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Mario Kostelac mariokostelac

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mariokostelac / croler.coords
Created January 11, 2015 23:35
/Users/mario/Downloads/results/K03455.fasta /Users/mario/Downloads/results/croler.fasta
NUCMER
[S1] [E1] | [S2] [E2] | [LEN 1] [LEN 2] | [% IDY] | [COV R] [COV Q] | [TAGS]
==========================================================================================================
6487 6744 | 1 255 | 258 255 | 89.15 | 2.65 98.08 | K03455 1
5344 5661 | 318 1 | 318 318 | 94.03 | 3.27 99.69 | K03455 2
6446 6704 | 258 3 | 259 256 | 90.35 | 2.66 99.22 | K03455 4
6499 6764 | 265 3 | 266 263 | 89.10 | 2.74 99.25 | K03455 7
9002 9222 | 190 410 | 221 221 | 91.86 | 2.27 53.90 | K03455 8
@mariokostelac
mariokostelac / nth_read.sh
Created August 20, 2015 11:48
#!/usr/bin/env bash
head -n $(($(($1+1))*2)) | tail -n 2
@mariokostelac
mariokostelac / extract_reads.sh
Created September 4, 2015 14:23
#!/usr/bin/env bash
output_dir=${1-.}
DONE=false
i=0
until $DONE; do
read header || DONE=true
read seq || DONE=true
echo $header > $output_dir/$i.fasta
@mariokostelac
mariokostelac / ovlstore2afg.sh
Created September 13, 2015 20:13
#!/usr/bin/env bash
awk '{printf "{OVL\nadj:%c\nrds:%d,%d\nahg:%d\nbhg:%d\n}\n", $3, $1-1, $2-1, $4, $5}'
@mariokostelac
mariokostelac / mhap2partial.sh
Last active September 15, 2015 21:49
#!/usr/bin/env bash
awk '
{printf "%d\t", $1 + 1} #Aiid
{printf "%d\t", $2 + 1} #Biid
{if ($5 == $9) { # orient
printf "f\t"
} else {
printf "r\t"
}}
@mariokostelac
mariokostelac / -
Created September 27, 2015 22:13
20| 10 (0.15%) ---
21| 21 (0.31%) ------
22| 45 (0.66%) ------------
23| 76 (1.12%) --------------------
24|130 (1.92%) -----------------------------------
25|200 (2.95%) -----------------------------------------------------
26|258 (3.81%) --------------------------------------------------------------------
27|308 (4.54%) ---------------------------------------------------------------------------------
28|360 (5.31%) -----------------------------------------------------------------------------------------------
29|444 (6.55%) ---------------------------------------------------------------------------------------------------------------------
@mariokostelac
mariokostelac / -
Created September 27, 2015 22:13
20| 10 (0.15%) ---
21| 21 (0.31%) ------
22| 45 (0.66%) ------------
23| 76 (1.12%) --------------------
24|130 (1.92%) -----------------------------------
25|200 (2.95%) -----------------------------------------------------
26|258 (3.81%) --------------------------------------------------------------------
27|308 (4.54%) ---------------------------------------------------------------------------------
28|360 (5.31%) -----------------------------------------------------------------------------------------------
29|444 (6.55%) ---------------------------------------------------------------------------------------------------------------------
@mariokostelac
mariokostelac / out.report
Created October 26, 2015 11:59
/data/reference/escherichia_coli_NCBI.fa /data/simulated_datasets/ecolli_15x/escherichia_coli_NCBI-e0.00/layout_20151026_115352/dnadiff_results/../contigs_fast.fasta
NUCMER
[REF] [QRY]
[Sequences]
TotalSeqs 1 1
AlignedSeqs 1(100.00%) 1(100.00%)
UnalignedSeqs 0(0.00%) 0(0.00%)
[Bases]
@mariokostelac
mariokostelac / make.log
Created November 11, 2015 20:27
mkdir -p obj_test/src/alignment/
g++-4.8 -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"libs/libdivsufsort-2.0.1/build/include" -I"libs/seqan-library-1.4.2/include" -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -Wuninitialized -pthread -march=native -o obj_test/src/alignment/opal.o src/alignment/opal.cpp
/var/folders/1v/mxp10j955jzc7s812dt7l9f80000gn/T//cc6Iljv3.s:156:no such instruction: `vpxor %xmm12, %xmm12,%xmm12'
/var/folders/1v/mxp10j955jzc7s812dt7l9f80000gn/T//cc6Iljv3.s:158:no such instruction: `vmovd %eax, %xmm0'
/var/folders/1v/mxp10j955jzc7s812dt7l9f80000gn/T//cc6Iljv3.s:162:no such instruction: `vpshufb %xmm12, %xmm0,%xmm12'
/var/folders/1v/mxp10j955jzc7s812dt7l9f80000gn/T//cc6Iljv3.s:206:no such instruction: `vpxor %xmm0, %xmm0,%xmm0'
/var/folders/1v/mxp10j955jzc7s812dt7l9f80000gn/T//cc6Iljv3.s:212:no such instruction: `vmovd %r14d, %xmm1'
/var/folders/1v/mxp10j955jzc7s812dt7l9f8000
@mariokostelac
mariokostelac / out.report
Created December 19, 2015 17:57
/Users/mario/bioinf/nmeth/../reference/escherichia_coli_NCBI.fa /Users/mario/bioinf/nmeth/contigs_fast.fasta
NUCMER
[REF] [QRY]
[Sequences]
TotalSeqs 1 1
AlignedSeqs 1(100.00%) 1(100.00%)
UnalignedSeqs 0(0.00%) 0(0.00%)
[Bases]