View fixFTDNAbam.sh
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#!/bin/bash | |
# | |
# Fixes FTDNA BAM version 1 files so can be processed by standard bioinformatic tools. | |
# Applies only to Bigy files (not needed for Bigy2 or Bigy3) | |
# | |
# This is handled behind the scenes (automagically) by WGS Extract (in the next release) | |
# Simply a stand-alone. simple scenario script installation for demonstration purposes here | |
# | |
# Relies on htslib bgzip and samtools; along with wget, python rm, zip and unzip. |
View countingNs.py
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# coding: utf8 | |
# Copyright (C) 2022 Randy Harr | |
# | |
# License: GNU General Public License v3 or later | |
# A copy of GNU GPL v3 should have been included in this software package in LICENSE.txt. | |
""" | |
Standalone script to process a reference model FASTA to determine the inclusion of N's in the base pair sequence. | |
Reads the compressed FASTA. Takes as a parameter the FASTA file. Also expects and reads in the DICT file determined | |
from the FASTA file name -- easier to do one pass if we have the sequence lengths. Processes all sequences. |