--- /dev/null
--- /dev/null
++- Add correct autopkgtests (still cloned from minimap)
++- Add man page
--- /dev/null
--- /dev/null
++fermi-lite (0.1-5) unstable; urgency=medium
++
++ [ Steffen Möller ]
++ * Add new d/u/metadata file
++
++ [ Sascha Steinbiss ]
++ * Update Vcs-* fields with Salsa addresses.
++ * Bump Standards-Version.
++ * Remove unnecessary Testsuite field.
++ * Use debhelper 11.
++
++ -- Sascha Steinbiss <satta@debian.org> Wed, 04 Jul 2018 23:40:50 +0200
++
++fermi-lite (0.1-4) unstable; urgency=medium
++
++ * Upload to unstable
++
++ -- Andreas Tille <tille@debian.org> Sun, 18 Jun 2017 08:12:35 +0200
++
++fermi-lite (0.1-3) experimental; urgency=medium
++
++ * Team upload.
++ * Avoid name space conflict with bwa
++
++ -- Andreas Tille <tille@debian.org> Thu, 02 Feb 2017 10:59:28 +0100
++
++fermi-lite (0.1-2) unstable; urgency=medium
++
++ * Autopkgtest: build example outside of upstream source tree.
++ * Restrict architectures to those with SSE2 support.
++ See also upstream's comment at https://github.com/lh3/fermi-lite/issues/4
++
++ -- Sascha Steinbiss <satta@debian.org> Thu, 04 Aug 2016 05:37:30 +0000
++
++fermi-lite (0.1-1) unstable; urgency=low
++
++ * Initial packaging (Closes: #832757)
++
++ -- Sascha Steinbiss <satta@debian.org> Thu, 28 Jul 2016 22:26:11 +0000
--- /dev/null
--- /dev/null
++11
--- /dev/null
--- /dev/null
++Source: fermi-lite
++Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
++Uploaders: Sascha Steinbiss <satta@debian.org>
++Section: science
++Priority: optional
++Build-Depends: debhelper (>= 11),
++ d-shlibs,
++ zlib1g-dev,
++ help2man
++Standards-Version: 4.1.4
++Vcs-Browser: https://salsa.debian.org/med-team/fermi-lite
++Vcs-Git: https://salsa.debian.org/med-team/fermi-lite.git
++Homepage: https://github.com/lh3/fermi-lite
++
++Package: fml-asm
++Architecture: any-amd64 x32
++Depends: ${misc:Depends},
++ ${shlibs:Depends},
++ zlib1g
++Description: tool for assembling Illumina short reads in small regions
++ Fml-asm is a command-line tool for assembling Illumina short reads in regions
++ from 100bp to 10 million bp in size, based on the fermi-lite library.
++ It is largely a light-weight in-memory version of fermikit without
++ generating any intermediate files. It inherits the performance, the relatively
++ small memory footprint and the features of fermikit. In particular, fermi-lite
++ is able to retain heterozygous events and thus can be used to assemble diploid
++ regions for the purpose of variant calling.
++
++Package: libfml0
++Section: libs
++Architecture: any-amd64 x32
++Depends: ${shlibs:Depends},
++ ${misc:Depends},
++ zlib1g
++Description: library for assembling Illumina short reads in small regions
++ Fermi-lite is a standalone C library tool for assembling Illumina short
++ reads in regions from 100bp to 10 million bp in size.
++ .
++ This package contains a shared library offering the fermi-lite API to custom C
++ programs.
++
++Package: libfml-dev
++Section: libdevel
++Architecture: any-amd64 x32
++Depends: ${shlibs:Depends},
++ ${misc:Depends},
++ libfml0 (= ${binary:Version}),
++ zlib1g-dev
++Description: development headers for libfml
++ Fermi-lite is a standalone C library tool for assembling Illumina short
++ reads in regions from 100bp to 10 million bp in size.
++ .
++ This package contains the C library headers for using libfml in custom tools,
++ along with a static library.
