--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ezBAMQC/src/htslib/cram/rANS_static.c	Thu Mar 24 17:12:52 2016 -0400
@@ -0,0 +1,841 @@
+/*
+ * Copyright (c) 2014 Genome Research Ltd.
+ * Author(s): James Bonfield
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ *
+ *    1. Redistributions of source code must retain the above copyright notice,
+ *       this list of conditions and the following disclaimer.
+ *
+ *    2. 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.
+ *
+ *    3. Neither the names Genome Research Ltd and Wellcome Trust Sanger
+ *       Institute nor the names of its contributors may be used to endorse
+ *       or promote products derived from this software without specific
+ *       prior written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD 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 GENOME RESEARCH
+ * LTD 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.
+ */
+
+/*
+ * Author: James Bonfield, Wellcome Trust Sanger Institute. 2014
+ */
+
+#include <stdint.h>
+#include <stdlib.h>
+#include <stdio.h>
+#include <unistd.h>
+#include <assert.h>
+#include <string.h>
+#include <sys/time.h>
+
+#include "cram/rANS_static.h"
+#include "cram/rANS_byte.h"
+
+#define TF_SHIFT 12
+#define TOTFREQ (1<<TF_SHIFT)
+
+#define ABS(a) ((a)>0?(a):-(a))
+#ifndef BLK_SIZE
+#  define BLK_SIZE 1024*1024
+#endif
+
+// Room to allow for expanded BLK_SIZE on worst case compression.
+#define BLK_SIZE2 ((int)(1.05*BLK_SIZE))
+
+/*-----------------------------------------------------------------------------
+ * Memory to memory compression functions.
+ *
+ * These are original versions without any manual loop unrolling. They
+ * are easier to understand, but can be up to 2x slower.
+ */
+
+unsigned char *rans_compress_O0(unsigned char *in, unsigned int in_size,
+				unsigned int *out_size) {
+    unsigned char *out_buf = malloc(1.05*in_size + 257*257*3 + 9);
+    unsigned char *cp, *out_end;
+    RansEncSymbol syms[256];
+    RansState rans0, rans1, rans2, rans3;
+    uint8_t* ptr;
+    int F[256] = {0}, i, j, tab_size, rle, x, fsum = 0;
+    int m = 0, M = 0;
+    uint64_t tr;
+
+    if (!out_buf)
+	return NULL;
+
+    ptr = out_end = out_buf + (int)(1.05*in_size) + 257*257*3 + 9;
+
+    // Compute statistics
+    for (i = 0; i < in_size; i++) {
+	F[in[i]]++;
+    }
+    tr = ((uint64_t)TOTFREQ<<31)/in_size + (1<<30)/in_size;
+
+    // Normalise so T[i] == TOTFREQ
+    for (m = M = j = 0; j < 256; j++) {
+	if (!F[j])
+	    continue;
+
+	if (m < F[j])
+	    m = F[j], M = j;
+
+	if ((F[j] = (F[j]*tr)>>31) == 0)
+	    F[j] = 1;
+	fsum += F[j];
+    }
+
+    fsum++;
+    if (fsum < TOTFREQ)
+	F[M] += TOTFREQ-fsum;
+    else
+	F[M] -= fsum-TOTFREQ;
+
+    //printf("F[%d]=%d\n", M, F[M]);
+    assert(F[M]>0);
+
+    // Encode statistics.
