[med-svn] [fermi-lite] 01/01: Try to take over patches from libSeqLib which needs separate bfc.h
Andreas Tille
tille at debian.org
Thu Feb 2 15:13:29 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository fermi-lite.
commit 394d461101796f26c32f609e870fea87ea7dbd6f
Author: Andreas Tille <tille at debian.org>
Date: Thu Feb 2 16:08:06 2017 +0100
Try to take over patches from libSeqLib which needs separate bfc.h
---
debian/patches/bcf_seqlib.patch | 346 ++++++++++++++++++++++++++++++++++++++++
debian/patches/series | 1 +
2 files changed, 347 insertions(+)
diff --git a/debian/patches/bcf_seqlib.patch b/debian/patches/bcf_seqlib.patch
new file mode 100644
index 0000000..cf8aa9e
--- /dev/null
+++ b/debian/patches/bcf_seqlib.patch
@@ -0,0 +1,346 @@
+Description: Try to take over patches from libSeqLib which needs separate bfc.h
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Thu, 02 Feb 2017 10:57:56 +0100
+
+--- a/bfc.c
++++ b/bfc.c
+@@ -7,24 +7,12 @@
+ #include "kmer.h"
+ #include "internal.h"
+ #include "fml.h"
++#include "bfc.h"
+
+ /*******************
+ *** BFC options ***
+ *******************/
+
+-typedef struct {
+- int n_threads, q, k, l_pre;
+- int min_cov; // a k-mer is considered solid if the count is no less than this
+-
+- int max_end_ext;
+- int win_multi_ec;
+- float min_trim_frac;
+-
+- // these ec options cannot be changed on the command line
+- int w_ec, w_ec_high, w_absent, w_absent_high;
+- int max_path_diff, max_heap;
+-} bfc_opt_t;
+-
+ void bfc_opt_init(bfc_opt_t *opt)
+ {
+ memset(opt, 0, sizeof(bfc_opt_t));
+@@ -46,26 +34,6 @@ void bfc_opt_init(bfc_opt_t *opt)
+ opt->max_heap = 100;
+ }
+
+-/**********************
+- *** K-mer counting ***
+- **********************/
+-
+-#define CNT_BUF_SIZE 256
+-
+-typedef struct { // cache to reduce locking
+- uint64_t y[2];
+- int is_high;
+-} insbuf_t;
+-
+-typedef struct {
+- int k, q;
+- int n_seqs;
+- const fml_seq1_t *seqs;
+- bfc_ch_t *ch;
+- int *n_buf;
+- insbuf_t **buf;
+-} cnt_step_t;
+-
+ bfc_kmer_t bfc_kmer_null = {{0,0,0,0}};
+
+ static int bfc_kmer_bufclear(cnt_step_t *cs, int forced, int tid)
+@@ -127,34 +95,6 @@ struct bfc_ch_s *fml_count(int n, const
+ return cs.ch;
+ }
+
+-/***************
+- *** Correct ***
+- ***************/
+-
+-#define BFC_MAX_KMER 63
+-#define BFC_MAX_BF_SHIFT 37
+-
+-#define BFC_MAX_PATHS 4
+-#define BFC_EC_HIST 5
+-#define BFC_EC_HIST_HIGH 2
+-
+-#define BFC_EC_MIN_COV_COEF .1
+-
+-/**************************
+- * Sequence struct for ec *
+- **************************/
+-
+-#include "kvec.h"
+-
+-typedef struct { // NOTE: unaligned memory
+- uint8_t b:3, q:1, ob:3, oq:1;
+- uint8_t dummy;
+- uint16_t lcov:6, hcov:6, solid_end:1, high_end:1, ec:1, absent:1;
+- int i;
+-} ecbase_t;
+-
+-typedef kvec_t(ecbase_t) ecseq_t;
+-
+ static int bfc_seq_conv(const char *s, const char *q, int qthres, ecseq_t *seq)
+ {
+ int i, l;
+@@ -264,53 +204,6 @@ uint64_t bfc_ec_best_island(int k, const
+ return max > 0? (uint64_t)(max_i - max - k + 1) << 32 | max_i : 0;
+ }
+
