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Changeset 7:890e9a40e2f1 (2014-12-12)

Previous changeset 6:f9f71cf4c3e3 (2014-12-11) Next changeset 8:087e196d6072 (2014-12-12)

Commit message:
Deleted selected files

diff -r f9f71cf4c3e3 -r 890e9a40e2f1 myTools/.git/HEAD
--- a/myTools/.git/HEAD Thu Dec 11 15:42:44 2014 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,1 +0,0 @@
-ref: refs/heads/master

diff -r f9f71cf4c3e3 -r 890e9a40e2f1 myTools/.git/config
--- a/myTools/.git/config Thu Dec 11 15:42:44 2014 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,13 +0,0 @@
-[core]
- repositoryformatversion = 0
- filemode = true
- bare = false
- logallrefupdates = true
- ignorecase = true
- precomposeunicode = true
-[remote "origin"]
- url = https://github.com/mvollger/TRTR.git
- fetch = +refs/heads/*:refs/remotes/origin/*
-[branch "master"]
- remote = origin
- merge = refs/heads/master

diff -r f9f71cf4c3e3 -r 890e9a40e2f1 myTools/.git/description
--- a/myTools/.git/description Thu Dec 11 15:42:44 2014 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,1 +0,0 @@
-Unnamed repository; edit this file 'description' to name the repository.

diff -r f9f71cf4c3e3 -r 890e9a40e2f1 myTools/.git/hooks/applypatch-msg.sample
--- a/myTools/.git/hooks/applypatch-msg.sample Thu Dec 11 15:42:44 2014 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,15 +0,0 @@
-#!/bin/sh
-#
-# An example hook script to check the commit log message taken by
-# applypatch from an e-mail message.
-#
-# The hook should exit with non-zero status after issuing an
-# appropriate message if it wants to stop the commit. The hook is
-# allowed to edit the commit message file.
-#
-# To enable this hook, rename this file to "applypatch-msg".
-
-. git-sh-setup
-test -x "$GIT_DIR/hooks/commit-msg" &&
- exec "$GIT_DIR/hooks/commit-msg" ${1+"$@"}
-:

diff -r f9f71cf4c3e3 -r 890e9a40e2f1 myTools/.git/hooks/commit-msg.sample
--- a/myTools/.git/hooks/commit-msg.sample Thu Dec 11 15:42:44 2014 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,24 +0,0 @@
-#!/bin/sh
-#
-# An example hook script to check the commit log message.
-# Called by "git commit" with one argument, the name of the file
-# that has the commit message. The hook should exit with non-zero
-# status after issuing an appropriate message if it wants to stop the
-# commit. The hook is allowed to edit the commit message file.
-#
-# To enable this hook, rename this file to "commit-msg".
-
-# Uncomment the below to add a Signed-off-by line to the message.
-# Doing this in a hook is a bad idea in general, but the prepare-commit-msg
-# hook is more suited to it.
-#
-# SOB=$(git var GIT_AUTHOR_IDENT | sed -n 's/^$.*>$.*$/Signed-off-by: \1/p')
-# grep -qs "^$SOB" "$1" || echo "$SOB" >> "$1"
-
-# This example catches duplicate Signed-off-by lines.
-
-test "" = "$(grep '^Signed-off-by: ' "$1" |
- sort | uniq -c | sed -e '/^[ ]*1[ ]/d')" || {
- echo >&2 Duplicate Signed-off-by lines.
- exit 1
-}

diff -r f9f71cf4c3e3 -r 890e9a40e2f1 myTools/.git/hooks/post-update.sample
--- a/myTools/.git/hooks/post-update.sample Thu Dec 11 15:42:44 2014 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,8 +0,0 @@
-#!/bin/sh
-#
-# An example hook script to prepare a packed repository for use over
-# dumb transports.
-#
-# To enable this hook, rename this file to "post-update".
-
-exec git update-server-info

diff -r f9f71cf4c3e3 -r 890e9a40e2f1 myTools/.git/hooks/pre-applypatch.sample
--- a/myTools/.git/hooks/pre-applypatch.sample Thu Dec 11 15:42:44 2014 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,14 +0,0 @@
-#!/bin/sh
-#
-# An example hook script to verify what is about to be committed
-# by applypatch from an e-mail message.
-#
-# The hook should exit with non-zero status after issuing an
-# appropriate message if it wants to stop the commit.
-#
-# To enable this hook, rename this file to "pre-applypatch".
-
-. git-sh-setup
-test -x "$GIT_DIR/hooks/pre-commit" &&
- exec "$GIT_DIR/hooks/pre-commit" ${1+"$@"}
-:

