Commit f5137c3d authored by Andreas Tille's avatar Andreas Tille
Browse files

New upstream version 1.2.10a

parent 624ab077

KMAspecification.pdf

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Makefile

+5 −4
Original line number Diff line number Diff line 
CFLAGS = -Wall -O3 -std=c99

LIBS = align.o alnfrags.o ankers.o assembly.o chain.o compdna.o compkmers.o compress.o decon.o ef.o filebuff.o frags.o hashmap.o hashmapindex.o hashmapkma.o hashmapkmers.o hashtable.o index.o kma.o kmapipe.o kmers.o kmmap.o loadupdate.o makeindex.o mt1.o nw.o pherror.o printconsensus.o qseqs.o qualcheck.o runinput.o runkma.o sam.o savekmers.o seq2fasta.o seqparse.o shm.o sparse.o spltdb.o stdnuc.o stdstat.o update.o updateindex.o updatescores.o valueshash.o vcf.o

LIBS = align.o alnfrags.o ankers.o assembly.o chain.o compdna.o compkmers.o compress.o decon.o ef.o filebuff.o frags.o hashmap.o hashmapindex.o hashmapkma.o hashmapkmers.o hashtable.o index.o kma.o kmapipe.o kmers.o kmmap.o loadupdate.o makeindex.o mt1.o nw.o pherror.o printconsensus.o qseqs.o qualcheck.o runinput.o runkma.o sam.o savekmers.o seq2fasta.o seqparse.o shm.o sparse.o spltdb.o stdnuc.o stdstat.o tmp.o update.o updateindex.o updatescores.o valueshash.o vcf.o

PROGS = kma kma_index kma_shm kma_update



.c .o:
@@ -43,7 +43,7 @@ hashmapkma.o: hashmapkma.h pherror.h 
hashmapkmers.o: hashmapkmers.h pherror.h

hashtable.o: hashtable.h hashmapkma.h hashmapkmers.h pherror.h

index.o: index.h compress.h decon.h hashmap.h hashmapkma.h loadupdate.h makeindex.h pherror.h stdstat.h version.h

kma.o: kma.h ankers.h assembly.h chain.h hashmapkma.h kmers.h mt1.h penalties.h pherror.h qseqs.h runinput.h runkma.h savekmers.h sparse.h spltdb.h version.h

kma.o: kma.h ankers.h assembly.h chain.h hashmapkma.h kmers.h mt1.h penalties.h pherror.h qseqs.h runinput.h runkma.h savekmers.h sparse.h spltdb.h tmp.h version.h

kmapipe.o: kmapipe.h pherror.h

kmers.o: kmers.h ankers.h compdna.h hashmapkma.h kmapipe.h pherror.h qseqs.h savekmers.h spltdb.h

kmmap.o: kmmap.h hashmapkma.h
@@ -56,16 +56,17 @@ printconsensus.o: printconsensus.h assembly.h 
qseqs.o: qseqs.h pherror.h

qualcheck.o: qualcheck.h compdna.h hashmap.h pherror.h stdnuc.h stdstat.h

runinput.o: runinput.h compdna.h filebuff.h pherror.h qseqs.h seqparse.h

runkma.o: runkma.h align.h alnfrags.h assembly.h chain.h compdna.h ef.h filebuff.h frags.h hashmapindex.h kmapipe.h nw.h pherror.h printconsensus.h qseqs.h stdnuc.h stdstat.h vcf.h

runkma.o: runkma.h align.h alnfrags.h assembly.h chain.h compdna.h ef.h filebuff.h frags.h hashmapindex.h kmapipe.h nw.h pherror.h printconsensus.h qseqs.h stdnuc.h stdstat.h tmp.h vcf.h

sam.o: sam.h nw.h pherror.h qseqs.h runkma.h

savekmers.o: savekmers.h ankers.h compdna.h hashmapkma.h penalties.h pherror.h qseqs.h stdnuc.h stdstat.h threader.h

