--- /dev/null
+- Add correct autopkgtests (still cloned from minimap)
+- Add man page
--- /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
+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
+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
+fml-asm /usr/bin
--- /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
+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
+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
+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
+make_shared_lib
+hardening
+rename_bseq1_t.patch
+bcf_seqlib.patch
--- /dev/null
+#!/usr/bin/make -f
+
+export DEB_BUILD_MAINT_OPTIONS = hardening=+bindnow
+
+%:
+ dh $@
+
+override_dh_auto_clean:
+ dh_auto_clean
+ rm -f fml-asm.1
+
+override_dh_auto_install:
+ ln -s libfml.so.* libfml.so
+ d-shlibmove --commit \
+ --multiarch \
+ --devunversioned \
+ --movedev "fml.h" /usr/include/ \
+ --movedev "bfc.h" /usr/include/fml \
+ --movedev "htab.h" /usr/include/fml \
+ --movedev "kmer.h" /usr/include/fml \
+ --movedev "internal.h" /usr/include/fml \
+ --movedev "khash.h" /usr/include/fml \
+ --movedev "kvec.h" /usr/include/fml \
+ --movedev "ksort.h" /usr/include/fml \
+ libfml.so
+
+override_dh_installman:
+ help2man --version-string='0.1' \
+ -n 'assemble Illumina short reads in small regions' \
+ -N --no-discard-stderr -h '' ./fml-asm > fml-asm.1
+ dh_installman
--- /dev/null
+3.0 (quilt)
--- /dev/null
+#!/bin/sh
+# autopkgtest check: Build and run a program against libfml
+# Author: Sascha Steinbiss <satta@debian.org>
+set -e
+
+SRC=$(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
+Tests: build-lib
+Depends: @, build-essential
+Restrictions: allow-stderr
--- /dev/null
+Registry:
+ - Name: OMICtools
+ Entry: OMICS_01087
+ - Name: bio.tools
+ Entry: flexbar
+ - Name: SciCrunch
+ Entry: SCR_013001
\ No newline at end of file
--- /dev/null
+version=3
+https://github.com/lh3/fermi-lite/releases .*/archive/v(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)
+
projects / fermi-lite.git / commitdiff