diff -r f9f71cf4c3e3 -r 890e9a40e2f1 myTools/.git/hooks/pre-commit.sample
--- a/myTools/.git/hooks/pre-commit.sample Thu Dec 11 15:42:44 2014 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,49 +0,0 @@
-#!/bin/sh
-#
-# An example hook script to verify what is about to be committed.
-# Called by "git commit" with no arguments.  The hook should
-# exit with non-zero status after issuing an appropriate message if
-# it wants to stop the commit.
-#
-# To enable this hook, rename this file to "pre-commit".
-
-if git rev-parse --verify HEAD >/dev/null 2>&1
-then
- against=HEAD
-else
- # Initial commit: diff against an empty tree object
- against=4b825dc642cb6eb9a060e54bf8d69288fbee4904
-fi
-
-# If you want to allow non-ASCII filenames set this variable to true.
-allownonascii=$(git config --bool hooks.allownonascii)
-
-# Redirect output to stderr.
-exec 1>&2
-
-# Cross platform projects tend to avoid non-ASCII filenames; prevent
-# them from being added to the repository. We exploit the fact that the
-# printable range starts at the space character and ends with tilde.
-if [ "$allownonascii" != "true" ] &&
- # Note that the use of brackets around a tr range is ok here, (it's
- # even required, for portability to Solaris 10's /usr/bin/tr), since
- # the square bracket bytes happen to fall in the designated range.
- test $(git diff --cached --name-only --diff-filter=A -z $against |
-   LC_ALL=C tr -d '[ -~]\0' | wc -c) != 0
-then
- cat <<\EOF
-Error: Attempt to add a non-ASCII file name.
-
-This can cause problems if you want to work with people on other platforms.
-
-To be portable it is advisable to rename the file.
-
-If you know what you are doing you can disable this check using:
-
-  git config hooks.allownonascii true
-EOF
- exit 1
-fi
-
-# If there are whitespace errors, print the offending file names and fail.
-exec git diff-index --check --cached $against --

diff -r f9f71cf4c3e3 -r 890e9a40e2f1 myTools/.git/hooks/pre-push.sample
--- a/myTools/.git/hooks/pre-push.sample Thu Dec 11 15:42:44 2014 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,54 +0,0 @@
-#!/bin/sh
-
-# An example hook script to verify what is about to be pushed.  Called by "git
-# push" after it has checked the remote status, but before anything has been
-# pushed.  If this script exits with a non-zero status nothing will be pushed.
-#
-# This hook is called with the following parameters:
-#
-# $1 -- Name of the remote to which the push is being done
-# $2 -- URL to which the push is being done
-#
-# If pushing without using a named remote those arguments will be equal.
-#
-# Information about the commits which are being pushed is supplied as lines to
-# the standard input in the form:
-#
-#   <local ref> <local sha1> <remote ref> <remote sha1>
-#
-# This sample shows how to prevent push of commits where the log message starts
-# with "WIP" (work in progress).
-
-remote="$1"
-url="$2"
-
-z40=0000000000000000000000000000000000000000
-
-IFS=' '
-while read local_ref local_sha remote_ref remote_sha
-do
- if [ "$local_sha" = $z40 ]
- then
- # Handle delete
- :
- else
- if [ "$remote_sha" = $z40 ]
- then
- # New branch, examine all commits
- range="$local_sha"
- else
- # Update to existing branch, examine new commits
- range="$remote_sha..$local_sha"
- fi
-
- # Check for WIP commit
- commit=`git rev-list -n 1 --grep '^WIP' "$range"`
- if [ -n "$commit" ]
- then
- echo >&2 "Found WIP commit in $local_ref, not pushing"
- exit 1
- fi
- fi
-done
-
-exit 0

