Commit 89afb8f0 authored by Andreas Tille's avatar Andreas Tille
Browse files

New upstream version 0.3+dfsg

parent 91ca2a64

Makefile

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CC=			gcc

CFLAGS=		-g -Wall -O2 -Wc++-compat -Wno-unused-function

CFLAGS=		-g -Wall -O2 -Wc++-compat

CPPFLAGS=

INCLUDES=	-I.

OBJS=		sys.o sdict.o paf.o asg.o common.o hit.o asm.o

PAF.md

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@@ -22,7 +22,7 @@ following predefined fields: 
If PAF is generated from an alignment, column 10 equals the number of sequence

matches, and column 11 equals the total number of sequence matches, mismatches,

insertions and deletions in the alignment. If alignment is not available,

column 10 and 11 are still required but can be approximate.

column 10 and 11 are still required but may be highly inaccurate.



A PAF file may optionally contain SAM-like typed key-value pairs at the end of

each line.

README.md

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*Warning: since r104, miniasm only works with minimap-r122 or later*



## Getting Started



```sh
@@ -7,10 +5,10 @@ 
wget -O- http://www.cbcb.umd.edu/software/PBcR/data/selfSampleData.tar.gz | tar zxf -

ln -s selfSampleData/pacbio_filtered.fastq reads.fq

# Install minimap and miniasm (requiring gcc and zlib)

git clone https://github.com/lh3/minimap && (cd minimap && make)

git clone https://github.com/lh3/minimap2 && (cd minimap2 && make)

git clone https://github.com/lh3/miniasm  && (cd miniasm  && make)

# Overlap

minimap/minimap -Sw5 -L100 -m0 -t8 reads.fq reads.fq | gzip -1 > reads.paf.gz

# Overlap for PacBio reads (or use "-x map-ont" for nanopore read overlapping)

minimap2/minimap2 -x map-pb -t8 pb-reads.fq pb-reads.fq | gzip -1 > reads.paf.gz

# Layout

miniasm/miniasm -f reads.fq reads.paf.gz > reads.gfa

```

asm.c

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@@ -45,10 +45,10 @@ void ma_sg_print(const asg_t *g, const sdict_t *d, const ma_sub_t *sub, FILE *fp 
		const asg_arc_t *p = &g->arc[i];

		if (sub) {

			const ma_sub_t *sq = &sub[p->ul>>33], *st = &sub[p->v>>1];

			fprintf(fp, "L\t%s:%d-%d\t%c\t%s:%d-%d\t%c\t%dM\tSD:i:%d\n", d->seq[p->ul>>33].name, sq->s + 1, sq->e, "+-"[p->ul>>32&1],

			fprintf(fp, "L\t%s:%d-%d\t%c\t%s:%d-%d\t%c\t%d:\tL1:i:%d\n", d->seq[p->ul>>33].name, sq->s + 1, sq->e, "+-"[p->ul>>32&1],

					d->seq[p->v>>1].name, st->s + 1, st->e, "+-"[p->v&1], p->ol, (uint32_t)p->ul);

		} else {

			fprintf(fp, "L\t%s\t%c\t%s\t%c\t%dM\tSD:i:%d\n", d->seq[p->ul>>33].name, "+-"[p->ul>>32&1],

			fprintf(fp, "L\t%s\t%c\t%s\t%c\t%d:\tL1:i:%d\n", d->seq[p->ul>>33].name, "+-"[p->ul>>32&1],

					d->seq[p->v>>1].name, "+-"[p->v&1], p->ol, (uint32_t)p->ul);

		}

	}

common.c

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@@ -8,7 +8,6 @@ void ma_opt_init(ma_opt_t *opt) 
	opt->min_match = 100;

	opt->min_dp = 3;

	opt->min_iden = .05;

	opt->cov_ratio = 0.;



	opt->max_hang = 1000;

	opt->min_ovlp = opt->min_span;