--- /dev/null
--- /dev/null
++Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
++Upstream-Name: fermi-lite
++Source: https://github.com/lh3/fermi-lite
++Upstream-Contact: Heng Li <hengli@broadinstitute.org>
++
++Files: *
++Copyright: © 2016 Broad Institute <hengli@broadinstitute.org>
++License: MIT
++
++Files: khash.h kseq.h
++Copyright: (c) 2008, 2009, 2011 Attractive Chaos <attractor@live.co.uk>
++License: MIT
++
++Files: ksort.h
++Copyright: (c) 2008, 2011 Attractive Chaos <attractor@live.co.uk>
++License: MIT
++
++Files: kstring.h
++Copyright: (c) Attractive Chaos <attractor@live.co.uk>
++License: MIT
++
++Files: ksw.h
++Copyright: (c) 2011 Attractive Chaos <attractor@live.co.uk>
++License: MIT
++
++Files: kvec.h
++Copyright: (c) 2008 Attractive Chaos <attractor@live.co.uk>
++License: MIT
++
++Files: debian/*
++Copyright: © 2016 Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
++License: GPL-3+
++
++License: MIT
++ Permission is hereby granted, free of charge, to any person obtaining
++ a copy of this software and associated documentation files (the
++ "Software"), to deal in the Software without restriction, including
++ without limitation the rights to use, copy, modify, merge, publish,
++ distribute, sublicense, and/or sell copies of the Software, and to
++ permit persons to whom the Software is furnished to do so, subject to
++ the following conditions:
++ .
++ The above copyright notice and this permission notice shall be
++ included in all copies or substantial portions of the Software.
++ .
++ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
++ EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
++ MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
++ NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
++ BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
++ ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
++ CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
++ SOFTWARE.
++
++License: GPL-3+
++ This package is free software; you can redistribute it and/or modify
++ it under the terms of the GNU General Public License as published by
++ the Free Software Foundation; either version 3 of the License, or
++ (at your option) any later version.
++ .
++ This package is distributed in the hope that it will be useful,
++ but WITHOUT ANY WARRANTY; without even the implied warranty of
++ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
++ GNU General Public License for more details.
++ .
++ You should have received a copy of the GNU General Public License
++ along with this program. If not, see <http://www.gnu.org/licenses/>
++ .
++ On Debian systems, the complete text of the GNU General
++ Public License version 3 can be found in "/usr/share/common-licenses/GPL-3".
++
--- /dev/null
--- /dev/null
++fml-asm /usr/bin
--- /dev/null
--- /dev/null
++*.1
--- /dev/null
--- /dev/null
++Description: Try to take over patches from libSeqLib which needs separate bfc.h
++ FIXME: Please check the FIXME at the end. I think I did things wrong to put a
++ static declaration into header file but I had no better idea to make
++ ec1buf_init known in libSeqLib
++Author: Andreas Tille <tille@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 +543,18 @@ float fml_correct_core(const fml_opt_t *
++ return kcov;
++ }
++
+++// Added by jwala for use in libSeqLib
+++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" ... this is actually included by htab.h */
+++#include "internal.h"
+++#include "fml.h"
+++#include "khash.h"
+++
+++/* Andreas Tille <tille@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
--- /dev/null
--- /dev/null
++Description: add hardening flags
++ Adds necessary build flags for hardening.
++Author: Sascha Steinbiss <sascha@steinbiss.name>
++Last-Update: 2016-01-08
++--- a/Makefile
+++++ b/Makefile
++@@ -1,6 +1,6 @@
++-CC= gcc
++-CFLAGS= -g -Wall -O2 -fPIC #-fno-inline-functions -fno-inline-functions-called-once
++-CPPFLAGS=
+++CC?= gcc
+++CFLAGS+= -g -Wall -O2 -fPIC #-fno-inline-functions -fno-inline-functions-called-once
+++#CPPFLAGS=
++ INCLUDES=
++ OBJS= kthread.o misc.o \
++ bseq.o htab.o bfc.o \
++@@ -18,7 +18,7 @@
++ all:$(PROG) libfml.so.$(SONUMBER)
++
++ fml-asm:libfml.a example.o
++- $(CC) $(CFLAGS) $^ -o $@ -L. -lfml $(LIBS)
+++ $(CC) $(CFLAGS) $^ -o $@ -L. -lfml $(LIBS) $(LDFLAGS)
++
++ libfml.a:$(OBJS)
++ $(AR) -csru $@ $(OBJS)
--- /dev/null
--- /dev/null
++Description: build shared library
++ Upstream only builds a static library, this adds a shared one.
