kbychkov

# Create `gh-pages` branch from scratch

cd <dir>
git init
git remote add origin <url>
git checkout --orphan gh-pages

git add .
git commit -m "build 1.0.0"
git push origin gh-pages

clausecker

#define _XOPEN_SOURCE 700
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <time.h>

extern void pospopcnt_reg(int accum[8], const char *buf, size_t len);
extern void pospopcnt_mem(int accum[8], const char *buf, size_t len);

extern void

clausecker

#include "textflag.h"

// func PospopcntMem(counts *[8]int32, buf []byte)
TEXT ·PospopcntMem(SB),NOSPLIT,$0-32
	MOVQ counts+0(FP), DI
	MOVQ buf_base+8(FP), SI		// SI = &buf[0]
	MOVQ buf_len+16(FP), CX		// CX = len(buf)

	SUBQ $32, CX			// pre-subtract 32 bit from CX
	JL scalar

pmenzel

#!/usr/bin/env perl
#
# rotates and (if necessary reverse complements) an assembly of a circular genome
# so that it starts with the sequence having the best blast hit to a gene database,
# e.g. dnaA
#
# depends on blastn being installed
#
# Example usage:
# rotate_assembly.pl assembly.fasta  dnaA.fa > rotated_assembly.fa

apcamargo

#!/usr/bin/env python

"""
This script processes SAM (Sequence Alignment/Map format) inputs from standard
input and extracts alignment information that is then provided in a tab-separated
table. The following fields are produced: query, target, query_length, query_start,
query_end, target_start, target_end, alignment_length, alignment_identity.

This script was designed for use with SAM files produced by minimap2. However,
it will work with any SAM data that: