annotate ezBAMQC/src/htslib/cram/cram_stats.c @ 17:161866cee2a2

wrapper rename

/*
Copyright (c) 2012-2013 Genome Research Ltd.
Author: James Bonfield <[e-mail]>

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.
*/

#ifdef HAVE_CONFIG_H
#include "io_lib_config.h"
#endif

#include <stdio.h>
#include <errno.h>
#include <assert.h>
#include <stdlib.h>
#include <string.h>
#include <zlib.h>
#include <sys/types.h>
#include <sys/stat.h>
#include <math.h>
#include <ctype.h>

#include "cram/cram.h"
#include "cram/os.h"

cram_stats *cram_stats_create(void) {
    return calloc(1, sizeof(cram_stats));
}

void cram_stats_add(cram_stats *st, int32_t val) {
    st->nsamp++;

    //assert(val >= 0);

    if (val < MAX_STAT_VAL && val >= 0) {
	st->freqs[val]++;
    } else {
	khint_t k;
	int r;

	if (!st->h) {
	    st->h = kh_init(m_i2i);
	}

	k = kh_put(m_i2i, st->h, val, &r);
	if (r == 0)
	    kh_val(st->h, k)++;
	else if (r != -1)
	    kh_val(st->h, k) = 1;
	else
	    ; // FIXME: handle error
    }
}

void cram_stats_del(cram_stats *st, int32_t val) {
    st->nsamp--;

    //assert(val >= 0);

    if (val < MAX_STAT_VAL && val >= 0) {
	st->freqs[val]--;
	assert(st->freqs[val] >= 0);
    } else if (st->h) {
	khint_t k = kh_get(m_i2i, st->h, val);

	if (k != kh_end(st->h)) {
	    if (--kh_val(st->h, k) == 0)
		kh_del(m_i2i, st->h, k);
	} else {
	    fprintf(stderr, "Failed to remove val %d from cram_stats\n", val);
	    st->nsamp++;
	}
    } else {
	fprintf(stderr, "Failed to remove val %d from cram_stats\n", val);
	st->nsamp++;
    }
}

void cram_stats_dump(cram_stats *st) {
    int i;
    fprintf(stderr, "cram_stats:\n");
    for (i = 0; i < MAX_STAT_VAL; i++) {
	if (!st->freqs[i])
	    continue;
	fprintf(stderr, "\t%d\t%d\n", i, st->freqs[i]);
    }
    if (st->h) {
	khint_t k;
	for (k = kh_begin(st->h); k != kh_end(st->h); k++) {
	    if (!kh_exist(st->h, k))
		continue;

	    fprintf(stderr, "\t%d\t%d\n", kh_key(st->h, k), kh_val(st->h, k));
	}
    }
}

#if 1
/* Returns the number of bits set in val; it the highest bit used */
static int nbits(int v) {
    static const int MultiplyDeBruijnBitPosition[32] = {
	1, 10, 2, 11, 14, 22, 3, 30, 12, 15, 17, 19, 23, 26, 4, 31,
	9, 13, 21, 29, 16, 18, 25, 8, 20, 28, 24, 7, 27, 6, 5, 32
    };

    v |= v >> 1; // first up to set all bits 1 after the first 1 */
    v |= v >> 2;
    v |= v >> 4;
    v |= v >> 8;
    v |= v >> 16;

    // DeBruijn magic to find top bit
    return MultiplyDeBruijnBitPosition[(uint32_t)(v * 0x07C4ACDDU) >> 27];
}
#endif

/*
 * Computes entropy from integer frequencies for various encoding methods and
 * picks the best encoding.
 *
 * FIXME: we could reuse some of the code here for the actual encoding
 * parameters too. Eg the best 'k' for SUBEXP or the code lengths for huffman.
 *
 * Returns the best codec to use.
 */
enum cram_encoding cram_stats_encoding(cram_fd *fd, cram_stats *st) {
    enum cram_encoding best_encoding = E_NULL;
    int best_size = INT_MAX, bits;
    int nvals, i, ntot = 0, max_val = 0, min_val = INT_MAX, k;
    int *vals = NULL, *freqs = NULL, vals_alloc = 0, *codes;

    //cram_stats_dump(st);

    /* Count number of unique symbols */
    for (nvals = i = 0; i < MAX_STAT_VAL; i++) {
	if (!st->freqs[i])
	    continue;
	if (nvals >= vals_alloc) {
	    vals_alloc = vals_alloc ? vals_alloc*2 : 1024;
	    vals  = realloc(vals,  vals_alloc * sizeof(int));
	    freqs = realloc(freqs, vals_alloc * sizeof(int));
	    if (!vals || !freqs) {
		if (vals)  free(vals);
		if (freqs) free(freqs);
		return E_HUFFMAN; // Cannot do much else atm
	    }
	}
	vals[nvals] = i;
	freqs[nvals] = st->freqs[i];
	ntot += freqs[nvals];
	if (max_val < i) max_val = i;
	if (min_val > i) min_val = i;
	nvals++;
    }
    if (st->h) {
	khint_t k;
	int i;