++Author: Sascha Steinbiss <sascha@steinbiss.name>
++Last-Update: 2016-01-08
++--- a/Makefile
+++++ b/Makefile
++@@ -1,5 +1,5 @@
++ CC= gcc
++-CFLAGS= -g -Wall -O2 -Wno-unused-function #-fno-inline-functions -fno-inline-functions-called-once
+++CFLAGS= -g -Wall -O2 -fPIC #-fno-inline-functions -fno-inline-functions-called-once
++ CPPFLAGS=
++ INCLUDES=
++ OBJS= kthread.o misc.o \
++@@ -8,13 +8,14 @@
++ unitig.o mag.o bubble.o ksw.o
++ PROG= fml-asm
++ LIBS= -lm -lz -lpthread
+++SONUMBER=0
++
++ .SUFFIXES:.c .o
++
++ .c.o:
++ $(CC) -c $(CFLAGS) $(CPPFLAGS) $(INCLUDES) $< -o $@
++
++-all:$(PROG)
+++all:$(PROG) libfml.so.$(SONUMBER)
++
++ fml-asm:libfml.a example.o
++ $(CC) $(CFLAGS) $^ -o $@ -L. -lfml $(LIBS)
++@@ -22,6 +23,10 @@
++ libfml.a:$(OBJS)
++ $(AR) -csru $@ $(OBJS)
++
+++libfml.so.$(SONUMBER): $(OBJS)
+++ $(CC) -shared -o $@ $(OBJS) -fPIC -Wl,-soname,libfml.so.$(SONUMBER) $(LIBS) $(LDFLAGS)
+++
+++
++ clean:
++ rm -fr gmon.out *.o ext/*.o a.out $(PROG) *~ *.a *.dSYM session*
++
--- /dev/null
--- /dev/null
++Description: Avoid name space conflict with bwa
++Bug-Upstream: https://github.com/lh3/fermi-lite/issues/5
++Author: Andreas Tille <tille@debian.org>
++Last-Update: Thu, 02 Feb 2017 10:57:56 +0100
++
++--- a/bfc.c
+++++ b/bfc.c
++@@ -60,7 +60,7 @@ typedef struct { // cache to reduce lock
++ typedef struct {
++ int k, q;
++ int n_seqs;
++- const bseq1_t *seqs;
+++ const fml_seq1_t *seqs;
++ bfc_ch_t *ch;
++ int *n_buf;
++ insbuf_t **buf;
++@@ -97,7 +97,7 @@ static void bfc_kmer_insert(cnt_step_t *
++ static void worker_count(void *_data, long k, int tid)
++ {
++ cnt_step_t *cs = (cnt_step_t*)_data;
++- const bseq1_t *s = &cs->seqs[k];
+++ const fml_seq1_t *s = &cs->seqs[k];
++ int i, l;
++ bfc_kmer_t x = bfc_kmer_null;
++ uint64_t qmer = 0, mask = (1ULL<<cs->k) - 1;
++@@ -111,7 +111,7 @@ static void worker_count(void *_data, lo
++ }
++ }
++
++-struct bfc_ch_s *fml_count(int n, const bseq1_t *seq, int k, int q, int l_pre, int n_threads)
+++struct bfc_ch_s *fml_count(int n, const fml_seq1_t *seq, int k, int q, int l_pre, int n_threads)
++ {
++ int i;
++ cnt_step_t cs;
++@@ -577,10 +577,10 @@ typedef struct {
++ bfc_ec1buf_t **e;
++ int64_t n_processed;
++ int n_seqs, flt_uniq;
++- bseq1_t *seqs;
+++ fml_seq1_t *seqs;
++ } ec_step_t;
++
++-static uint64_t max_streak(int k, const bfc_ch_t *ch, const bseq1_t *s)
+++static uint64_t max_streak(int k, const bfc_ch_t *ch, const fml_seq1_t *s)
++ {
++ int i, l;
++ uint64_t max = 0, t = 0;
++@@ -602,7 +602,7 @@ static uint64_t max_streak(int k, const
++ static void worker_ec(void *_data, long k, int tid)
++ {
++ ec_step_t *es = (ec_step_t*)_data;
++- bseq1_t *s = &es->seqs[k];
+++ fml_seq1_t *s = &es->seqs[k];
++ if (es->flt_uniq) {
++ uint64_t max;
++ max = max_streak(es->opt->k, es->ch, s);