+    cp = out_buf+9;
+
+    for (x = rle = j = 0; j < 256; j++) {
+	if (F[j]) {
+	    // j
+	    if (rle) {
+		rle--;
+	    } else {
+		*cp++ = j;
+		if (!rle && j && F[j-1])  {
+		    for(rle=j+1; rle<256 && F[rle]; rle++)
+			;
+		    rle -= j+1;
+		    *cp++ = rle;
+		}
+		//fprintf(stderr, "%d: %d %d\n", j, rle, N[j]);
+	    }
+
+	    // F[j]
+	    if (F[j]<128) {
+		*cp++ = F[j];
+	    } else {
+		*cp++ = 128 | (F[j]>>8);
+		*cp++ = F[j]&0xff;
+	    }
+	    RansEncSymbolInit(&syms[j], x, F[j], TF_SHIFT);
+	    x += F[j];
+	}
+    }
+    *cp++ = 0;
+
+    //write(1, out_buf+4, cp-(out_buf+4));
+    tab_size = cp-out_buf;
+
+    RansEncInit(&rans0);
+    RansEncInit(&rans1);
+    RansEncInit(&rans2);
+    RansEncInit(&rans3);
+
+    switch (i=(in_size&3)) {
+    case 3: RansEncPutSymbol(&rans2, &ptr, &syms[in[in_size-(i-2)]]);
+    case 2: RansEncPutSymbol(&rans1, &ptr, &syms[in[in_size-(i-1)]]);
+    case 1: RansEncPutSymbol(&rans0, &ptr, &syms[in[in_size-(i-0)]]);
+    case 0:
+	break;
+    }
+    for (i=(in_size &~3); i>0; i-=4) {
+	RansEncSymbol *s3 = &syms[in[i-1]];
+	RansEncSymbol *s2 = &syms[in[i-2]];
+	RansEncSymbol *s1 = &syms[in[i-3]];
+	RansEncSymbol *s0 = &syms[in[i-4]];
+
+	RansEncPutSymbol(&rans3, &ptr, s3);
+	RansEncPutSymbol(&rans2, &ptr, s2);
+	RansEncPutSymbol(&rans1, &ptr, s1);
+	RansEncPutSymbol(&rans0, &ptr, s0);
+    }
+
+    RansEncFlush(&rans3, &ptr);
+    RansEncFlush(&rans2, &ptr);
+    RansEncFlush(&rans1, &ptr);
+    RansEncFlush(&rans0, &ptr);
+
+    // Finalise block size and return it
+    *out_size = (out_end - ptr) + tab_size;
+
+    cp = out_buf;
+
+    *cp++ = 0; // order
+    *cp++ = ((*out_size-9)>> 0) & 0xff;
+    *cp++ = ((*out_size-9)>> 8) & 0xff;
+    *cp++ = ((*out_size-9)>>16) & 0xff;
+    *cp++ = ((*out_size-9)>>24) & 0xff;
+
+    *cp++ = (in_size>> 0) & 0xff;
+    *cp++ = (in_size>> 8) & 0xff;
+    *cp++ = (in_size>>16) & 0xff;
+    *cp++ = (in_size>>24) & 0xff;
+
+    memmove(out_buf + tab_size, ptr, out_end-ptr);
+
+    return out_buf;
+}
+
+typedef struct {
+    struct {
+	int F;
+	int C;
+    } fc[256];
+    unsigned char *R;
+} ari_decoder;
+
+unsigned char *rans_uncompress_O0(unsigned char *in, unsigned int in_size,
+				  unsigned int *out_size) {
+    /* Load in the static tables */
+    unsigned char *cp = in + 9;
+    int i, j, x, out_sz, in_sz, rle;
+    char *out_buf;
+    ari_decoder D;
+    RansDecSymbol syms[256];
+
+    memset(&D, 0, sizeof(D));
+
+    if (*in++ != 0) // Order-0 check
+	return NULL;
+    
+    in_sz  = ((in[0])<<0) | ((in[1])<<8) | ((in[2])<<16) | ((in[3])<<24);
+    out_sz = ((in[4])<<0) | ((in[5])<<8) | ((in[6])<<16) | ((in[7])<<24);
+    if (in_sz != in_size-9)
+	return NULL;
+
+    out_buf = malloc(out_sz);
+    if (!out_buf)
+	return NULL;
+
+    //fprintf(stderr, "out_sz=%d\n", out_sz);
+
+    // Precompute reverse lookup of frequency.