diff -r f9f71cf4c3e3 -r 890e9a40e2f1 myTools/.git/hooks/pre-rebase.sample
--- a/myTools/.git/hooks/pre-rebase.sample Thu Dec 11 15:42:44 2014 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,169 +0,0 @@
-#!/bin/sh
-#
-# Copyright (c) 2006, 2008 Junio C Hamano
-#
-# The "pre-rebase" hook is run just before "git rebase" starts doing
-# its job, and can prevent the command from running by exiting with
-# non-zero status.
-#
-# The hook is called with the following parameters:
-#
-# $1 -- the upstream the series was forked from.
-# $2 -- the branch being rebased (or empty when rebasing the current branch).
-#
-# This sample shows how to prevent topic branches that are already
-# merged to 'next' branch from getting rebased, because allowing it
-# would result in rebasing already published history.
-
-publish=next
-basebranch="$1"
-if test "$#" = 2
-then
- topic="refs/heads/$2"
-else
- topic=`git symbolic-ref HEAD` ||
- exit 0 ;# we do not interrupt rebasing detached HEAD
-fi
-
-case "$topic" in
-refs/heads/??/*)
- ;;
-*)
- exit 0 ;# we do not interrupt others.
- ;;
-esac
-
-# Now we are dealing with a topic branch being rebased
-# on top of master.  Is it OK to rebase it?
-
-# Does the topic really exist?
-git show-ref -q "$topic" || {
- echo >&2 "No such branch $topic"
- exit 1
-}
-
-# Is topic fully merged to master?
-not_in_master=`git rev-list --pretty=oneline ^master "$topic"`
-if test -z "$not_in_master"
-then
- echo >&2 "$topic is fully merged to master; better remove it."
- exit 1 ;# we could allow it, but there is no point.
-fi
-
-# Is topic ever merged to next?  If so you should not be rebasing it.
-only_next_1=`git rev-list ^master "^$topic" ${publish} | sort`
-only_next_2=`git rev-list ^master           ${publish} | sort`
-if test "$only_next_1" = "$only_next_2"
-then
- not_in_topic=`git rev-list "^$topic" master`
- if test -z "$not_in_topic"
- then
- echo >&2 "$topic is already up-to-date with master"
- exit 1 ;# we could allow it, but there is no point.
- else
- exit 0
- fi
-else
- not_in_next=`git rev-list --pretty=oneline ^${publish} "$topic"`
- /usr/bin/perl -e '
- my $topic = $ARGV[0];
- my $msg = "* $topic has commits already merged to public branch:\n";
- my (%not_in_next) = map {
- /^([0-9a-f]+) /;
- ($1 => 1);
- } split(/\n/, $ARGV[1]);
- for my $elem (map {
- /^([0-9a-f]+) (.*)$/;
- [$1 => $2];
- } split(/\n/, $ARGV[2])) {
- if (!exists $not_in_next{$elem->[0]}) {
- if ($msg) {
- print STDERR $msg;
- undef $msg;
- }
- print STDERR " $elem->[1]\n";
- }
- }
- ' "$topic" "$not_in_next" "$not_in_master"
- exit 1
-fi
-
-exit 0
-
-################################################################
-
-This sample hook safeguards topic branches that have been
-published from being rewound.
-
-The workflow assumed here is:
-
- * Once a topic branch forks from "master", "master" is never
-   merged into it again (either directly or indirectly).
-
- * Once a topic branch is fully cooked and merged into "master",
-   it is deleted.  If you need to build on top of it to correct
-   earlier mistakes, a new topic branch is created by forking at
-   the tip of the "master".  This is not strictly necessary, but
-   it makes it easier to keep your history simple.
-
- * Whenever you need to test or publish your changes to topic
-   branches, merge them into "next" branch.
-
-The script, being an example, hardcodes the publish branch name
-to be "next", but it is trivial to make it configurable via
-$GIT_DIR/config mechanism.
-
-With this workflow, you would want to know:
-
-(1) ... if a topic branch has ever been merged to "next".  Young
-    topic branches can have stupid mistakes you would rather
-    clean up before publishing, and things that have not been
-    merged into other branches can be easily rebased without
-    affecting other people.  But once it is published, you would
-    not want to rewind it.
-
-(2) ... if a topic branch has been fully merged to "master".
-    Then you can delete it.  More importantly, you should not
-    build on top of it -- other people may already want to
-    change things related to the topic as patches against your
-    "master", so if you need further changes, it is better to
-    fork the topic (perhaps with the same name) afresh from the
-    tip of "master".
-
-Let's look at this example:
-
-    o---o---o---o---o---o---o---o---o---o "next"
-   /       /           /           /
- /   a---a---b A     /           /
- /   /               /           /
-        /   /   c---c---c---c B         /
-       /   /   /             \         /
-      /   /   /   b---b C     \       /
-     /   /   /   /             \     /
-    ---o---o---o---o---o---o---o---o---o---o---o "master"
-
-
-A, B and C are topic branches.
-
- * A has one fix since it was merged up to "next".
-
- * B has finished.  It has been fully merged up to "master" and "next",
-   and is ready to be deleted.
-
- * C has not merged to "next" at all.
-
-We would want to allow C to be rebased, refuse A, and encourage
-B to be deleted.
-
-To compute (1):
-
- git rev-list ^master ^topic next
- git rev-list ^master        next
-
- if these match, topic has not merged in next at all.
-
-To compute (2):
-
- git rev-list master..topic
-
- if this is empty, it is fully merged to "master".

