLevel, isMultiOverlapAllowed, isStrandChecked, (char *)argv[3] , isReadSummaryReport, isBothEndRequired, isChimericDisallowed, isPEDistChecked, nameFeatureTypeColumn, nameGeneIDColumn, minMappingQualityScore,isMultiMappingAllowed, 0, alias_file_name, cmd_rebuilt, isInputFileResortNeeded, feature_block_size, isCVersion, fiveEndExtension, thre [...]
+ fc_thread_init_global_context(& global_context, FEATURECOUNTS_BUFFER_SIZE, thread_number, MAX_LINE_LENGTH, isPE, minPEDistance, maxPEDistance,isGeneLevel, isMultiOverlapAllowed, isStrandChecked, (char *)argv[3] , isReadSummaryReport, isBothEndRequired, isChimericDisallowed, isPEDistChecked, nameFeatureTypeColumn, nameGeneIDColumn, minMappingQualityScore,isMultiMappingAllowed, 0, alias_file_name, cmd_rebuilt, isInputFileResortNeeded, feature_block_size, isCVersion, fiveEndExtension, thre [...]
- if( global_context.is_multi_mapping_allowed != ALLOW_ALL_MULTI_MAPPING && global_context.use_fraction_multi_mapping)
+ if( global_context.is_multi_mapping_allowed != ALLOW_ALL_MULTI_MAPPING && (!isMultiOverlapAllowed) && global_context.use_fraction_multi_mapping)
{
- SUBREADprintf("ERROR: '--fraction' option should be used together with '-M'.\nThis option should not be used when multi-mapping reads are disallowed or the primary mapping is only counted.\n");
+ SUBREADprintf("ERROR: '--fraction' option should be used together with '-M' or '-O'. Please change the parameters to allow multi-mapping reads and/or multi-overlapping features.\n");
return -1;
}
- print_FC_configuration(&global_context, argv[1], argv[2], argv[3], global_context.is_SAM_file, isGTF, & n_input_files, isReadSummaryReport);
+ if( print_FC_configuration(&global_context, argv[1], argv[2], argv[3], global_context.is_SAM_file, isGTF, & n_input_files, isReadSummaryReport) )
+ return -1;
//print_in_box(80,0,0,"IG=%d, IS=%d", isGeneLevel, isSplitOrExonicOnly);
if(0)if(isSplitOrExonicOnly && ( isGeneLevel || !isMultiOverlapAllowed) )
{
- print_in_box(80,0,0,"NOTICE --countSplitAlignmentsOnly is specified, but '-O' and '-f' are not");
+ print_in_box(80,0,0,"NOTICE --splitOnly is specified, but '-O' and '-f' are not");
print_in_box(80,0,0," both specified. Please read the manual for details.");
print_in_box(80,0,0,"");
}
@@ -4195,6 +4655,8 @@ int readSummary(int argc,char *argv[]){
if(ret_fq){
print_in_box(80,0,0," WARNING unable to open the FASTA file.");
print_in_box(80,0,0,"");
+ free(global_context.fasta_contigs);
+ global_context.fasta_contigs = NULL;
}else{
print_in_box(80,0,0," %lu contigs were loaded", global_context.fasta_contigs -> contig_table -> numOfElements);
print_in_box(80,0,0,"");
@@ -4308,11 +4770,14 @@ int readSummary(int argc,char *argv[]){
free(file_list_used);
- if(isGeneLevel)
- fc_write_final_gene_results(&global_context, geneid, chr, start, stop, sorted_strand, argv[3], nexons, table_columns, argv[2], n_input_files , loaded_features, isCVersion);
- else
- fc_write_final_results(&global_context, argv[3], nexons, table_columns, argv[2], n_input_files ,loaded_features, isCVersion);
-
+ if(global_context.is_input_bad_format){
+ SUBREADprintf("\nFATAL Error: an input file has wrong format! The program has to terminate and no counting file is generated.\n\n");
+ }else{
+ if(isGeneLevel)
+ fc_write_final_gene_results(&global_context, geneid, chr, start, stop, sorted_strand, argv[3], nexons, table_columns, argv[2], n_input_files , loaded_features, isCVersion);
+ else