+    rle = x = 0;
+    j = *cp++;
+    do {
+	if ((D.fc[j].F = *cp++) >= 128) {
+	    D.fc[j].F &= ~128;
+	    D.fc[j].F = ((D.fc[j].F & 127) << 8) | *cp++;
+	}
+	D.fc[j].C = x;
+
+	RansDecSymbolInit(&syms[j], D.fc[j].C, D.fc[j].F);
+
+	/* Build reverse lookup table */
+	if (!D.R) D.R = (unsigned char *)malloc(TOTFREQ);
+	memset(&D.R[x], j, D.fc[j].F);
+
+	x += D.fc[j].F;
+
+	if (!rle && j+1 == *cp) {
+	    j = *cp++;
+	    rle = *cp++;
+	} else if (rle) {
+	    rle--;
+	    j++;
+	} else {
+	    j = *cp++;
+	}
+    } while(j);
+
+    assert(x < TOTFREQ);
+
+    RansState rans0, rans1, rans2, rans3;
+    uint8_t *ptr = cp;
+    RansDecInit(&rans0, &ptr);
+    RansDecInit(&rans1, &ptr);
+    RansDecInit(&rans2, &ptr);
+    RansDecInit(&rans3, &ptr);
+
+    int out_end = (out_sz&~3);
+
+    RansState R[4];
+    R[0] = rans0;
+    R[1] = rans1;
+    R[2] = rans2;
+    R[3] = rans3;
+    uint32_t mask = (1u << TF_SHIFT)-1;
+
+    for (i=0; i < out_end; i+=4) {
+	uint32_t m[4] = {R[0] & mask,
+			 R[1] & mask,
+			 R[2] & mask,
+			 R[3] & mask};
+	uint8_t c[4] = {D.R[m[0]],
+			D.R[m[1]],
+			D.R[m[2]],
+			D.R[m[3]]};
+	out_buf[i+0] = c[0];
+	out_buf[i+1] = c[1];
+	out_buf[i+2] = c[2];
+	out_buf[i+3] = c[3];
+
+	// RansDecAdvanceSymbolStep(&R[0], &syms[c[0]], TF_SHIFT);
+	// RansDecAdvanceSymbolStep(&R[1], &syms[c[1]], TF_SHIFT);
+	// RansDecAdvanceSymbolStep(&R[2], &syms[c[2]], TF_SHIFT);
+	// RansDecAdvanceSymbolStep(&R[3], &syms[c[3]], TF_SHIFT);
+	R[0] = syms[c[0]].freq * (R[0]>>TF_SHIFT);
+	R[1] = syms[c[1]].freq * (R[1]>>TF_SHIFT);
+	R[2] = syms[c[2]].freq * (R[2]>>TF_SHIFT);
+	R[3] = syms[c[3]].freq * (R[3]>>TF_SHIFT);
+
+	R[0] += m[0] - syms[c[0]].start;
+	R[1] += m[1] - syms[c[1]].start;
+	R[2] += m[2] - syms[c[2]].start;
+	R[3] += m[3] - syms[c[3]].start;
+
+	RansDecRenorm(&R[0], &ptr);
+	RansDecRenorm(&R[1], &ptr);
+	RansDecRenorm(&R[2], &ptr);
+	RansDecRenorm(&R[3], &ptr);
+    }
+
+    rans0 = R[0];
+    rans1 = R[1];
+    rans2 = R[2];
+    rans3 = R[3];
+
+    switch(out_sz&3) {
+	unsigned char c;
+    case 0:
+	break;
+    case 1:
+	c = D.R[RansDecGet(&rans0, TF_SHIFT)];
+	RansDecAdvanceSymbol(&rans0, &ptr, &syms[c], TF_SHIFT);
+	out_buf[out_end] = c;
+	break;
+
+    case 2:
+	c = D.R[RansDecGet(&rans0, TF_SHIFT)];
+	RansDecAdvanceSymbol(&rans0, &ptr, &syms[c], TF_SHIFT);
+	out_buf[out_end] = c;
+
+	c = D.R[RansDecGet(&rans1, TF_SHIFT)];
