New upstream version 2.0.0 (7871ef7d) · Commits · Debian Med / falcon

.travis.yml

+53 −0

Original line number	Diff line number	Diff line
		@@ -28,3 +28,56 @@ script: ./travis.sh
		notifications:
		email: false
		sudo: false


		# Copied from https://github.com/nim-lang/Nim/wiki/TravisCI
		#language: c
		env:
		# Build and test against the master and devel branches of Nim
		#- BRANCH=master
		- BRANCH=devel
		#- BRANCH=v0.17.2
		compiler:
		# Build and test using both gcc and clang
		- gcc
		#- clang
		#matrix:
		# allow_failures:
		# # Ignore failures when building against the devel Nim branch
		# - env: BRANCH=devel
		# fast_finish: true
		install:
		- \|
		if [ ! -x nim-$BRANCH/bin/nim ]; then
		git clone -b $BRANCH --depth 1 git://github.com/nim-lang/nim nim-$BRANCH/
		cd nim-$BRANCH
		git clone --depth 1 git://github.com/nim-lang/csources csources/
		cd csources
		sh build.sh
		cd ..
		rm -rf csources
		bin/nim c koch
		./koch boot -d:release
		else
		cd nim-$BRANCH
		git fetch origin
		if ! git merge FETCH_HEAD \| grep "Already up-to-date"; then
		bin/nim c koch
		./koch boot -d:release
		fi
		fi
		cd ..
		before_script:
		- export PATH="$(pwd)/nim-$BRANCH/bin${PATH:+:$PATH}"
		#script:
		# # Replace uppercase strings!
		# - nim c --cc:$CC --verbosity:0 -r MYFILE.nim
		# # Optional: build docs.
		# - nim doc --docSeeSrcUrl:https://github.com/AUTHOR/MYPROJECT/blob/master --project MYFILE.nim
		cache:
		directories:
		#- nim-master
		- nim-devel
		branches:
		except:
		- gh-pages

DALIGNER/LA4Falcon.c

+39 −1

Original line number	Diff line number	Diff line
		@@ -62,6 +62,13 @@
		#include <stdio.h>
		#include <stdlib.h>
		#include <string.h>
		// debugging
		#include <time.h>
		//#include <locale.h>
		#include <stdbool.h>
		// end debugging



		#define MAX_OVERLAPS 50000

		@@ -552,6 +559,13 @@ int main(int argc, char *argv[])

		// For each record do

		// debugging
		// setlocale(LC_NUMERIC, ""); // for commas in numbers with %'d, but this can cause other problems
		fprintf(stderr, "\nabout to go into loop with novl = %lld %s\n", novl, argv[3]);
		time_t timeLast;
		time(&timeLast);
		// end debugging

		blast = -1;
		match = 0;
		seen = 0;
		@@ -559,7 +573,25 @@ int main(int argc, char *argv[])
		for (j = 0; j < novl; j++)
		// Read it in

		{ Read_Overlap(input,ovl);
		{

		// debugging
		time_t timeCurrent;
		time(&timeCurrent);
		double diff_t = difftime(timeCurrent, timeLast);


		if ( ( diff_t > 60.0 ) \|\| ( j < 10) \|\| ( j % 1000000 == 0 ) ) {
		time_t mytime = time(NULL);
		fprintf(stderr, "before Read_Overlap record j = %d out of %lld at %s %s", j, novl, argv[3], ctime(&mytime));
		fflush(stderr);
		timeLast = timeCurrent;
		}
		// end debugging



		Read_Overlap(input,ovl);
		if (ovl->path.tlen > tmax)
		{ tmax = ((int) 1.2*ovl->path.tlen) + 100;
		trace = (uint16 ) Realloc(trace,sizeof(uint16)tmax,"Allocating trace vector");
		@@ -831,6 +863,12 @@ int main(int argc, char *argv[])
		}
		}

		// debugging
		time_t mytime = time(NULL);
		fprintf(stderr, "\ncompleted loop record j = %d out of %lld at %s %s\n", j, novl, argv[3], ctime(&mytime));
		// end debugging


		if (FALCON && hit_count != -1)
		{
		print_hits(hit_count, dbx2, bbuffer, buffer, (int64)sizeof(buffer), MAX_HIT_COUNT);