+ fc_write_final_results(&global_context, argv[3], nexons, table_columns, argv[2], n_input_files ,loaded_features, isCVersion);
+ }
if(global_context.do_junction_counting)
fc_write_final_junctions(&global_context, argv[3], table_columns, argv[2], n_input_files , junction_global_table_list, splicing_global_table_list);
@@ -4333,7 +4798,7 @@ int readSummary(int argc,char *argv[]){
free(table_columns);
- print_FC_results(&global_context);
+ if(global_context.is_input_bad_format == 0) print_FC_results(&global_context);
KeyValuePair * cursor;
int bucket;
for(bucket=0; bucket < global_context.exontable_chro_table -> numOfBuckets; bucket++)
@@ -4441,13 +4906,6 @@ void sort_bucket_table(fc_thread_global_context_t * global_context){
-
-
-
-
-
-
-
int readSummary_single_file(fc_thread_global_context_t * global_context, read_count_type_t * column_numbers, int nexons, int * geneid, char ** chr, long * start, long * stop, unsigned char * sorted_strand, char * anno_chr_2ch, char ** anno_chrs, long * anno_chr_head, long * block_end_index, long * block_min_start , long * block_max_end, fc_read_counters * my_read_counter, HashTable * junction_global_table, HashTable * splicing_global_table)
{
FILE *fp_in = NULL;
@@ -4549,6 +5007,7 @@ int readSummary_single_file(fc_thread_global_context_t * global_context, read_co
global_context -> sambam_chro_table = NULL;
free(line);
+ if(global_context -> is_input_bad_format) return -1;
return 0;
}
@@ -4559,8 +5018,9 @@ int main(int argc, char ** argv)
int feature_count_main(int argc, char ** argv)
#endif
{
- char * Rargv[40];
+ char * Rargv[42];
char annot_name[300];
+ char temp_dir[300];
char * out_name = malloc(300);
char * fasta_contigs_name = malloc(300);
char * alias_file_name = malloc(300);
@@ -4607,7 +5067,8 @@ int feature_count_main(int argc, char ** argv)
int c;
int very_long_file_names_size = 200;
int fiveEndExtension = 0, threeEndExtension = 0, minFragmentOverlap = 1;
- char strFiveEndExtension[11], strThreeEndExtension[11], strMinFragmentOverlap[11];
+ float fracOverlap = 0.0;
+ char strFiveEndExtension[11], strThreeEndExtension[11], strMinFragmentOverlap[11], fracOverlapStr[20];
very_long_file_names = malloc(very_long_file_names_size);
very_long_file_names [0] = 0;
fasta_contigs_name[0]=0;
@@ -4617,6 +5078,7 @@ int feature_count_main(int argc, char ** argv)
strcpy(nameFeatureTypeColumn,"exon");
strcpy(nameGeneIDColumn,"gene_id");
+ strcpy(temp_dir, "<use output directory>");
annot_name[0]=0;out_name[0]=0;
@@ -4635,7 +5097,6 @@ int feature_count_main(int argc, char ** argv)
opterr=1;
optopt=63;
strcpy(max_M_str, "10");
-
strcpy(Pair_Orientations,"fr");
while ((c = getopt_long (argc, argv, "G:A:g:t:T:o:a:d:D:L:Q:pbF:fs:S:CBJPMORv?", long_options, &option_index)) != -1)
@@ -4775,6 +5236,13 @@ int feature_count_main(int argc, char ** argv)
threeEndExtension = max(0, threeEndExtension);
}
+ if(strcmp("fracOverlap", long_options[option_index].name)==0)
+ {
+ if(!is_valid_float(optarg, "fracOverlap"))
+ STANDALONE_exit(-1);
+ fracOverlap = atof(optarg);
+ }
+
if(strcmp("minOverlap", long_options[option_index].name)==0)
{
if(!is_valid_digit(optarg, "minOverlap"))
@@ -4797,6 +5265,9 @@ int feature_count_main(int argc, char ** argv)
{
use_fraction_multimapping = 1;
}
+ if(strcmp("tmpDir", long_options[option_index].name)==0){
+ strcpy(temp_dir, optarg);
+ }
if(strcmp("maxMOp", long_options[option_index].name)==0){
if(!is_valid_digit_range(optarg, "maxMOp", 1 , 64))
STANDALONE_exit(-1);