+	RansDecAdvanceSymbol(&rans1, &ptr, &syms[c], TF_SHIFT);
+	out_buf[out_end+1] = c;
+	break;
+
+    case 3:
+	c = D.R[RansDecGet(&rans0, TF_SHIFT)];
+	RansDecAdvanceSymbol(&rans0, &ptr, &syms[c], TF_SHIFT);
+	out_buf[out_end] = c;
+
+	c = D.R[RansDecGet(&rans1, TF_SHIFT)];
+	RansDecAdvanceSymbol(&rans1, &ptr, &syms[c], TF_SHIFT);
+	out_buf[out_end+1] = c;
+
+	c = D.R[RansDecGet(&rans2, TF_SHIFT)];
+	RansDecAdvanceSymbol(&rans2, &ptr, &syms[c], TF_SHIFT);
+	out_buf[out_end+2] = c;
+	break;
+    }
+
+    *out_size = out_sz;
+
+    if (D.R) free(D.R);
+
+    return (unsigned char *)out_buf;
+}
+
+unsigned char *rans_compress_O1(unsigned char *in, unsigned int in_size,
+				unsigned int *out_size) {
+    unsigned char *out_buf, *out_end, *cp;
+    unsigned int last_i, tab_size, rle_i, rle_j;
+    RansEncSymbol syms[256][256];
+
+    if (in_size < 4)
+	return rans_compress_O0(in, in_size, out_size);
+
+    out_buf = malloc(1.05*in_size + 257*257*3 + 9);
+    if (!out_buf)
+	return NULL;
+
+    out_end = out_buf + (int)(1.05*in_size) + 257*257*3 + 9;
+    cp = out_buf+9;
+
+    int F[256][256], T[256], i, j;
+    unsigned char c;
+
+    memset(F, 0, 256*256*sizeof(int));
+    memset(T, 0, 256*sizeof(int));
+    //for (last = 0, i=in_size-1; i>=0; i--) {
+    //	F[last][c = in[i]]++;
+    //	T[last]++;
+    //	last = c;
+    //}
+
+    for (last_i=i=0; i<in_size; i++) {
+	F[last_i][c = in[i]]++;
+	T[last_i]++;
+	last_i = c;
+    }
+    F[0][in[1*(in_size>>2)]]++;
+    F[0][in[2*(in_size>>2)]]++;
+    F[0][in[3*(in_size>>2)]]++;
+    T[0]+=3;
+
+    // Normalise so T[i] == TOTFREQ
+    for (rle_i = i = 0; i < 256; i++) {
+	int t2, m, M;
+	unsigned int x;
+
+	if (T[i] == 0)
+	    continue;
+
+	//uint64_t p = (TOTFREQ * TOTFREQ) / t;
+	double p = ((double)TOTFREQ)/T[i];
+	for (t2 = m = M = j = 0; j < 256; j++) {
+	    if (!F[i][j])
+		continue;
+
+	    if (m < F[i][j])
+		m = F[i][j], M = j;
+
+	    //if ((F[i][j] = (F[i][j] * p) / TOTFREQ) == 0)
+	    if ((F[i][j] *= p) == 0)
+		F[i][j] = 1;
+	    t2 += F[i][j];
+	}
+
+	t2++;
+	if (t2 < TOTFREQ)
+	    F[i][M] += TOTFREQ-t2;
+	else
+	    F[i][M] -= t2-TOTFREQ;
+
+	// Store frequency table
+	// i
+	if (rle_i) {
+	    rle_i--;
+	} else {
+	    *cp++ = i;
+	    // FIXME: could use order-0 statistics to observe which alphabet
+	    // symbols are present and base RLE on that ordering instead.