diff -r f9f71cf4c3e3 -r 890e9a40e2f1 myTools/.git/hooks/prepare-commit-msg.sample
--- a/myTools/.git/hooks/prepare-commit-msg.sample Thu Dec 11 15:42:44 2014 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,36 +0,0 @@
-#!/bin/sh
-#
-# An example hook script to prepare the commit log message.
-# Called by "git commit" with the name of the file that has the
-# commit message, followed by the description of the commit
-# message's source.  The hook's purpose is to edit the commit
-# message file.  If the hook fails with a non-zero status,
-# the commit is aborted.
-#
-# To enable this hook, rename this file to "prepare-commit-msg".
-
-# This hook includes three examples.  The first comments out the
-# "Conflicts:" part of a merge commit.
-#
-# The second includes the output of "git diff --name-status -r"
-# into the message, just before the "git status" output.  It is
-# commented because it doesn't cope with --amend or with squashed
-# commits.
-#
-# The third example adds a Signed-off-by line to the message, that can
-# still be edited.  This is rarely a good idea.
-
-case "$2,$3" in
-  merge,)
-    /usr/bin/perl -i.bak -ne 's/^/# /, s/^# #/#/ if /^Conflicts/ .. /#/; print' "$1" ;;
-
-# ,|template,)
-#   /usr/bin/perl -i.bak -pe '
-#      print "\n" . `git diff --cached --name-status -r`
-# if /^#/ && $first++ == 0' "$1" ;;
-
-  *) ;;
-esac
-
-# SOB=$(git var GIT_AUTHOR_IDENT | sed -n 's/^$.*>$.*$/Signed-off-by: \1/p')
-# grep -qs "^$SOB" "$1" || echo "$SOB" >> "$1"

diff -r f9f71cf4c3e3 -r 890e9a40e2f1 myTools/.git/hooks/update.sample
--- a/myTools/.git/hooks/update.sample Thu Dec 11 15:42:44 2014 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,128 +0,0 @@
-#!/bin/sh
-#
-# An example hook script to blocks unannotated tags from entering.
-# Called by "git receive-pack" with arguments: refname sha1-old sha1-new
-#
-# To enable this hook, rename this file to "update".
-#
-# Config
-# ------
-# hooks.allowunannotated
-#   This boolean sets whether unannotated tags will be allowed into the
-#   repository.  By default they won't be.
-# hooks.allowdeletetag
-#   This boolean sets whether deleting tags will be allowed in the
-#   repository.  By default they won't be.
-# hooks.allowmodifytag
-#   This boolean sets whether a tag may be modified after creation. By default
-#   it won't be.
-# hooks.allowdeletebranch
-#   This boolean sets whether deleting branches will be allowed in the
-#   repository.  By default they won't be.
-# hooks.denycreatebranch
-#   This boolean sets whether remotely creating branches will be denied
-#   in the repository.  By default this is allowed.
-#
-
-# --- Command line
-refname="$1"
-oldrev="$2"
-newrev="$3"
-
-# --- Safety check
-if [ -z "$GIT_DIR" ]; then
- echo "Don't run this script from the command line." >&2
- echo " (if you want, you could supply GIT_DIR then run" >&2
- echo "  $0 <ref> <oldrev> <newrev>)" >&2
- exit 1
-fi
-
-if [ -z "$refname" -o -z "$oldrev" -o -z "$newrev" ]; then
- echo "usage: $0 <ref> <oldrev> <newrev>" >&2
- exit 1
-fi
-
-# --- Config
-allowunannotated=$(git config --bool hooks.allowunannotated)
-allowdeletebranch=$(git config --bool hooks.allowdeletebranch)
-denycreatebranch=$(git config --bool hooks.denycreatebranch)
-allowdeletetag=$(git config --bool hooks.allowdeletetag)
-allowmodifytag=$(git config --bool hooks.allowmodifytag)
-
-# check for no description
-projectdesc=$(sed -e '1q' "$GIT_DIR/description")
-case "$projectdesc" in
-"Unnamed repository"* | "")
- echo "*** Project description file hasn't been set" >&2
- exit 1
- ;;
-esac
-
-# --- Check types
-# if $newrev is 0000...0000, it's a commit to delete a ref.
-zero="0000000000000000000000000000000000000000"
-if [ "$newrev" = "$zero" ]; then
- newrev_type=delete
-else
- newrev_type=$(git cat-file -t $newrev)
-fi
-
-case "$refname","$newrev_type" in
- refs/tags/*,commit)
- # un-annotated tag
- short_refname=${refname##refs/tags/}
- if [ "$allowunannotated" != "true" ]; then
- echo "*** The un-annotated tag, $short_refname, is not allowed in this repository" >&2
- echo "*** Use 'git tag [ -a | -s ]' for tags you want to propagate." >&2
- exit 1
- fi
- ;;
- refs/tags/*,delete)
- # delete tag
- if [ "$allowdeletetag" != "true" ]; then
- echo "*** Deleting a tag is not allowed in this repository" >&2
- exit 1
- fi
- ;;
- refs/tags/*,tag)
- # annotated tag
- if [ "$allowmodifytag" != "true" ] && git rev-parse $refname > /dev/null 2>&1
- then
- echo "*** Tag '$refname' already exists." >&2
- echo "*** Modifying a tag is not allowed in this repository." >&2
- exit 1
- fi
- ;;
- refs/heads/*,commit)
- # branch
- if [ "$oldrev" = "$zero" -a "$denycreatebranch" = "true" ]; then
- echo "*** Creating a branch is not allowed in this repository" >&2
- exit 1
- fi
- ;;
- refs/heads/*,delete)
- # delete branch
- if [ "$allowdeletebranch" != "true" ]; then
- echo "*** Deleting a branch is not allowed in this repository" >&2
- exit 1
- fi
- ;;
- refs/remotes/*,commit)
- # tracking branch
- ;;
- refs/remotes/*,delete)
- # delete tracking branch
- if [ "$allowdeletebranch" != "true" ]; then
- echo "*** Deleting a tracking branch is not allowed in this repository" >&2
- exit 1
- fi
- ;;
- *)
- # Anything else (is there anything else?)
- echo "*** Update hook: unknown type of update to ref $refname of type $newrev_type" >&2
- exit 1
- ;;
-esac
-
-# --- Finished
-exit 0