	for (k = kh_begin(st->h); k != kh_end(st->h); k++) {
	    if (!kh_exist(st->h, k))
		continue;

	    if (nvals >= vals_alloc) {
		vals_alloc = vals_alloc ? vals_alloc*2 : 1024;
		vals  = realloc(vals,  vals_alloc * sizeof(int));
		freqs = realloc(freqs, vals_alloc * sizeof(int));
		if (!vals || !freqs)
		    return E_HUFFMAN; // Cannot do much else atm
	    }
	    i = kh_key(st->h, k);
	    vals[nvals]=i;
	    freqs[nvals] = kh_val(st->h, k);
	    ntot += freqs[nvals];
	    if (max_val < i) max_val = i;
	    if (min_val > i) min_val = i;
	    nvals++;
	}
    }

    st->nvals = nvals;
    assert(ntot == st->nsamp);

    if (nvals <= 1) {
	free(vals);
	free(freqs);
	return E_HUFFMAN;
    }

    if (fd->verbose > 1)
	fprintf(stderr, "Range = %d..%d, nvals=%d, ntot=%d\n",
		min_val, max_val, nvals, ntot);

    /* Theoretical entropy */
//    if (fd->verbose > 1) {
//	double dbits = 0;
//	for (i = 0; i < nvals; i++) {
//	    dbits += freqs[i] * log((double)freqs[i]/ntot);
//	}
//	dbits /= -log(2);
//	if (fd->verbose > 1)
//	    fprintf(stderr, "Entropy = %f\n", dbits);
//    }

    if (nvals > 1 && ntot > 256) {
#if 0
	/*
	 * CRUDE huffman estimator. Round to closest and round up from 0
	 * to 1 bit.
	 *
	 * With and without ITF8 incase we have a few discrete values but with
	 * large magnitude.
	 *
	 * Note rans0/arith0 and Z_HUFFMAN_ONLY vs internal huffman can be
	 * compared in this way, but order-1 (eg rans1) or maybe LZ77 modes
	 * may detect the correlation of high bytes to low bytes in multi-
	 * byte values. So this predictor breaks down.
	 */
	double dbits = 0;  // entropy + ~huffman
	double dbitsH = 0;
	double dbitsE = 0; // external entropy + ~huffman
	double dbitsEH = 0;
	int F[256] = {0}, n = 0;
	double e = 0; // accumulated error bits
	for (i = 0; i < nvals; i++) {
	    double x; int X;
	    unsigned int v = vals[i];

	    //Better encoding would cope with sign.
	    //v = ABS(vals[i])*2+(vals[i]<0);

	    if (!(v & ~0x7f)) {
		F[v]             += freqs[i], n+=freqs[i];
	    } else if (!(v & ~0x3fff)) {
		F[(v>>8) |0x80] += freqs[i];
		F[ v     &0xff] += freqs[i], n+=2*freqs[i];
	    } else if (!(v & ~0x1fffff)) {
		F[(v>>16)|0xc0] += freqs[i];
		F[(v>>8 )&0xff] += freqs[i];
		F[ v     &0xff] += freqs[i], n+=3*freqs[i];
	    } else if (!(v & ~0x0fffffff)) {
		F[(v>>24)|0xe0] += freqs[i];
		F[(v>>16)&0xff] += freqs[i];
		F[(v>>8 )&0xff] += freqs[i];
		F[ v     &0xff] += freqs[i], n+=4*freqs[i];
	    } else {
		F[(v>>28)|0xf0] += freqs[i];
		F[(v>>20)&0xff] += freqs[i];
		F[(v>>12)&0xff] += freqs[i];
		F[(v>>4 )&0xff] += freqs[i];
		F[ v     &0x0f] += freqs[i], n+=5*freqs[i];
	    }

	    x = -log((double)freqs[i]/ntot)/.69314718055994530941;
	    X = x+0.5;
	    if ((int)(x+((double)e/freqs[i])+.5)>X) {
		X++;
	    } else if ((int)(x+((double)e/freqs[i])+.5)<X) {
		X--;
	    }
	    e-=freqs[i]*(X-x);
	    X += (X==0);

	    //fprintf(stderr, "Val %d = %d x %d (ent %f, %d) e %f\n", i, v, freqs[i], x, X, e);

	    dbits  += freqs[i] * x;
	    dbitsH += freqs[i] * X;
	}

	for (i = 0; i < 256; i++) {
	    if (F[i]) {
		double x = -log((double)F[i]/n)/.69314718055994530941;
		int X = x+0.5;
		X += (X==0);
		dbitsE  += F[i] * x;
		dbitsEH += F[i] * X;