+	    if (i && T[i-1]) {
+		for(rle_i=i+1; rle_i<256 && T[rle_i]; rle_i++)
+		    ;
+		rle_i -= i+1;
+		*cp++ = rle_i;
+	    }
+	}
+
+	int *F_i_ = F[i];
+	x = 0;
+	rle_j = 0;
+	for (j = 0; j < 256; j++) {
+	    if (F_i_[j]) {
+		//fprintf(stderr, "F[%d][%d]=%d, x=%d\n", i, j, F_i_[j], x);
+
+		// j
+		if (rle_j) {
+		    rle_j--;
+		} else {
+		    *cp++ = j;
+		    if (!rle_j && j && F_i_[j-1]) {
+			for(rle_j=j+1; rle_j<256 && F_i_[rle_j]; rle_j++)
+			    ;
+			rle_j -= j+1;
+			*cp++ = rle_j;
+		    }
+		}
+
+		// F_i_[j]
+		if (F_i_[j]<128) {
+		    *cp++ = F_i_[j];
+		} else {
+		    *cp++ = 128 | (F_i_[j]>>8);
+		    *cp++ = F_i_[j]&0xff;
+		}
+
+		RansEncSymbolInit(&syms[i][j], x, F_i_[j], TF_SHIFT);
+		x += F_i_[j];
+	    }
+	}
+	*cp++ = 0;
+    }
+    *cp++ = 0;
+
+    //write(1, out_buf+4, cp-(out_buf+4));
+    tab_size = cp - out_buf;
+    assert(tab_size < 257*257*3);
+
+    RansState rans0, rans1, rans2, rans3;
+    RansEncInit(&rans0);
+    RansEncInit(&rans1);
+    RansEncInit(&rans2);
+    RansEncInit(&rans3);
+
+    uint8_t* ptr = out_end;
+
+    int isz4 = in_size>>2;
+    int i0 = 1*isz4-2;
+    int i1 = 2*isz4-2;
+    int i2 = 3*isz4-2;
+    int i3 = 4*isz4-2;
+
+    unsigned char l0 = in[i0+1];
+    unsigned char l1 = in[i1+1];
+    unsigned char l2 = in[i2+1];
+    unsigned char l3 = in[i3+1];
+
+    // Deal with the remainder
+    l3 = in[in_size-1];
+    for (i3 = in_size-2; i3 > 4*isz4-2; i3--) {
+	unsigned char c3 = in[i3];
+	RansEncPutSymbol(&rans3, &ptr, &syms[c3][l3]);
+	l3 = c3;
+    }
+
+    for (; i0 >= 0; i0--, i1--, i2--, i3--) {
+	unsigned char c0, c1, c2, c3;
+	RansEncSymbol *s3 = &syms[c3 = in[i3]][l3];
+	RansEncSymbol *s2 = &syms[c2 = in[i2]][l2];
+	RansEncSymbol *s1 = &syms[c1 = in[i1]][l1];
+	RansEncSymbol *s0 = &syms[c0 = in[i0]][l0];
+
+	RansEncPutSymbol(&rans3, &ptr, s3);
+	RansEncPutSymbol(&rans2, &ptr, s2);
+	RansEncPutSymbol(&rans1, &ptr, s1);
+	RansEncPutSymbol(&rans0, &ptr, s0);
+
+	l0 = c0;
+	l1 = c1;
+	l2 = c2;
+	l3 = c3;
+    }
+
+    RansEncPutSymbol(&rans3, &ptr, &syms[0][l3]);
+    RansEncPutSymbol(&rans2, &ptr, &syms[0][l2]);
+    RansEncPutSymbol(&rans1, &ptr, &syms[0][l1]);
+    RansEncPutSymbol(&rans0, &ptr, &syms[0][l0]);
+
+    RansEncFlush(&rans3, &ptr);
+    RansEncFlush(&rans2, &ptr);