@@ -4821,7 +5292,7 @@ int feature_count_main(int argc, char ** argv)
do_not_sort = 1;
}
- if(strcmp("countSplitAlignmentsOnly", long_options[option_index].name)==0)
+ if(strcmp("splitOnly", long_options[option_index].name)==0)
{
is_Split_or_Exonic_Only = 1;
}
@@ -4830,7 +5301,7 @@ int feature_count_main(int argc, char ** argv)
{
is_Restrictedly_No_Overlap = 1;
}
- if(strcmp("countNonSplitAlignmentsOnly", long_options[option_index].name)==0)
+ if(strcmp("nonSplitOnly", long_options[option_index].name)==0)
{
is_Split_or_Exonic_Only = 2;
}
@@ -4881,6 +5352,7 @@ int feature_count_main(int argc, char ** argv)
sprintf(min_qual_score_str,"%d", min_qual_score);
sprintf(feature_block_size_str,"%d", feature_block_size);
sprintf(Strand_Sensitive_Str,"%d", Strand_Sensitive_Mode);
+ sprintf(fracOverlapStr, "%g", fracOverlap);
Rargv[0] = "CreadSummary";
Rargv[1] = annot_name;
Rargv[2] = very_long_file_names;
@@ -4921,7 +5393,9 @@ int feature_count_main(int argc, char ** argv)
Rargv[37] = fasta_contigs_name;
Rargv[38] = max_M_str;
Rargv[39] = is_Restrictedly_No_Overlap?"1":"0";
- int retvalue = readSummary(40, Rargv);
+ Rargv[40] = fracOverlapStr;
+ Rargv[41] = temp_dir;
+ int retvalue = readSummary(42, Rargv);
free(very_long_file_names);
free(out_name);
diff --git a/test/featureCounts/data/corner-MinOverlap.ora b/test/featureCounts/data/corner-MinOverlap.ora
index 0645697..cc98f9d 100644
--- a/test/featureCounts/data/corner-MinOverlap.ora
+++ b/test/featureCounts/data/corner-MinOverlap.ora
@@ -1,8 +1,8 @@
-geNeiD 0
+Geneid data/test-junc.sam
simu_gene1 0
simu_gene2 0
simu_gene3 0
simu_gene4 0
-simu_gene5 15
-simu_gene6 19
-simu_gene7 157
+simu_gene5 13
+simu_gene6 21
+simu_gene7 145
diff --git a/test/featureCounts/data/corner-fractions.SAF b/test/featureCounts/data/corner-fractions.SAF
new file mode 100644
index 0000000..0ca01b5
--- /dev/null
+++ b/test/featureCounts/data/corner-fractions.SAF
@@ -0,0 +1,5 @@
+g1 chr3 1000 2000 +
+g1 chr3 5000 6000 +
+g2 chr3 1000 2000 +
+g2 chr3 3000 4000 +
+g3 chr3 1000 2000 +
diff --git a/test/featureCounts/data/corner-fractions.ora b/test/featureCounts/data/corner-fractions.ora
new file mode 100644
index 0000000..1735eef
--- /dev/null
+++ b/test/featureCounts/data/corner-fractions.ora
@@ -0,0 +1,3 @@
+g1 0.78
+g2 1.28
+g3 0.44
diff --git a/test/featureCounts/data/corner-fractions.sam b/test/featureCounts/data/corner-fractions.sam
new file mode 100644
index 0000000..909f4fd
--- /dev/null
+++ b/test/featureCounts/data/corner-fractions.sam
@@ -0,0 +1,7 @@
+ at SQ SN:chr3 LN:999950
+R1 0 chr3 1000 40 100M * 0 0 N I NH:i:3 HI:i:1
+R1 0 chr3 3000 40 100M * 0 0 N I NH:i:3 HI:i:2
+R1 0 chr3 5000 40 100M * 0 0 N I NH:i:3 HI:i:3
+R2 0 chr3 1000 40 100M * 0 0 N I NH:i:1 HI:i:1
+R3 0 chr3 3000 40 100M * 0 0 N I NH:i:2 HI:i:1
+R3 0 chr3 9000 40 100M * 0 0 N I NH:i:2 HI:i:2
diff --git a/test/featureCounts/data/test-fracOverlap.ora b/test/featureCounts/data/test-fracOverlap.ora
new file mode 100644
index 0000000..e522f8c
--- /dev/null
+++ b/test/featureCounts/data/test-fracOverlap.ora
@@ -0,0 +1,4 @@
+Geneid test-fracOverlap.sam
+g1 1
+g2 0
+g3 0
diff --git a/test/featureCounts/data/test-fracOverlap.sam b/test/featureCounts/data/test-fracOverlap.sam
new file mode 100644
index 0000000..47d2fc7
--- /dev/null
+++ b/test/featureCounts/data/test-fracOverlap.sam
@@ -0,0 +1,4 @@
+read1 99 chr3 4950 40 60M300N40M = 4970 120 N I
+read1 147 chr3 4970 40 40M300N60M = 4950 120 N I
+read1 99 chr3 4955 40 60M300N40M = 4975 120 N I
