git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@74874 bc3139a8-67e5-0310-9ffc-ced21a209358
Michael Lawrence authored on 26/03/2013 21:40:15
| ... | ... |
@@ -14,6 +14,7 @@ setClass("BamTallyParam",
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| 14 | 14 |
concordant_only = "logical", |
| 15 | 15 |
unique_only = "logical", |
| 16 | 16 |
primary_only = "logical", |
| 17 |
+ ignore_duplicates = "logical", |
|
| 17 | 18 |
min_depth = "integer", |
| 18 | 19 |
variant_strand = "integer", |
| 19 | 20 |
ignore_query_Ns = "logical", |
| ... | ... |
@@ -36,7 +37,7 @@ BamTallyParam <- function(genome, which = RangesList(), |
| 36 | 37 |
high_base_quality = 0L, |
| 37 | 38 |
minimum_mapq = 0L, |
| 38 | 39 |
concordant_only = FALSE, unique_only = FALSE, |
| 39 |
- primary_only = FALSE, |
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| 40 |
+ primary_only = FALSE, ignore_duplicates = FALSE, |
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| 40 | 41 |
min_depth = 0L, variant_strand = 0L, |
| 41 | 42 |
ignore_query_Ns = FALSE, |
| 42 | 43 |
indels = FALSE) |
| ... | ... |
@@ -116,7 +116,7 @@ normArgTRUEorFALSE <- function(x) {
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| 116 | 116 |
minimum_mapq = 0L, good_unique_mapq = 35L, |
| 117 | 117 |
maximum_nhits = 1000000L, |
| 118 | 118 |
concordant_only = FALSE, unique_only = FALSE, |
| 119 |
- primary_only = FALSE, |
|
| 119 |
+ primary_only = FALSE, ignore_duplicates = FALSE, |
|
| 120 | 120 |
min_depth = 0L, variant_strand = 0L, |
| 121 | 121 |
ignore_query_Ns = FALSE, |
| 122 | 122 |
indels = FALSE, |
| ... | ... |
@@ -153,6 +153,7 @@ normArgTRUEorFALSE <- function(x) {
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| 153 | 153 |
normArgTRUEorFALSE(concordant_only), |
| 154 | 154 |
normArgTRUEorFALSE(unique_only), |
| 155 | 155 |
normArgTRUEorFALSE(primary_only), |
| 156 |
+ normArgTRUEorFALSE(ignore_duplicates), |
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| 156 | 157 |
normArgSingleInteger(min_depth), |
| 157 | 158 |
normArgSingleInteger(variant_strand), |
| 158 | 159 |
normArgTRUEorFALSE(ignore_query_Ns), |
| ... | ... |
@@ -18,7 +18,7 @@ |
| 18 | 18 |
high_base_quality = 0L, |
| 19 | 19 |
minimum_mapq = 0L, |
| 20 | 20 |
concordant_only = FALSE, unique_only = FALSE, |
| 21 |
- primary_only = FALSE, |
|
| 21 |
+ primary_only = FALSE, ignore_duplicates = FALSE, |
|
| 22 | 22 |
min_depth = 0L, variant_strand = 0L, |
| 23 | 23 |
ignore_query_Ns = FALSE, |
| 24 | 24 |
indels = FALSE) |
| ... | ... |
@@ -41,6 +41,9 @@ |
| 41 | 41 |
} |
| 42 | 42 |
\item{unique_only}{Consider only the uniquly mapped reads.}
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| 43 | 43 |
\item{primary_only}{Consider only primary pairs.}
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+ \item{ignore_duplicates}{Whether to ignore the reads flagged as
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|
| 45 |
+ PCR/optical duplicates. |
|
| 46 |
+ } |
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| 44 | 47 |
\item{min_depth}{The minimum number of reads overlapping a position for
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| 45 | 48 |
it to be counted.} |
| 46 | 49 |
\item{variant_strand}{The number of strands on which a variant must be
|