+    RansEncFlush(&rans1, &ptr);
+    RansEncFlush(&rans0, &ptr);
+
+    *out_size = (out_end - ptr) + tab_size;
+
+    cp = out_buf;
+    *cp++ = 1; // order
+
+    *cp++ = ((*out_size-9)>> 0) & 0xff;
+    *cp++ = ((*out_size-9)>> 8) & 0xff;
+    *cp++ = ((*out_size-9)>>16) & 0xff;
+    *cp++ = ((*out_size-9)>>24) & 0xff;
+
+    *cp++ = (in_size>> 0) & 0xff;
+    *cp++ = (in_size>> 8) & 0xff;
+    *cp++ = (in_size>>16) & 0xff;
+    *cp++ = (in_size>>24) & 0xff;
+
+    memmove(out_buf + tab_size, ptr, out_end-ptr);
+
+    return out_buf;
+}
+
+unsigned char *rans_uncompress_O1(unsigned char *in, unsigned int in_size,
+				  unsigned int *out_size) {
+    /* Load in the static tables */
+    unsigned char *cp = in + 9;
+    int i, j = -999, x, out_sz, in_sz, rle_i, rle_j;
+    char *out_buf;
+    ari_decoder D[256];
+    RansDecSymbol syms[256][256];
+
+    memset(D, 0, 256*sizeof(*D));
+
+    if (*in++ != 1) // Order-1 check
+	return NULL;
+
+    in_sz  = ((in[0])<<0) | ((in[1])<<8) | ((in[2])<<16) | ((in[3])<<24);
+    out_sz = ((in[4])<<0) | ((in[5])<<8) | ((in[6])<<16) | ((in[7])<<24);
+    if (in_sz != in_size-9)
+	return NULL;
+
+    out_buf = malloc(out_sz);
+    if (!out_buf)
+	return NULL;
+
+    //fprintf(stderr, "out_sz=%d\n", out_sz);
+
+    //i = *cp++;
+    rle_i = 0;
+    i = *cp++;
+    do {
+	rle_j = x = 0;
+	j = *cp++;
+	do {
+	    if ((D[i].fc[j].F = *cp++) >= 128) {
+		D[i].fc[j].F &= ~128;
+		D[i].fc[j].F = ((D[i].fc[j].F & 127) << 8) | *cp++;
+	    }
+	    D[i].fc[j].C = x;
+
+	    //fprintf(stderr, "i=%d j=%d F=%d C=%d\n", i, j, D[i].fc[j].F, D[i].fc[j].C);
+
+	    if (!D[i].fc[j].F)
+		D[i].fc[j].F = TOTFREQ;
+
+	    RansDecSymbolInit(&syms[i][j], D[i].fc[j].C, D[i].fc[j].F);
+
+	    /* Build reverse lookup table */
+	    if (!D[i].R) D[i].R = (unsigned char *)malloc(TOTFREQ);
+	    memset(&D[i].R[x], j, D[i].fc[j].F);
+
+	    x += D[i].fc[j].F;
+	    assert(x <= TOTFREQ);
+
+	    if (!rle_j && j+1 == *cp) {
+		j = *cp++;
+		rle_j = *cp++;
+	    } else if (rle_j) {
+		rle_j--;
+		j++;
+	    } else {
+		j = *cp++;
+	    }
+	} while(j);
+
+	if (!rle_i && i+1 == *cp) {
+	    i = *cp++;
+	    rle_i = *cp++;
+	} else if (rle_i) {
+	    rle_i--;
+	    i++;
+	} else {
+	    i = *cp++;
+	}
+    } while (i);
+
+    // Precompute reverse lookup of frequency.