+read1 147 chr3 4975 40 40M300N60M = 4955 120 N I
diff --git a/test/featureCounts/test_corner_cases.sh b/test/featureCounts/test_corner_cases.sh
index 12c9843..340a60c 100644
--- a/test/featureCounts/test_corner_cases.sh
+++ b/test/featureCounts/test_corner_cases.sh
@@ -21,7 +21,8 @@ $SH_CMD data/compare.sh data/test-junc.sam data/corner-BothEnds.ora data/test-mi
$SH_CMD data/compare.sh data/test-junc.sam data/corner-Chimeric.ora data/test-minimum.SAF "-p -F SAF -C " "disallowing chimeric fragments"
$SH_CMD data/compare.sh data/test-junc.sam data/corner-MultiMapping.ora data/test-minimum.SAF "-p -F SAF -M " "Allowing multi-mapped reads"
$SH_CMD data/compare.sh data/test-junc.sam data/corner-DoNotSort.ora data/test-minimum.SAF " -p -F SAF --donotsort " "not sorting input file"
-$SH_CMD data/compare.sh data/test-junc.sam data/corner-MinOverlap.ora data/test-minimum.SAF " --minOverlap 185 -p -F SAF " "minimum overlapping length"
+$SH_CMD data/compare.sh data/test-junc.sam data/corner-MinOverlap.ora data/test-minimum.SAF " --minOverlap 125 -p -F SAF " "minimum overlapping length"
+$SH_CMD data/compare.sh data/test-fracOverlap.sam data/test-fracOverlap.ora data/corner-fractions.SAF " --fracOverlap 0.62 -O -p -F SAF " "minimum overlapping fraction"
$SH_CMD data/compare.sh data/test-junc.sam data/corner-LargestOverlap.ora data/test-minimum.SAF "-p -F SAF --largestOverlap" "Largest Overlapping"
$SH_CMD data/compare.sh data/test-junc.sam data/corner-PEdist.ora data/test-minimum.SAF " -p -F SAF -B -C -P -d 130 -D 770 " "paired-end distance"
$SH_CMD data/compare.sh data/test-junc.sam data/corner-Read2Pos5.ora data/test-minimum.SAF " -p -F SAF --read2pos 5 " "Read to position (5' end)"
@@ -32,6 +33,7 @@ $SH_CMD data/compare.sh data/test-junc.sam data/corner-MaxOPs.ora data/test-mini
$SH_CMD data/compare.sh data/test-junc.sam data/corner-MinMAPQ.ora data/test-minimum.SAF " -p -F SAF -Q 58" "minimum mapping quality"
$SH_CMD data/compare.sh data/test-dup.sam data/corner-IgnoreDup.ora data/test-minimum.SAF "-p -F SAF --ignoreDup " "Ignoring duplicated reads"
$SH_CMD data/compare.sh data/test-junc.sam data/corner-Fraction.ora data/test-minimum.SAF "-p -F SAF --fraction -M " "Fraction counting"
+$SH_CMD data/compare.sh data/corner-fractions.sam data/corner-fractions.ora data/corner-fractions.SAF " -O -M -F SAF --fraction " "Advanced fractions"
$SH_CMD data/compare.sh data/test-junc.sam data/corner-Jcounts.ora data/test-minimum.SAF "-p -F SAF -J " "Junction counting" JC
if test -f /usr/local/work/liao/subread/chromosomes/all_34_alt.fa
@@ -57,7 +59,7 @@ $SH_CMD data/compare.sh data/test-minimum.sam data/test-minimum-UNSTR.ora data/t
# test 5' and 3' end extension
$SH_CMD data/compare.sh data/test-chrname.sam data/test-minimum-dup.ora data/test-minimum.GTF " -p --ignoreDup " "Ignoring duplicate fragments"
-$SH_CMD data/compare.sh data/corner-JUNC.sam data/corner-JUNC-ONLY.ora data/test-minimum.GTF "--countSplitAlignmentsOnly -O -f " "Junction reads only" FL
-$SH_CMD data/compare.sh data/corner-JUNC.sam data/corner-EXON-ONLY.ora data/test-minimum.GTF "--countNonSplitAlignmentsOnly -p " "Exonic reads only"
+$SH_CMD data/compare.sh data/corner-JUNC.sam data/corner-JUNC-ONLY.ora data/test-minimum.GTF " --splitOnly -O -f " "Junction reads only" FL
+$SH_CMD data/compare.sh data/corner-JUNC.sam data/corner-EXON-ONLY.ora data/test-minimum.GTF " --nonSplitOnly -p " "Exonic reads only"
echo
--
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