		//fprintf(stderr, "Val %d = %d x %d (e %f, %d)\n", i, i, F[i], x, X);
	    }
	}

	//fprintf(stderr, "CORE Entropy = %f, %f\n", dbits/8, dbitsH/8);
	//fprintf(stderr, "Ext. Entropy = %f, %f\n", dbitsE/8, dbitsEH/8);

	if (dbitsE < 1000 || dbitsE / dbits > 1.1) {
	    //fprintf(stderr, "=> %d < 200 ? E_HUFFMAN : E_BETA\n", nvals);
	    free(vals); free(freqs);
	    return nvals < 200 ? E_HUFFMAN : E_BETA;
	}
#endif
	free(vals); free(freqs);
	return E_EXTERNAL;
    }

    /*
     * Avoid complex stats for now, just do heuristic of HUFFMAN for small
     * alphabets and BETA for anything large.
     */
    free(vals); free(freqs);
    return nvals < 200 ? E_HUFFMAN : E_BETA;
    //return E_HUFFMAN;
    //return E_EXTERNAL;


    /* We only support huffman now anyway... */
    //free(vals); free(freqs); return E_HUFFMAN;

    /* Beta */
    bits = nbits(max_val - min_val) * ntot;
    if (fd->verbose > 1)
	fprintf(stderr, "BETA    = %d\n", bits);
    if (best_size > bits)
	best_size = bits, best_encoding = E_BETA;

#if 0
    /* Unary */
    if (min_val >= 0) {
	for (bits = i = 0; i < nvals; i++)
	    bits += freqs[i]*(vals[i]+1);
	if (fd->verbose > 1)
	    fprintf(stderr, "UNARY   = %d\n", bits);
	if (best_size > bits)
	    best_size = bits, best_encoding = E_NULL; //E_UNARY;
    }

    /* Gamma */
    for (bits = i = 0; i < nvals; i++)
	bits += ((nbits(vals[i]-min_val+1)-1) + nbits(vals[i]-min_val+1)) * freqs[i];
    if (fd->verbose > 1)
	fprintf(stderr, "GAMMA   = %d\n", bits);
    if (best_size > bits)
	best_size = bits, best_encoding = E_GAMMA;

    /* Subexponential */
    for (k = 0; k < 10; k++) {
	for (bits = i = 0; i < nvals; i++) {
	    if (vals[i]-min_val < (1<<k))
		bits += (1 + k)*freqs[i];
	    else
		bits += (nbits(vals[i]-min_val)*2-k)*freqs[i];
	}

	if (fd->verbose > 1)
	    fprintf(stderr, "SUBEXP%d = %d\n", k, bits);
	if (best_size > bits)
	    best_size = bits, best_encoding = E_SUBEXP;
    }
#endif

    /* byte array len */

    /* byte array stop */

    /* External? Guesswork! */

    /* Huffman */
//    qsort(freqs, nvals, sizeof(freqs[0]), sort_freqs);
//    for (i = 0; i < nvals; i++) {
//	fprintf(stderr, "%d = %d\n", i, freqs[i]);
//	vals[i] = 0;
//    }

    /* Grow freqs to 2*freqs, to store sums */
    /* Vals holds link data */
    freqs = realloc(freqs, 2*nvals*sizeof(*freqs));
    codes = calloc(2*nvals, sizeof(*codes));
    if (!freqs || !codes)
	return E_HUFFMAN; // Cannot do much else atm

    /* Inefficient, use pointers to form chain so we can insert and maintain
     * a sorted list? This is currently O(nvals^2) complexity.
     */
    for (;;) {
	int low1 = INT_MAX, low2 = INT_MAX;
	int ind1 = 0, ind2 = 0;
	for (i = 0; i < nvals; i++) {
	    if (freqs[i] < 0)
		continue;
	    if (low1 > freqs[i]) 
		low2 = low1, ind2 = ind1, low1 = freqs[i], ind1 = i;
	    else if (low2 > freqs[i])
		low2 = freqs[i], ind2 = i;
	}
	if (low2 == INT_MAX)
	    break;

	//fprintf(stderr, "Merge ind %d (%d), %d (%d) = %d+%d, => %d=%d\n",
	//	ind1, vals[ind1], ind2, vals[ind2], low1, low2,
	//	nvals, low1+low2);

	freqs[nvals] = low1 + low2;
	codes[ind1] = nvals;
	codes[ind2] = nvals;
	freqs[ind1] *= -1;
	freqs[ind2] *= -1;
	nvals++;
    }
    nvals = nvals/2+1;

    for (i = 0; i < nvals; i++) {
	int code_len = 0;
	for (k = codes[i]; k; k = codes[k])
	    code_len++;
	codes[i] = code_len;
	freqs[i] *= -1;
	//fprintf(stderr, "%d / %d => %d\n", vals[i], freqs[i], codes[i]);
    }

    for (bits = i = 0; i < nvals; i++) {
	bits += freqs[i] * codes[i];
    }
    if (fd->verbose > 1)
	fprintf(stderr, "HUFFMAN = %d\n", bits);
    if (best_size >= bits)
	best_size = bits, best_encoding = E_HUFFMAN;
    free(codes);

    free(vals);
    free(freqs);

    return best_encoding;
}

void cram_stats_free(cram_stats *st) {
    if (st->h)
	kh_destroy(m_i2i, st->h);
    free(st);
}