+
+    RansState rans0, rans1, rans2, rans3;
+    uint8_t *ptr = cp;
+    RansDecInit(&rans0, &ptr);
+    RansDecInit(&rans1, &ptr);
+    RansDecInit(&rans2, &ptr);
+    RansDecInit(&rans3, &ptr);
+
+    int isz4 = out_sz>>2;
+    int l0 = 0;
+    int l1 = 0;
+    int l2 = 0;
+    int l3 = 0;
+    int i4[] = {0*isz4, 1*isz4, 2*isz4, 3*isz4};
+
+    RansState R[4];
+    R[0] = rans0;
+    R[1] = rans1;
+    R[2] = rans2;
+    R[3] = rans3;
+
+    for (; i4[0] < isz4; i4[0]++, i4[1]++, i4[2]++, i4[3]++) {
+	uint32_t m[4] = {R[0] & ((1u << TF_SHIFT)-1),
+			 R[1] & ((1u << TF_SHIFT)-1),
+			 R[2] & ((1u << TF_SHIFT)-1),
+			 R[3] & ((1u << TF_SHIFT)-1)};
+
+	uint8_t c[4] = {D[l0].R[m[0]],
+			D[l1].R[m[1]],
+			D[l2].R[m[2]],
+			D[l3].R[m[3]]};
+
+	out_buf[i4[0]] = c[0];
+	out_buf[i4[1]] = c[1];
+	out_buf[i4[2]] = c[2];
+	out_buf[i4[3]] = c[3];
+
+	//RansDecAdvanceSymbolStep(&R[0], &syms[l0][c[0]], TF_SHIFT);
+	//RansDecAdvanceSymbolStep(&R[1], &syms[l1][c[1]], TF_SHIFT);
+	//RansDecAdvanceSymbolStep(&R[2], &syms[l2][c[2]], TF_SHIFT);
+	//RansDecAdvanceSymbolStep(&R[3], &syms[l3][c[3]], TF_SHIFT);
+
+	R[0] = syms[l0][c[0]].freq * (R[0]>>TF_SHIFT);
+	R[1] = syms[l1][c[1]].freq * (R[1]>>TF_SHIFT);
+	R[2] = syms[l2][c[2]].freq * (R[2]>>TF_SHIFT);
+	R[3] = syms[l3][c[3]].freq * (R[3]>>TF_SHIFT);
+
+	R[0] += m[0] - syms[l0][c[0]].start;
+	R[1] += m[1] - syms[l1][c[1]].start;
+	R[2] += m[2] - syms[l2][c[2]].start;
+	R[3] += m[3] - syms[l3][c[3]].start;
+
+	RansDecRenorm(&R[0], &ptr);
+	RansDecRenorm(&R[1], &ptr);
+	RansDecRenorm(&R[2], &ptr);
+	RansDecRenorm(&R[3], &ptr);
+
+	l0 = c[0];
+	l1 = c[1];
+	l2 = c[2];
+	l3 = c[3];
+    }
+
+    rans0 = R[0];
+    rans1 = R[1];
+    rans2 = R[2];
+    rans3 = R[3];
+
+    // Remainder
+    for (; i4[3] < out_sz; i4[3]++) {
+	unsigned char c3 = D[l3].R[RansDecGet(&rans3, TF_SHIFT)];
+	out_buf[i4[3]] = c3;
+	RansDecAdvanceSymbol(&rans3, &ptr, &syms[l3][c3], TF_SHIFT);
+	l3 = c3;
+    }
+
+    *out_size = out_sz;
+
+    for (i = 0; i < 256; i++)
+	if (D[i].R) free(D[i].R);
+
+    return (unsigned char *)out_buf;
+}
+
+/*-----------------------------------------------------------------------------
+ * Simple interface to the order-0 vs order-1 encoders and decoders.
