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Wort john patch 1 #1

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8296ab6
Update gcstats.R read.R and MD5 files
WortJohn Dec 17, 2024
df12a27
Update gcstats.R read.R and MD5 files
WortJohn Dec 17, 2024
59d840c
Update gcstats.R read.R and MD5 files
WortJohn Dec 17, 2024
8bd3ac8
Create README.md
WortJohn Dec 17, 2024
b46aa6d
Update README.md
WortJohn Dec 17, 2024
28c12d0
Update README.md
WortJohn Dec 17, 2024
ccb9983
Update README.md
WortJohn Dec 18, 2024
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4 changes: 2 additions & 2 deletions MD5
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Original file line number Diff line number Diff line change
Expand Up @@ -4,12 +4,12 @@ dc74f3941cd7eb5d5d2820a78e855291 *NEWS
0090c3e305006e38f8ec8cef5616a3e2 *R/bayes.R
1c95cfc1a6597466e42c386b0c6a6196 *R/extract.R
c37085ee8b851dfd42eea66341904e82 *R/fit.R
06b55a573555d6e0315478fb47fd48c0 *R/gcstats.R
594c9ccd9c0816666791fb018756c2b2 *R/gcstats.R
3ad97d0891d98e23cd5be6b4417067c5 *R/graphics.R
79624c9cf668bfb2b05e8a339e98f393 *R/misc.R
4b7f3320bad5b252cc0727ba9e019ab8 *R/model.R
8ab48098af7628c6d2f155b8f9f24b74 *R/mutations.R
1415cb2b3e892624fb7ea4ff76a2c46f *R/read.R
574485fa2da5de558b74b117512a84a7 *R/read.R
bfe91a98d0c94dab8ae8bcb554eb5acd *R/results.R
f763a946f45e700642201c486263b969 *R/segments.R
0359f75dbcc67975a0a8654cc04e32a3 *R/solutions.R
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2 changes: 1 addition & 1 deletion R/gcstats.R
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Expand Up @@ -22,7 +22,7 @@ gc.sample.stats <- function(file, col_types = "c--dd----d----",
message("Collecting GC information ", appendLF = FALSE)
}
res <- chunk.apply(input = con, FUN = parse_chunck, col_types = col_types,
CH.MAX.SIZE = buffer, parallel = parallel)
CH.MAX.SIZE = buffer, CH.PARALLEL = parallel)
close(con)
if (verbose){
message(" done\n")
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2 changes: 1 addition & 1 deletion R/read.R
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Expand Up @@ -43,7 +43,7 @@ read.seqz.chr <- function(file, chr_name, col_names,
}
res <- chunk.apply(input = con, FUN = parse_chunck, chr_name = chr_name,
col_names = col_names, col_types = col_types, CH.MAX.SIZE = buffer,
parallel = parallel)
CH.PARALLEL = parallel)
close(con)
res
}
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11 changes: 11 additions & 0 deletions README.md
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@@ -0,0 +1,11 @@
Solve the following issues:
<br>
Collecting GC information Error in (function (x, col_types) : unused argument (parallel = 1)
<br>
Calls: main ... preprocess.seqz -> sequenza.extract -> gc.sample.stats -> chunk.apply
<br>
Execution halted

The reason:
<br>
The "chunk.apply" function from R iotools package with new version does not have "parallel" parameter which has been changed to "CH.PARALLEL"