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|
#!/bin/sh
#
# Suitable for Version 1996.3 onwards
#
# Script to assemble data into a gap4 database using a file of file
# names. No vector screening is performed.
# Startup gap4 with this script. The backslash here fools tcl into thinking
# the next line is a comment, thus enabling the script to be both bourne shell
# and tcl compatible. \
exec stash "$0" ${@+"$@"} || exit 1
proc open_database {name} {
if {[set dot [string last . $name]] == -1} {
puts "ERROR: Invalid database name '$name'"
return ""
}
set db_name [string range $name 0 [expr $dot-1]]
set version_num [string range $name [expr $dot+1] end]
if {[file exists $name.BUSY]} {
puts "ERROR: Database is busy"
return ""
}
# Make backup if the database already exists.
if {[file exists $name]} {
exec cp $name $db_name.X
exec cp $name.aux $db_name.X.aux
set c 0
} else {
set c 1
}
return [open_db -name $db_name -version $version_num -access rw -create $c]
}
# Set up the gap4 defaults
load_package gap
# Turn off the annoyance bell ringing when writing readings to the fail file
error_bell 0
# Check arguments
if {$argc != 2 && $argc != 3} {
puts "Usage: assemble database.version file_of_filenames {failure_file}"
exit 1
}
set dbname [lindex $argv 0]
set fofn [lindex $argv 1]
if {$argc == 3} {
set fails [lindex $argv 2]
} else {
set fails $fofn.fails
}
# Open the database
if {[set io [open_database $dbname]] == ""} {
puts "ERROR: Couldn't open database '[lindex $argv 0]'"
exit 1
}
# Shotgun assembly
set result [assemble_shotgun \
-io $io \
-files [ListLoad $fofn files] \
-min_match [keylget gap_defs AUTO_ASSEMBLE.MINMATCH.VALUE] \
-max_pads [keylget gap_defs AUTO_ASSEMBLE.MAXPADS.VALUE] \
-max_pmismatch [keylget gap_defs AUTO_ASSEMBLE.MISMATCH.VALUE]]
ListCreate2 fails $result
ListSave $fails fails
# Close the database
close_db -io $io
exit
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