diff -r f9f71cf4c3e3 -r 890e9a40e2f1 myTools/.git/index

Binary file myTools/.git/index has changed

diff -r f9f71cf4c3e3 -r 890e9a40e2f1 myTools/.git/info/exclude
--- a/myTools/.git/info/exclude Thu Dec 11 15:42:44 2014 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,6 +0,0 @@
-# git ls-files --others --exclude-from=.git/info/exclude
-# Lines that start with '#' are comments.
-# For a project mostly in C, the following would be a good set of
-# exclude patterns (uncomment them if you want to use them):
-# *.[oa]
-# *~

diff -r f9f71cf4c3e3 -r 890e9a40e2f1 myTools/.git/logs/HEAD
--- a/myTools/.git/logs/HEAD Thu Dec 11 15:42:44 2014 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,1 +0,0 @@
-0000000000000000000000000000000000000000 18ed489cf4214dad15282176452bb12ce7d91e6e Mitchell <mrvollger@gmail.com> 1418330085 -0500 clone: from https://github.com/mvollger/TRTR.git

diff -r f9f71cf4c3e3 -r 890e9a40e2f1 myTools/.git/logs/refs/heads/master
--- a/myTools/.git/logs/refs/heads/master Thu Dec 11 15:42:44 2014 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,1 +0,0 @@
-0000000000000000000000000000000000000000 18ed489cf4214dad15282176452bb12ce7d91e6e Mitchell <mrvollger@gmail.com> 1418330085 -0500 clone: from https://github.com/mvollger/TRTR.git

diff -r f9f71cf4c3e3 -r 890e9a40e2f1 myTools/.git/logs/refs/remotes/origin/HEAD
--- a/myTools/.git/logs/refs/remotes/origin/HEAD Thu Dec 11 15:42:44 2014 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,1 +0,0 @@
-0000000000000000000000000000000000000000 18ed489cf4214dad15282176452bb12ce7d91e6e Mitchell <mrvollger@gmail.com> 1418330085 -0500 clone: from https://github.com/mvollger/TRTR.git