++@@ -624,7 +624,7 @@ static void worker_ec(void *_data, long
++ } else bfc_ec1(es->e[tid], s->seq, s->qual);
++ }
++
++-float fml_correct_core(const fml_opt_t *opt, int flt_uniq, int n, bseq1_t *seq)
+++float fml_correct_core(const fml_opt_t *opt, int flt_uniq, int n, fml_seq1_t *seq)
++ {
++ bfc_ch_t *ch;
++ int i, mode;
++@@ -663,12 +663,12 @@ float fml_correct_core(const fml_opt_t *
++ return kcov;
++ }
++
++-float fml_correct(const fml_opt_t *opt, int n, bseq1_t *seq)
+++float fml_correct(const fml_opt_t *opt, int n, fml_seq1_t *seq)
++ {
++ return fml_correct_core(opt, 0, n, seq);
++ }
++
++-float fml_fltuniq(const fml_opt_t *opt, int n, bseq1_t *seq)
+++float fml_fltuniq(const fml_opt_t *opt, int n, fml_seq1_t *seq)
++ {
++ return fml_correct_core(opt, 1, n, seq);
++ }
++--- a/bseq.c
+++++ b/bseq.c
++@@ -6,10 +6,10 @@
++ #include "kseq.h"
++ KSEQ_INIT(gzFile, gzread)
++
++-bseq1_t *bseq_read(const char *fn, int *n_)
+++fml_seq1_t *fml_seq_read(const char *fn, int *n_)
++ {
++ gzFile fp;
++- bseq1_t *seqs;
+++ fml_seq1_t *seqs;
++ kseq_t *ks;
++ int m, n;
++ uint64_t size = 0;
++@@ -21,10 +21,10 @@ bseq1_t *bseq_read(const char *fn, int *
++
++ m = n = 0; seqs = 0;
++ while (kseq_read(ks) >= 0) {
++- bseq1_t *s;
+++ fml_seq1_t *s;
++ if (n >= m) {
++ m = m? m<<1 : 256;
++- seqs = realloc(seqs, m * sizeof(bseq1_t));
+++ seqs = realloc(seqs, m * sizeof(fml_seq1_t));
++ }
++ s = &seqs[n];
++ s->seq = strdup(ks->seq.s);
++--- a/misc.c
+++++ b/misc.c
++@@ -40,7 +40,7 @@ void fml_opt_init(fml_opt_t *opt)
++ opt->mag_opt.flag = MAG_F_NO_SIMPL;
++ }
++
++-void fml_opt_adjust(fml_opt_t *opt, int n_seqs, const bseq1_t *seqs)
+++void fml_opt_adjust(fml_opt_t *opt, int n_seqs, const fml_seq1_t *seqs)
++ {
++ int i, log_len;
++ uint64_t tot_len = 0;
++@@ -62,7 +62,7 @@ static inline int is_rev_same(int l, con
++ return (i == l>>1);
++ }
++
++-struct rld_t *fml_fmi_gen(int n, bseq1_t *seq, int is_mt)
+++struct rld_t *fml_fmi_gen(int n, fml_seq1_t *seq, int is_mt)
++ {
++ mrope_t *mr;
++ kstring_t str = {0,0,0};
++@@ -75,7 +75,7 @@ struct rld_t *fml_fmi_gen(int n, bseq1_t
++ mr = mr_init(ROPE_DEF_MAX_NODES, ROPE_DEF_BLOCK_LEN, MR_SO_RCLO);
++ for (k = 0; k < n; ++k) {
++ int i;
++- bseq1_t *s = &seq[k];
+++ fml_seq1_t *s = &seq[k];
++ if (s->l_seq == 0) continue;
++ free(s->qual);
++ for (i = 0; i < s->l_seq; ++i)
++@@ -116,7 +116,7 @@ struct rld_t *fml_fmi_gen(int n, bseq1_t
++ return e;
++ }
++
++-struct rld_t *fml_seq2fmi(const fml_opt_t *opt, int n, bseq1_t *seq)
+++struct rld_t *fml_seq2fmi(const fml_opt_t *opt, int n, fml_seq1_t *seq)
++ {
++ return fml_fmi_gen(n, seq, opt->n_threads > 1? 1 : 0);
++ }
++@@ -251,7 +251,7 @@ void fml_utg_destroy(int n, fml_utg_t *u
++
++ #define MAG_MIN_NSR_COEF .1
++
++-fml_utg_t *fml_assemble(const fml_opt_t *opt0, int n_seqs, bseq1_t *seqs, int *n_utg)