seq2fasta.o: seq2fasta.h pherror.h qseqs.h runkma.h stdnuc.h

seqparse.o: seqparse.h filebuff.h qseqs.h

shm.o: shm.h pherror.h hashmapkma.h version.h

sparse.o: sparse.h compkmers.h hashtable.h kmapipe.h pherror.h runinput.h savekmers.h stdnuc.h stdstat.h

spltdb.o: spltdb.h align.h alnfrags.h assembly.h chain.h compdna.h ef.h filebuff.h frags.h hashmapindex.h kmapipe.h nw.h pherror.h printconsensus.h qseqs.h runkma.h stdnuc.h stdstat.h vcf.h

spltdb.o: spltdb.h align.h alnfrags.h assembly.h chain.h compdna.h ef.h filebuff.h frags.h hashmapindex.h kmapipe.h nw.h pherror.h printconsensus.h qseqs.h runkma.h stdnuc.h stdstat.h tmp.h vcf.h

stdnuc.o: stdnuc.h

stdstat.o: stdstat.h

tmp.o: tmp.h pherror.h threader.h

update.o: update.h hashmapkma.h pherror.h stdnuc.h

updateindex.o: updateindex.h compdna.h hashmap.h hashmapindex.h pherror.h qualcheck.h stdnuc.h pherror.h

updatescores.o: updatescores.h qseqs.h

align.c

+6 −0
Original line number Diff line number Diff line
@@ -48,6 +48,7 @@ AlnScore KMA(const HashMap_index *template_index, const unsigned char *qseq, int 
	mask = 0;

	mask = (~mask) >> (sizeof(long unsigned) * sizeof(long unsigned) - (kmersize << 1));

	key = 0;

	

	/* circular, skip boundaries */

	if(min < max) {

		min = 0;
@@ -757,6 +758,7 @@ int anker_rc(const HashMap_index *template_index, unsigned char *qseq, int q_len 
			if(end == -1) {

				end = q_len;

			}

			

			if(i < end - kmersize) {

				key = makeKmer(qseq, i, kmersize - 1);

				i += (kmersize - 1);
@@ -767,6 +769,7 @@ int anker_rc(const HashMap_index *template_index, unsigned char *qseq, int q_len 
			while(i < end) {

				key = ((key << 2) | qseq[i]) & mask;

				value = hashMap_index_get_bound(template_index, key, 0, t_len, shifter);

				

				if(value == 0) {

					++i;

				} else if(0 < value) {
@@ -870,6 +873,8 @@ int anker_rc(const HashMap_index *template_index, unsigned char *qseq, int q_len 
						

						stop = hashMap_index_getNextDubPos(template_index, key, 0, t_len, stop, shifter);

					}

					/* add best anker score */

					score_r += (bias - i);

					i = bias + 1;

					

					/* update position */
@@ -883,6 +888,7 @@ int anker_rc(const HashMap_index *template_index, unsigned char *qseq, int q_len 
			}

			i = end + 1;

		}

		

		if(bestScore < score_r) {

			bestScore = score_r;

		}

compress.c

+1 −0
Original line number Diff line number Diff line
@@ -702,6 +702,7 @@ HashMapKMA * compressKMA_megaDB(HashMap *templates, FILE *out) { 
		fprintf(stderr, "# Overflow bypassed.\n");

	}

	free(templates->values);

	

	/* convert valuesHash to a linked list */

	table = 0;

	i = shmValues->size;

frags.c

+2 −1
Original line number Diff line number Diff line
@@ -24,6 +24,7 @@ 
#include "pherror.h"

#include "qseqs.h"

#include "threader.h"

#include "tmp.h"



FILE * printFrags(Frag **alignFrags, int DB_size) {
@@ -31,7 +32,7 @@ FILE * printFrags(Frag **alignFrags, int DB_size) { 
	FILE *OUT;

	Frag *alignFrag, *next;

	

	if(!(OUT = tmpfile())) {

	if(!(OUT = tmpF(0))) {

		fprintf(stderr, "Could not create tmp files.\n");

		ERROR();

	}