diff -r f9f71cf4c3e3 -r 890e9a40e2f1 myTools/.git/objects/10/78740a0afb61b2ac8a8928fae3c4f467eaf7d3
--- a/myTools/.git/objects/10/78740a0afb61b2ac8a8928fae3c4f467eaf7d3 Thu Dec 11 15:42:44 2014 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,1 +0,0 @@
-xE�QN$1D�F�?-Hp�]�pwWw%v6v��qz�ݿ8��U/Cց�_��d䪙�˄e��ܴd2ҙ6��D��dL�D'��]{��׆#$��}��Ӥ��*��ˮPmX��yg�i�k�a�B�gWJ"<�[c��c4r�v��~��}��QY|�H��f�C�mz�r�R ��D��O��4��#nI�w��'u"۸��$�@�8��?�#�L{��ti\�Q��r��'�Vw��B��<8t;��HtwDO}&�D�w��M�M��<o��,�;j\��eȧ��v��OC0��
\ No newline at end of file

diff -r f9f71cf4c3e3 -r 890e9a40e2f1 myTools/.git/objects/18/ed489cf4214dad15282176452bb12ce7d91e6e

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-# pack-refs with: peeled fully-peeled
-18ed489cf4214dad15282176452bb12ce7d91e6e refs/remotes/origin/master

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-ref: refs/remotes/origin/master

diff -r f9f71cf4c3e3 -r 890e9a40e2f1 myTools/README.md
--- a/myTools/README.md Thu Dec 11 15:42:44 2014 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,7 +0,0 @@
-This tool removes tandem repeats from ends of unaligned sequencing reads (leaving one copy). This prevents reads that don't span the repeated region from overlapping and leading to innaccurate SNPs calls.
-
-The maximimum repeat length is adjustable (use 1 to trim only homopolymers).
-
-The "aggressive" option should not be touched in general. Setting to 0 will prevent the program from trimming to exactly 1 copy of the repeat, instead leaving between 1 and 2 copies.
-
-This could also be a useful first step before assembly. More testing needs to be done.