+++fml_utg_t *fml_assemble(const fml_opt_t *opt0, int n_seqs, fml_seq1_t *seqs, int *n_utg)
++ {
++ rld_t *e;
++ mag_t *g;
++--- a/example.c
+++++ b/example.c
++@@ -7,7 +7,7 @@ int main(int argc, char *argv[])
++ {
++ fml_opt_t opt;
++ int c, n_seqs, n_utg;
++- bseq1_t *seqs;
+++ fml_seq1_t *seqs;
++ fml_utg_t *utg;
++
++ fml_opt_init(&opt);
++@@ -34,7 +34,7 @@ int main(int argc, char *argv[])
++ fprintf(stderr, " -A discard heterozygotes (apply this to assemble bacterial genomes)\n");
++ return 1;
++ }
++- seqs = bseq_read(argv[optind], &n_seqs);
+++ seqs = fml_seq_read(argv[optind], &n_seqs);
++ utg = fml_assemble(&opt, n_seqs, seqs, &n_utg);
++ fml_utg_print(n_utg, utg);
++ fml_utg_destroy(n_utg, utg);
++--- a/internal.h
+++++ b/internal.h
++@@ -12,7 +12,7 @@ extern "C" {
++ void kt_for(int n_threads, void (*func)(void*,long,int), void *data, long n);
++ void seq_reverse(int l, unsigned char *s);
++ void seq_revcomp6(int l, unsigned char *s);
++-struct bfc_ch_s *fml_count(int n, const bseq1_t *seq, int k, int q, int l_pre, int n_threads);
+++struct bfc_ch_s *fml_count(int n, const fml_seq1_t *seq, int k, int q, int l_pre, int n_threads);
++
++ #ifdef __cplusplus
++ }
++--- a/fml.h
+++++ b/fml.h
++@@ -8,7 +8,7 @@
++ typedef struct {
++ int32_t l_seq;
++ char *seq, *qual;
++-} bseq1_t;
+++} fml_seq1_t;
++
++ #define MAG_F_AGGRESSIVE 0x20
++ #define MAG_F_NO_SIMPL 0x80
++@@ -60,7 +60,7 @@ extern "C" {
++ *
++ * @return array of sequences
++ */
++-bseq1_t *bseq_read(const char *fn, int *n);
+++fml_seq1_t *fml_seq_read(const char *fn, int *n);
++
++ /**
++ * Initialize default parameters
++@@ -79,7 +79,7 @@ void fml_opt_init(fml_opt_t *opt);
++ *
++ * @return array of unitigs
++ */
++-fml_utg_t *fml_assemble(const fml_opt_t *opt, int n_seqs, bseq1_t *seqs, int *n_utg);
+++fml_utg_t *fml_assemble(const fml_opt_t *opt, int n_seqs, fml_seq1_t *seqs, int *n_utg);
++
++ /**
++ * Free unitigs
++@@ -100,7 +100,7 @@ void fml_utg_destroy(int n_utg, fml_utg_
++ * @param n_seqs number of sequences
++ * @param seqs array of sequences
++ */
++-void fml_opt_adjust(fml_opt_t *opt, int n_seqs, const bseq1_t *seqs);
+++void fml_opt_adjust(fml_opt_t *opt, int n_seqs, const fml_seq1_t *seqs);
++
++ /**
++ * Error correction
++@@ -111,8 +111,8 @@ void fml_opt_adjust(fml_opt_t *opt, int
++ *
++ * @return k-mer coverage
++ */
++-float fml_correct(const fml_opt_t *opt, int n, bseq1_t *seq);
++-float fml_fltuniq(const fml_opt_t *opt, int n, bseq1_t *seq);
+++float fml_correct(const fml_opt_t *opt, int n, fml_seq1_t *seq);
+++float fml_fltuniq(const fml_opt_t *opt, int n, fml_seq1_t *seq);
++
++ /**
++ * Construct FMD-index
++@@ -123,7 +123,7 @@ float fml_fltuniq(const fml_opt_t *opt,
++ *
++ * @return FMD-index
++ */
++-struct rld_t *fml_seq2fmi(const fml_opt_t *opt, int n, bseq1_t *seq);