DALIGNER/LAmerge.c

+23 −5

Original line number	Diff line number	Diff line
		@@ -48,6 +48,24 @@ static char *Usage = "[-va] <merge:las> <parts:las> ...";
		else \
		bigger = 0;

		static void Fwrite(const void ptr, size_t size, size_t nmemb, FILE stream) {
		size_t rc = fwrite(ptr, size, nmemb, stream);
		if (rc != nmemb) {
		EPRINTF(EPLACE," Error writing %zu elements (of size %zu)\n", nmemb, size);
		exit(1);
		}
		}

		static void Fclose(FILE *stream) {
		// An error in fclose() could be caused by an earlier failure in fwrite().
		// 'man fclose' for details.
		int rc = fclose(stream);
		if (rc != 0) {
		EPRINTF(EPLACE," Error closing stream.\n");
		exit(1);
		}
		}

		static void reheap(int s, Overlap **heap, int hsize)
		{ int c, l, r;
		int bigger;
		@@ -288,8 +306,8 @@ int main(int argc, char *argv[])
		free(pwd);
		free(root);

		fwrite(&totl,sizeof(int64),1,output);
		fwrite(&tspace,sizeof(int),1,output);
		Fwrite(&totl,sizeof(int64),1,output);
		Fwrite(&tspace,sizeof(int),1,output);

		oblock = block+fway*bsize;
		optr = oblock;
		@@ -351,7 +369,7 @@ int main(int argc, char *argv[])
		if (src->ptr + span > src->top)
		ovl_reload(src,bsize);
		if (optr + span > otop)
		{ fwrite(oblock,1,optr-oblock,output);
		{ Fwrite(oblock,1,optr-oblock,output);
		optr = oblock;
		}

		@@ -375,8 +393,8 @@ int main(int argc, char *argv[])
		// Flush output buffer and wind up

		if (optr > oblock)
		fwrite(oblock,1,optr-oblock,output);
		fclose(output);
		Fwrite(oblock,1,optr-oblock,output);
		Fclose(output);

		for (i = 0; i < fway; i++)
		fclose(in[i].stream);

DALIGNER/LAsort.c

+23 −5

Original line number	Diff line number	Diff line
		@@ -25,6 +25,24 @@ static char *Usage = "[-va] <align:las> ...";

		static char *IBLOCK;

		static void Fwrite(const void ptr, size_t size, size_t nmemb, FILE stream) {
		size_t rc = fwrite(ptr, size, nmemb, stream);
		if (rc != nmemb) {
		EPRINTF(EPLACE," Error writing %zu elements (of size %zu)\n", nmemb, size);
		exit(1);
		}
		}

		static void Fclose(FILE *stream) {
		// An error in fclose() could be caused by an earlier failure in fwrite().
		// 'man fclose' for details.
		int rc = fclose(stream);
		if (rc != 0) {
		EPRINTF(EPLACE," Error closing stream.\n");
		exit(1);
		}
		}

		static int SORT_OVL(const void x, const void y)
		{ int64 l = ((int64 ) x);
		int64 r = ((int64 ) y);
		@@ -182,8 +200,8 @@ int main(int argc, char *argv[])
		if (foutput == NULL)
		exit (1);

		fwrite(&novl,sizeof(int64),1,foutput);
		fwrite(&tspace,sizeof(int),1,foutput);
		Fwrite(&novl,sizeof(int64),1,foutput);
		Fwrite(&tspace,sizeof(int),1,foutput);

		free(pwd);
		free(root);
		@@ -258,7 +276,7 @@ int main(int argc, char *argv[])
		{ tsize = w->path.tlen*tbytes;
		span = ovlsize + tsize;
		if (fptr + span > ftop)
		{ fwrite(fblock,1,fptr-fblock,foutput);
		{ Fwrite(fblock,1,fptr-fblock,foutput);
		fptr = fblock;
		}
		memcpy(fptr,((char *) w)+ptrsize,ovlsize);
		@@ -270,11 +288,11 @@ int main(int argc, char *argv[])
		while (wo < iend && CHAIN_NEXT(w->flags));
		}
		if (fptr > fblock)
		fwrite(fblock,1,fptr-fblock,foutput);
		Fwrite(fblock,1,fptr-fblock,foutput);
		}

		free(perm);
		fclose(foutput);
		Fclose(foutput);
		}

		if (iblock != NULL)

DALIGNER/README

+14 −0

Original line number	Diff line number	Diff line
		@@ -519,3 +519,17 @@ G: 62,654 records
		1 464 n [ 0.. 1,942] x [12,416..14,281] : < 411 diffs ( 19 trace pts)

		...

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