Add fapack and fapacks (lowercase)

.gitignore

@@ -1 +1,3 @@
 fastqz
+fapack
+fapacks

Makefile

@@ -1,4 +1,7 @@
-default: fastqz
+default: fastqz fapack fapacks
 
 fastqz: fastqz15.cpp libzpaq.3.pod libzpaq.cpp libzpaq.h
 	g++ -O3 -msse2 -s -lpthread fastqz15.cpp libzpaq.cpp -o $@
+
+clean:
+	- rm -f fastqz fapack fapacks

fapack.cpp

@@ -0,0 +1,71 @@
+/* fapack.cpp - pack FASTA 4 bases per byte
+
+  Copyright (C) 2012, Matt Mahoney, Dell Inc.
+  All rights reserved.
+
+  Redistribution and use in source and binary forms, with or without
+  modification, are permitted provided that the following conditions are met:
+
+  Redistributions of source code must retain the above copyright notice,
+  this list of conditions and the following disclaimer.
+
+  Redistributions in binary form must reproduce the above copyright notice,
+  this list of conditions and the following disclaimer in the documentation
+  and/or other materials provided with the distribution.
+
+  THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+  AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+  IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+  ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
+  LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+  CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+  SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+  INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+  CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+  ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+  POSSIBILITY OF SUCH DAMAGE.
+
+This program produces packed DNA sequences from FASTA files.
+The output may be used as a reference genome for the program fastqz.
+
+To use: fapack output *.fa
+
+where *.fa is a list of FASTA input files. For each file,
+input lines starting with ">" are ignored. For all other lines,
+the letters A,C,G,T are packed MSB first with A=00,C=01,G=10,T=11.
+All other characters are ignored. The last partial byte is discarded.
+
+To compile: g++ -O3 fapack.cpp -o fapack
+*/
+
+#include <stdio.h>
+#include <stdlib.h>
+
+int main(int argc, char** argv) {
+  if (argc<3)
+    printf("To pack FASTA files: fapack output *.fa\n"), exit(1);
+  FILE *out=fopen(argv[1], "wb");
+  int b=1, c;
+  for (int i=2; i<argc; ++i) {
+    printf("%s\n", argv[i]);
+    FILE *in=fopen(argv[i], "rb");
+    if (!in) continue;
+    bool dna=true;
+    while ((c=getc(in))!=EOF) {
+      if (c=='>') dna=false;
+      else if (c==10) dna=true;
+      if (dna) {
+        if (c=='A') b=b*4;
+        if (c=='C') b=b*4+1;
+        if (c=='G') b=b*4+2;
+        if (c=='T') b=b*4+3;
+        if (b>=256) putc(b&255, out), b=1;
+      }
+    }
+    if (in) fclose(in);
+  }
+  fclose(out);
+  return 0;
+}
+
+

fapacks.cpp

@@ -0,0 +1,65 @@
+/* fapacks.cpp - pack FASTA 4 bases per byte
+   includes lowercase a,c,g,t
+
+  Copyright (C) 2012, Matt Mahoney, Dell Inc.
+  All rights reserved.
+
+  Redistribution and use in source and binary forms, with or without
+  modification, are permitted provided that the following conditions are met:
+
+  Redistributions of source code must retain the above copyright notice,
+  this list of conditions and the following disclaimer.
+
+  Redistributions in binary form must reproduce the above copyright notice,
+  this list of conditions and the following disclaimer in the documentation
+  and/or other materials provided with the distribution.
+
+  THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+  AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+  IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+  ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
+  LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+  CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+  SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+  INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+  CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+  ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+  POSSIBILITY OF SUCH DAMAGE.
+
+This program produces packed DNA sequences from FASTA files.
+The output may be used as a reference genome for the program fastqz.
+*/
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <ctype.h>
+
+int main(int argc, char** argv) {
+  if (argc<3)
+    printf("To pack FASTA files: fapack output *.fa\n"), exit(1);
+  FILE *out=fopen(argv[1], "wb");
+  int b=1, c;
+  for (int i=2; i<argc; ++i) {
+    printf("%s\n", argv[i]);
+    FILE *in=fopen(argv[i], "rb");
+    if (!in) continue;
+    bool dna=true;
+    while ((c=getc(in))!=EOF) {
+      if (c=='>') dna=false;
+      else if (c==10) dna=true;
+      if (islower(c)) c=toupper(c);
+      if (dna) {
+        if (c=='A') b=b*4;
+        if (c=='C') b=b*4+1;
+        if (c=='G') b=b*4+2;
+        if (c=='T') b=b*4+3;
+        if (b>=256) putc(b&255, out), b=1;
+      }
+    }
+    if (in) fclose(in);
+  }
+  fclose(out);
+  return 0;
+}
+
+