+++struct rld_t *fml_seq2fmi(const fml_opt_t *opt, int n, fml_seq1_t *seq);
++
++ /**
++ * Generate initial overlap graph
++--- a/README.md
+++++ b/README.md
++@@ -29,11 +29,11 @@ sketch of the example:
++ int main(int argc, char *argv[])
++ {
++ int i, n_seqs, n_utgs;
++- bseq1_t *seqs; // array of input sequences
+++ fml_seq1_t *seqs; // array of input sequences
++ fml_utg_t *utgs; // array of output unitigs
++ fml_opt_t opt;
++ if (argc == 1) return 1; // do nothing if there is no input file
++- seqs = bseq_read(argv[1], &n_seqs); // or fill the array with callers' functions
+++ seqs = fml_seq_read(argv[1], &n_seqs); // or fill the array with callers' functions
++ fml_opt_init(&opt); // initialize parameters
++ utgs = fml_assemble(&opt, n_seqs, seqs, &n_utgs); // assemble!
++ for (i = 0; i < n_utgs; ++i) // output in fasta
--- /dev/null
--- /dev/null
++make_shared_lib
++hardening
++rename_bseq1_t.patch
++bcf_seqlib.patch
--- /dev/null
--- /dev/null
++#!/usr/bin/make -f
++
++export DEB_BUILD_MAINT_OPTIONS = hardening=+bindnow
++
++%:
++ dh $@
++
++override_dh_auto_clean:
++ dh_auto_clean
++ rm -f fml-asm.1
++
++override_dh_auto_install:
++ ln -s libfml.so.* libfml.so
++ d-shlibmove --commit \
++ --multiarch \
++ --devunversioned \
++ --movedev "fml.h" /usr/include/ \
++ --movedev "bfc.h" /usr/include/fml \
++ --movedev "htab.h" /usr/include/fml \
++ --movedev "kmer.h" /usr/include/fml \
++ --movedev "internal.h" /usr/include/fml \
++ --movedev "khash.h" /usr/include/fml \
++ --movedev "kvec.h" /usr/include/fml \
++ --movedev "ksort.h" /usr/include/fml \
++ libfml.so
++
++override_dh_installman:
++ help2man --version-string='0.1' \
++ -n 'assemble Illumina short reads in small regions' \
++ -N --no-discard-stderr -h '' ./fml-asm > fml-asm.1
++ dh_installman
--- /dev/null
--- /dev/null
++3.0 (quilt)
--- /dev/null
--- /dev/null
++#!/bin/sh
++# autopkgtest check: Build and run a program against libfml
++# Author: Sascha Steinbiss <satta@debian.org>
++set -e
++
++SRC=$(pwd)/example.c
++DATADIR=$(pwd)/test
++WORKDIR=$(mktemp -d)
++trap "rm -rf $WORKDIR" 0 INT QUIT ABRT PIPE TERM
++cd $WORKDIR
++
++cp $SRC .
++gcc -O2 -o fermi-lite example.c -lfml -lz -lm -lpthread
++[ -x fermi-lite ]
++echo "build: OK"
++
++./fermi-lite $DATADIR/MT-simu.fq.gz > out
++ldd fermi-lite
++echo "run: OK"
--- /dev/null
--- /dev/null
++Tests: build-lib
++Depends: @, build-essential
++Restrictions: allow-stderr
--- /dev/null
--- /dev/null
++Registry:
++ - Name: OMICtools
++ Entry: OMICS_01087
++ - Name: bio.tools
++ Entry: flexbar
++ - Name: SciCrunch
++ Entry: SCR_013001
--- /dev/null
--- /dev/null
++version=3
++https://github.com/lh3/fermi-lite/releases .*/archive/v(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)
++
projects / fermi-lite.git / commitdiff