| ... | ... |
@@ -140,14 +140,29 @@ lastz <- function(assemblyTarget, assemblyQuery, |
| 140 | 140 |
"-", gsub("|", "\\|", chrQuery, fixed=TRUE),
|
| 141 | 141 |
".", sub("\\..*$", "", basename(assemblyQuery)),
|
| 142 | 142 |
".", format)) |
| 143 |
- cmd <- paste0(binary, " ", assemblyTarget, "/", |
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| 144 |
- gsub("|", "\\|", chrTarget, fixed=TRUE), " ",
|
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- assemblyQuery, "/", |
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| 146 |
- gsub("|", "\\|", chrQuery, fixed=TRUE), " ",
|
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| 147 |
- lastzOptions[[distance]], |
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| 148 |
- " --format=", format, |
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| 149 |
- " --output=", output, |
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- " --markend") |
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| 143 |
+ |
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| 144 |
+ if(identical(paste(assemblyTarget, chrTarget), |
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| 145 |
+ paste(assemblyQuery, chrQuery))){
|
|
| 146 |
+ ## Self-alignment |
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+ cmd <- paste0(binary, " ", assemblyTarget, "/", |
|
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+ gsub("|", "\\|", chrTarget, fixed=TRUE), " ",
|
|
| 149 |
+ "--self --nomirror", |
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+ lastzOptions[[distance]], |
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| 151 |
+ " --format=", format, |
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+ " --output=", output, |
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| 153 |
+ " --markend") |
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+ }else{
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+ ## No self-alignment |
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+ cmd <- paste0(binary, " ", assemblyTarget, "/", |
|
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+ gsub("|", "\\|", chrTarget, fixed=TRUE), " ",
|
|
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+ assemblyQuery, "/", |
|
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+ gsub("|", "\\|", chrQuery, fixed=TRUE), " ",
|
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| 160 |
+ lastzOptions[[distance]], |
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| 161 |
+ " --format=", format, |
|
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+ " --output=", output, |
|
| 163 |
+ " --markend") |
|
| 164 |
+ } |
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+ |
|
| 151 | 166 |
if(echoCommand){
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| 152 | 167 |
output <- cmd |
| 153 | 168 |
}else{
|