+-/********************
+- * Correct one read *
+- ********************/
+-
+-#include "ksort.h"
+-
+-#define ECCODE_MISC 1
+-#define ECCODE_MANY_N 2
+-#define ECCODE_NO_SOLID 3
+-#define ECCODE_UNCORR_N 4
+-#define ECCODE_MANY_FAIL 5
+-
+-typedef struct {
+- uint32_t ec_code:3, brute:1, n_ec:14, n_ec_high:14;
+- uint32_t n_absent:24, max_heap:8;
+-} ecstat_t;
+-
+-typedef struct {
+- uint8_t ec:1, ec_high:1, absent:1, absent_high:1, b:4;
+-} bfc_penalty_t;
+-
+-typedef struct {
+- int tot_pen;
+- int i; // base position
+- int k; // position in the stack
+- int32_t ecpos_high[BFC_EC_HIST_HIGH];
+- int32_t ecpos[BFC_EC_HIST];
+- bfc_kmer_t x;
+-} echeap1_t;
+-
+-typedef struct {
+- int parent, i, tot_pen;
+- uint8_t b;
+- bfc_penalty_t pen;
+- uint16_t cnt;
+-} ecstack1_t;
+-
+-typedef struct {
+- const bfc_opt_t *opt;
+- const bfc_ch_t *ch;
+- kvec_t(echeap1_t) heap;
+- kvec_t(ecstack1_t) stack;
+- ecseq_t seq, tmp, ec[2];
+- int mode;
+- ecstat_t ori_st;
+-} bfc_ec1buf_t;
+-
+ #define heap_lt(a, b) ((a).tot_pen > (b).tot_pen)
+ KSORT_INIT(ec, echeap1_t, heap_lt)
+
+@@ -567,19 +460,6 @@ ecstat_t bfc_ec1(bfc_ec1buf_t *e, char *
+ return s;
+ }
+
+-/********************
+- * Error correction *
+- ********************/
+-
+-typedef struct {
+- const bfc_opt_t *opt;
+- const bfc_ch_t *ch;
+- bfc_ec1buf_t **e;
+- int64_t n_processed;
+- int n_seqs, flt_uniq;
+- fml_seq1_t *seqs;
+-} ec_step_t;
+-
+ static uint64_t max_streak(int k, const bfc_ch_t *ch, const fml_seq1_t *s)
+ {
+ int i, l;
+@@ -663,6 +543,21 @@ float fml_correct_core(const fml_opt_t *
+ return kcov;
+ }
+
++//jwala added here (linker issues)
++// copied from fml_correct_core
++/* Andreas Tille <tille at debian.org>: uncomment for the moment - would like to see what linker issues might actually happen
++void kmer_correct(ec_step_t * es, int mode, bfc_ch_t * ch) {
++ int i = 0;
++ es->e = (bfc_ec1buf_t**)calloc(es->opt->n_threads, sizeof(void*)); //jwala added cast
++ for (i = 0; i < es->opt->n_threads; ++i)
++ es->e[i] = ec1buf_init(es->opt, ch), es->e[i]->mode = mode;
++ kt_for(es->opt->n_threads, worker_ec, es, es->n_seqs);
++ for (i = 0; i < es->opt->n_threads; ++i)
++ ec1buf_destroy(es->e[i]);
++ free(es->e);
++}
++*/
++
+ float fml_correct(const fml_opt_t *opt, int n, fml_seq1_t *seq)
+ {
+ return fml_correct_core(opt, 0, n, seq);
+--- /dev/null
++++ b/bfc.h
+@@ -0,0 +1,153 @@
++#ifndef AC_BFC_H__
++#define AC_BFC_H__
++
++#include <stdlib.h>
++#include <string.h>
++#include <assert.h>
++#include <limits.h>
++#include <stdio.h>
++#include "htab.h"
++#include "kmer.h"
++#include "internal.h"
++#include "fml.h"
++#include "khash.h"
++
++/* Andreas Tille <tille at debian.org>: Its not clear where jwala took this from and what its purpose might be - commenting out for the moment
++#define _cnt_eq(a, b) ((a)>>14 == (b)>>14)
++#define _cnt_hash(a) ((a)>>14)
++KHASH_INIT(cnt, uint64_t, char, 0, _cnt_hash, _cnt_eq)
++typedef khash_t(cnt) cnthash_t;
++
++struct bfc_ch_s {
++ int k;
++ cnthash_t **h;
++ // private