diff -r f9f71cf4c3e3 -r 890e9a40e2f1 myTools/test-data/medium.fastq
--- a/myTools/test-data/medium.fastq Thu Dec 11 15:42:44 2014 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b"@@ -1,30000 +0,0 @@\n-@HWI-ST387:145:B013JABXX:1:1101:1428:2120 1:N:0:\n-TTCTCCTTGCGGGGTCCCGGCTGGGGCCGGGACTAAATATTTTATATATTTATTAATTAAATATTTATCTATTAAATAAAAATTATTAGATAAATTAAGTT\n-+\n-@@@DDDDDFFFFFI:DGI:D@0:FFI6A;BD//;>@BAABDDD;A@BD>BD;>B>B>A>@B3::BD>BAABDD:B@@ABBBB<AAAD>:ABBAB@B>>::>\n-@HWI-ST387:145:B013JABXX:1:1101:1385:2185 1:N:0:\n-TTGAGAAATATCATCAAAAAAAAAAAGTGCGACATCACAATGAGACATCAATACTATCAACCACAACCGATGTATTATCAACCACAACCGCAACCTATATA\n-+\n-@@@BDDDEHFHH?FHIIIIIDGIIIID.8B;4';@;=)7?E=)73;;3?>(6@C>;;55;;(5?B<?B=-5;8@CA(+(:@CABDBDD80<9<@<>C:ADD\n-@HWI-ST387:145:B013JABXX:1:1101:1701:2127 1:N:0:\n-CGTTATTGATGCTCCAGGTCACAGAGATTTCATCAAGAACATGATTACTGGTACTTCTCAAGCTGACTGTGCTATCTTGATTATTGCTGGTGGTGTCGGTG\n-+\n-@@@DFDDF<FHH>EEGAHCE>FH@HHFEHF>>C?EGGGHGGCGIGIIAF9909?BD?DCHBA<CGGHGG@FFHGGCEEEAAHEEE;?B?@B@?A=;@B?85\n-@HWI-ST387:145:B013JABXX:1:1101:1619:2127 1:N:0:\n-CTGTCTTTTTCACCGCCAAAGAAATGCGCAGCATGTAAAAACTTCTCCGGAGAAAACGCCTACGGATGGGCAGATCGATCGAATTTCCCCGTGCCTAAATT\n-+\n-CCCFFDFFHHHHHJEHJJIGIJJJIJIGJIJIJIJIJIJJIIIIJIJJJHGHHFEHHFFDECDDDDDDDDA<??C>B@BD3<A>?C3>CC3559A@AAC>@\n-@HWI-ST387:145:B013JABXX:1:1101:1670:2202 1:N:0:\n-CCTGGCCATTACTAGAAGAAGAGAAACAATTAGTGTATTGGATTCGACAAGAGGCAAGCAAGGGAGCCAAGTTTTCCGCATGTCTGGAAGGCAGATCAAAG\n-+\n-@@@FFFFFGHDHFHIIJJCGIIJIJJIIDIJJJCFCGIJJIGIJIIGIIJJHGIEIICHGIGGIIG:E;BB?@>CCECD/>BCDDD?5>ABBBD?CDCCDD\n-@HWI-ST387:145:B013JABXX:1:1101:1716:2203 1:N:0:\n-ATTCTTTTAATACCACAGGAACAAAGCGGGCATCGTGGTAGCGGGCCAATCAGGTTGCAGTAAATGAAGAGATATAGAGGAGGACTCTGCTAAAGACCATA\n-+\n-@@@BDFFFGGFAFBHIIII;ECFGGGI1EGGHEHEDGGIGC>@AH<A(6.(-(5>A39>>55>;@;:(5,(3:@@::>CB@89?<ACC::@C34@><3?:@\n-@HWI-ST387:145:B013JABXX:1:1101:1522:2237 1:N:0:\n-ACATACAAAACATACAAAATATACCTTTCTCACACAAGAAATATATGCTACTTGCAAAATATCATACCAAAAAACTTTTCACAACCGAAACCAAAACCAAC\n-+\n-?1?AD?DDDD?DD@:CEEDEEDF9,<9+A++A:C@DD3CDD9D4B<?B*?<D9DDC<D)?B48==BC##################################\n-@HWI-ST387:145:B013JABXX:1:1101:1971:2120 1:N:0:\n-AAGGAACCTACCACTATAACCGGAACTGATAACTTCTTGAGTGAGCTCCACGACGATAATTTAATGCCGTTTAATATAATGTTCCCCACAACCTTTGTACT\n-+\n-@@<DFFFFHHHDADHEIIIEGEA@FFA??@FHHIIIIIBBG?BGGIIIBDCFGIIEHEE>B)?@3?BCACBCB:>@BDCA>5@5@><ABB8??C::@CDCD\n-@HWI-ST387:145:B013JABXX:1:1101:1842:2127 1:N:0:\n-TAAATCAATAGTGAATGATTCCAAATATGCCTTCTTTAAAATGGACTCTGGGTTCTTCGCAGTATAAGTCTGTATGGTATGCGAAAGAAAGTGTTTTCTTA\n-+\n-CCCFFFFFHHHHHJJJIJJJJJJJJJJJJJIJJJJJJIIIJJJJJJJJJIJJDGIJJJIJJJIJIJIGHGJJJJJIJDHIHHHDFFDEECDDD;BCDDDDD\n-@HWI-ST387:145:B013JABXX:1:1101:1956:2170 1:N:0:\n-TACGTCGTCTCTGAATTGAGCAACGATGTTGCTATCTGCAGGACCGATTACCCGGGTACCGAAAACATGGTGATTCCTACATATGTGCAAGCAGGTGACTC\n-+\n-CCCFDFFFHGHHHFHHIHGJGIJIIIEIJJJJJIJIJJJJJJEGHIGGIJJJJGGF=BCEDD?BDCDCCC>CCDEDDDDDCCEDECDCCCDDDDD?CC>CC\n-@HWI-ST387:145:B013JABXX:1:1101:1752:2191 1:N:0:\n-GCTCTTGGTGCCTGCATCTCGACTTTGGGAGAAGATGAGACCGATGTTTGTCTCTGACTCAGACTCGAACAGGAATTCTCAGTTTGACAACAACAACAGCG\n-+\n-@@CFFFDDHHFHDBGGGHIIIJJGGIIGGJIGJJIGIGI@DFGIIGIGHGCHEEH=DHH;?)3?B@BAAAC?B??