(OK) v0.4.4: add temp folder name selection (-t)

README.md

@@ -57,7 +57,7 @@ unzip mt1x.zip
 /usr/bin/wmsa -i mt1x.fasta -o mt1x.wmsa.fasta -T 16 -c 0.9
 ```
 
-The arugments in last line means the input file ( `-i` ) is  `mt1x.fasta `, the output file ( `-o` ) is  `mt1x.wmsa.fasta `, use `16 `threads (` -T` ) and the similarity of cd-hit (` -c` ) in  `wmsa `is `0.9`.
+The arugments in last line means the input file ( `-i` ) is `mt1x.fasta`, the output file ( `-o` ) is `mt1x.wmsa.fasta`, use `16` threads ( `-T` ) and the similarity of cd-hit ( `-c` ) in  `wmsa `is `0.9`.
 
 For dataset from www.drive5.com/bench, see [here](https://github.com/malabz/WMSA-dataset/blob/main/benchmark/README.md) for testing in `wmsa` .
 

constants.c

@@ -23,7 +23,8 @@ char centerfile[maxf];
 char cmdstr[maxf], cmdstr2[maxf], cmdstr3[maxf];
 
 // tmp directory
-char tmpdir[maxf] = "./swap/";
+char tmpdir[maxf] = "./swap/", *readtmpdir;
+int tmpinthisdir;
 
 char orderprotein[20] = {'A', 'R', 'N', 'D', 'C', 'Q', 'E', 'G', 'H', 'I', 'L', 'K', 'M', 'F', 'P', 'S', 'T', 'W', 'Y', 'V'};
 int BLOSUM62[20][20] = {

msa.h

@@ -33,7 +33,8 @@ extern char centerfile[];
 extern char cmdstr[], cmdstr2[], cmdstr3[];
 
 // tmp directory
-extern char tmpdir[]; 
+extern char tmpdir[], *readtmpdir;
+extern int tmpinthisdir;
 
 extern char orderprotein[], orderDNA[];
 extern int BLOSUM62[20][20], trans[4][4];

msa_main.c

@@ -7,7 +7,7 @@
 #if REPORTCOSTS
 #include <time.h>
 #endif
-#define VERSION "0.4.3"
+#define VERSION "0.4.4"
 #define SHOWVERSION reporterr( "%s (%s, %d-bit) Version " VERSION "\n\n", "MSA align", (seq_type == 1) ? "nuc" : ((seq_type == 0) ? "unknown" : "aa"), sizeof(int *) * 8 )
 // #define FILESAVE
 #define MIN(X, Y) ((X) > (Y) ? (Y) : (X))
@@ -31,6 +31,7 @@ void print_help_message()
     reporterr("-d: print debug info on profilealign, staralign and cd-hit*\n");
     reporterr("-s: do not simply check the result is ok\n");
     reporterr("-v: only print version\n");
+    reporterr("-t: temp folder name\n");
     reporterr("== MAFFT common arguments ==\n");
     reporterr("-V, -f, -S: ppenalty_dist, penalty, nmax_shift\n");
     reporterr("-z, -w: fftthreshold, fftWinsize\n");
@@ -78,6 +79,7 @@ void arguments(int argc, char *argv[])
     BLOSUM = 62;
     simplycheck = 1;
     profilealignthread = NOTKNOWNINT;
+    tmpinthisdir = 0;
     while(--argc > 0 && (*++ argv)[0] == '-' )
 	{
         while ( (c = *++ argv[0]) )
@@ -93,6 +95,10 @@ void arguments(int argc, char *argv[])
                     outputfile = *++ argv;
                     -- argc;
                     goto nextoption;
+                case 't':
+                    readtmpdir = *++ argv;
+                    -- argc;
+                    goto nextoption;
                 // Sequence type
                 case 'P':
                     seq_type = 2;
@@ -231,6 +237,11 @@ int main(int argc, char **argv)
     programfolder = get_exe_path(programfolder, PATH_MAX + 100);
     if(printdebug) puts(programfolder);
     // now the value programfolder is the right value, and the last place of the folder name is not '/'.
+    if(readtmpdir != NULL)
+    {
+        if(tmpinthisdir) sprintf(tmpdir, "./%s/", readtmpdir);
+        else sprintf(tmpdir, "%s/", readtmpdir);
+    }
     if(maketmpfolder())
     {
         reporterr("Warning: cannot make folder %s\n", tmpdir);