++ int l_pre;
++};
++*/
++
++typedef struct {
++ int n_threads, q, k, l_pre;
++ int min_cov; // a k-mer is considered solid if the count is no less than this
++
++ int max_end_ext;
++ int win_multi_ec;
++ float min_trim_frac;
++
++ // these ec options cannot be changed on the command line
++ int w_ec, w_ec_high, w_absent, w_absent_high;
++ int max_path_diff, max_heap;
++} bfc_opt_t;
++
++/**********************
++ *** K-mer counting ***
++ **********************/
++
++#define CNT_BUF_SIZE 256
++
++typedef struct { // cache to reduce locking
++ uint64_t y[2];
++ int is_high;
++} insbuf_t;
++
++typedef struct {
++ int k, q;
++ int n_seqs;
++ const fml_seq1_t *seqs;
++ bfc_ch_t *ch;
++ int *n_buf;
++ insbuf_t **buf;
++} cnt_step_t;
++
++/***************
++ *** Correct ***
++ ***************/
++
++#define BFC_MAX_KMER 63
++#define BFC_MAX_BF_SHIFT 37
++
++#define BFC_MAX_PATHS 4
++#define BFC_EC_HIST 5
++#define BFC_EC_HIST_HIGH 2
++
++#define BFC_EC_MIN_COV_COEF .1
++
++/**************************
++ * Sequence struct for ec *
++ **************************/
++
++#include "kvec.h"
++
++typedef struct { // NOTE: unaligned memory
++ uint8_t b:3, q:1, ob:3, oq:1;
++ uint8_t dummy;
++ uint16_t lcov:6, hcov:6, solid_end:1, high_end:1, ec:1, absent:1;
++ int i;
++} ecbase_t;
++
++typedef kvec_t(ecbase_t) ecseq_t;
++
++/********************
++ * Correct one read *
++ ********************/
++
++#include "ksort.h"
++
++#define ECCODE_MISC 1
++#define ECCODE_MANY_N 2
++#define ECCODE_NO_SOLID 3
++#define ECCODE_UNCORR_N 4
++#define ECCODE_MANY_FAIL 5
++
++typedef struct {
++ uint32_t ec_code:3, brute:1, n_ec:14, n_ec_high:14;
++ uint32_t n_absent:24, max_heap:8;
++} ecstat_t;
++
++typedef struct {
++ uint8_t ec:1, ec_high:1, absent:1, absent_high:1, b:4;
++} bfc_penalty_t;
++
++typedef struct {
++ int tot_pen;
++ int i; // base position
++ int k; // position in the stack
++ int32_t ecpos_high[BFC_EC_HIST_HIGH];
++ int32_t ecpos[BFC_EC_HIST];
++ bfc_kmer_t x;
++} echeap1_t;
++
++typedef struct {
++ int parent, i, tot_pen;
++ uint8_t b;
++ bfc_penalty_t pen;
++ uint16_t cnt;
++} ecstack1_t;
++
++typedef struct {
++ const bfc_opt_t *opt;
++ const bfc_ch_t *ch;
++ kvec_t(echeap1_t) heap;
++ kvec_t(ecstack1_t) stack;
++ ecseq_t seq, tmp, ec[2];
++ int mode;
++ ecstat_t ori_st;
++} bfc_ec1buf_t;
++
++/********************
++ * Error correction *
++ ********************/
++
++typedef struct {
++ const bfc_opt_t *opt;
++ const bfc_ch_t *ch;
++ bfc_ec1buf_t **e;
++ int64_t n_processed;
++ int n_seqs, flt_uniq;
++ fml_seq1_t *seqs;
++} ec_step_t;
++
++//void kmer_correct(ec_step_t * es, int mode, bfc_ch_t * ch);
++void bfc_opt_init(bfc_opt_t *opt);
++
++#endif
diff --git a/debian/patches/series b/debian/patches/series
index 763f067..4642b14 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,3 +1,4 @@
make_shared_lib
hardening
rename_bseq1_t.patch
+bcf_seqlib.patch
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/fermi-lite.git
More information about the debian-med-commit
mailing list