+ */
+unsigned char *rans_compress(unsigned char *in, unsigned int in_size,
+			     unsigned int *out_size, int order) {
+    return order
+	? rans_compress_O1(in, in_size, out_size)
+	: rans_compress_O0(in, in_size, out_size);
+}
+
+unsigned char *rans_uncompress(unsigned char *in, unsigned int in_size,
+			       unsigned int *out_size) {
+    return in[0]
+	? rans_uncompress_O1(in, in_size, out_size)
+	: rans_uncompress_O0(in, in_size, out_size);
+}
+
+
+#ifdef TEST_MAIN
+/*-----------------------------------------------------------------------------
+ * Main.
+ *
+ * This is a simple command line tool for testing order-0 and order-1
+ * compression using the rANS codec. Simply compile with
+ *
+ * gcc -DTEST_MAIN -O3 -I. cram/rANS_static.c -o cram/rANS_static
+ *
+ * Usage: cram/rANS_static -o0 < file    > file.o0
+ *        cram/rANS_static -d  < file.o0 > file2
+ *
+ *        cram/rANS_static -o1 < file    > file.o1
+ *        cram/rANS_static -d  < file.o1 > file2
+ */
+int main(int argc, char **argv) {
+    int opt, order = 0;
+    unsigned char in_buf[BLK_SIZE2+257*257*3];
+    int decode = 0;
+    FILE *infp = stdin, *outfp = stdout;
+    struct timeval tv1, tv2;
+    size_t bytes = 0;
+
+    extern char *optarg;
+    extern int optind;
+
+    while ((opt = getopt(argc, argv, "o:d")) != -1) {
+	switch (opt) {
+	case 'o':
+	    order = atoi(optarg);
+	    break;
+
+	case 'd':
+	    decode = 1;
+	    break;
+	}
+    }
+
+    order = order ? 1 : 0; // Only support O(0) and O(1)
+
+    if (optind < argc) {
+	if (!(infp = fopen(argv[optind], "rb"))) {
+	    perror(argv[optind]);
+	    return 1;
+	}
+	optind++;
+    }
+
+    if (optind < argc) {
+	if (!(outfp = fopen(argv[optind], "wb"))) {
+	    perror(argv[optind]);
+	    return 1;
+	}
+	optind++;
+    }
+
+    gettimeofday(&tv1, NULL);
+
+    if (decode) {
+	// Only used in some test implementations of RC_GetFreq()
+	//RC_init();
+	//RC_init2();
+
+	for (;;) {
+	    uint32_t in_size, out_size;
+	    unsigned char *out;
+
+	    if (4 != fread(&in_size, 1, 4, infp))
+		break;
+	    if (in_size != fread(in_buf, 1, in_size, infp)) {
+		fprintf(stderr, "Truncated input\n");
+		exit(1);
+	    }
+	    out = rans_uncompress(in_buf, in_size, &out_size);
+	    if (!out)
+		abort();
+
+	    fwrite(out, 1, out_size, outfp);
+	    free(out);
+
+	    bytes += out_size;
+	}
+    } else {
+	for (;;) {
+	    uint32_t in_size, out_size;
+	    unsigned char *out;
+
+	    in_size = fread(in_buf, 1, BLK_SIZE, infp);
+	    if (in_size <= 0)
+		break;
+
+	    out = rans_compress(in_buf, in_size, &out_size, order);
+
+	    fwrite(&out_size, 1, 4, outfp);
+	    fwrite(out, 1, out_size, outfp);
+	    free(out);
+
+	    bytes += in_size;
+	}
+    }
+
+    gettimeofday(&tv2, NULL);
+
+    fprintf(stderr, "Took %ld microseconds, %5.1f MB/s\n",
+	    (long)(tv2.tv_sec - tv1.tv_sec)*1000000 +
+	    tv2.tv_usec - tv1.tv_usec,
+	    (double)bytes / ((long)(tv2.tv_sec - tv1.tv_sec)*1000000 +
+			     tv2.tv_usec - tv1.tv_usec));
+    return 0;
+}
+#endif