>>CD@;@:>@@CAA:A<??<BAA?BD\n-@HWI-ST387:145:B013JABXX:1:1101:1833:2202 1:N:0:\n-GGTATCTGTTTGGTGGAACCTGATTAGAGGAAACTCAAAGAGTGCTATGGTATGGTGACGGAGTGCGCTGGTCAAGAGTGTAAAAGCTTTTTGAACAGAGA\n-+\n-?@?DAA>D::?BACG;?ED=GGGIIIB<E<ADEEEGIGHI9??@?FAFBD@FGGE?4B=C/4@EC:A<:BE6;;;;6=@C5(;;3555@@CCB<>@39>??\n-@HWI-ST387:145:B013JABXX:1:1101:1881:2210 1:N:0:\n-ATTGTTCAAATAACTTCAATAGTTTGTCCATGTTTAATATATTTATATGCAATAGGATTTTTTGAATATGTTATAACAATTGTATATAACATTCAAGATAC\n-+\n-CCCFFFFFHHHHHJJJJJJJJJJJJJIJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJIHIJJJIJJJJIIIJJJHHHGHHHHFFFFFFEDEEEE\n-@HWI-ST387:145:B013JABXX:1:1101:1823:2238 1:N:0:\n-CTATGTCTATTCATCTTTCATCTGACTACCTAATACTATGCAAAAATGTAAAATCATCACACAAAACATAAACAATCAAAATCAGCCATTTCCGCACCTTT\n-+\n-CCCFFFFFHGHGGJGJJIGGJIIAGIJIJJEHGIIIIGIIIJIIGGIIDGGGFIIJJIIGHEAGHGHGHGGFEIIIHIFHECEFHFCFDBCEECDDBBCDD\n-@HWI-ST387:145:B013JABXX:1:1101:2164:2119 1:N:0:\n-CTTCTAAATTGGCAAAACTTGGTATTAAGCAAGATAATTCAGTTTTCAAAGAGTTCGATCCAATATCTAAACAACAAGAAGAAAAAACTTTACATGAGGCA\n-+\n-CCCFFFFFHHHGHJJJJJJJJJHIIJIJJJJJJJIJIJJJJJIDFHIJJIHIJFIHJCIIJJJIJJIJJIIIIIJJGHHHFHDFBEC?C@ADCCDCCDABD\n-@HWI-ST387:145:B013JABXX:1:1101:2245:2133 1:N:0:\n-TAGTACATATTGACCTTCTGCACAAGAAGCCATATTGACAGAG"..b"GAAGACG\n-+\n-C@CFFFFFHDHFGJJJJJJGJHIIIJJJIHIJJJFFHJJJIJIJJJJJJIJGIFGIIGJJJJJIJIEGIFHBB<D>>ACEDDDDDDDDDD?<@BC@@CDCD\n-@HWI-ST387:145:B013JABXX:1:1101:6486:5286 1:N:0:\n-AAAATTAGCTAACAAAAAAAAACTAAAATTTTTTCAAATTCCATCAGTTAGTTTGAGAAGTTGTCGGTAAGCAACCTATAGAACAAGTGTTTCCAGTCAAA\n-+\n-CCCFFFFFHHHHHJJJJJJJJJJJIJJIJJJJJJJJJJJJJJJJJJIHHJHEHHHHFFFFCEECEDD@BDDDDDDBDCDDEDDDDDDCCCDCDDEDDDCDC\n-@HWI-ST387:145:B013JABXX:1:1101:6379:5312 1:N:0:\n-CATTATATTGCAAATTTGCCAGGGTCACAATGTCGTTTGCCTCTTGGGTATCAGATTGCATTTTTTCAATACTTTTGGAAAGAATTTTCATGATATCCGTA\n-+\n-C@CFFFFFHHHHHJJJJJJJIJJJAFGGIIJJIJJIJIJJJJGIIJIJDFHIGHIGIIGHHGJJJJH>@DCHHHHGFDCDEECBEEDDEDEDCCDDCCBBB\n-@HWI-ST387:145:B013JABXX:1:1101:6481:5382 1:N:0:\n-AAATTCCAATCCTCTCCCTTACTACTTTTTGGAGAAGACGACTTAGAATTACCAGAATACTCTCTTCGAGATAAGGCATGGGGCTCTGAAAGTATCTTTGA\n-+\n-@@@D?D:=4CF?<ACAEBBF@GA:CBFB?FFI9:::C*C@?@D@FFFBBFCFD@CFAFA8@FEEI>A=(..;@??;76;;>;?'3(>@55::A;(;@B@@:\n-@HWI-ST387:145:B013JABXX:1:1101:6314:5413 1:N:0:\n-TGAAAATGGATTTTTTTGTTTTGGCAAGAGCATGAGAGCTTTTACTGGGCAAGAAGACAAGAGATGGAGAGTCCAGCCGGGCCTGCGCTTAAGTGCGCGGC\n-+\n-??1ADDDADCDFHHIEAGAE?FCAHCEHEGIGGIC@9BDGGHECFIGECHCAEG;@9CH>.?D>@CDCA;A-;-(;?B?;@BBB?89>><<CC########\n-@HWI-ST387:145:B013JABXX:1:1101:6442:5451 1:N:0:\n-ATAATATATAATAATAAATTATAAATAAATTTTAATTAAAAGTAGTATTAACATATTATAAATAGACAAAAGAGTCTAAAGGTTAAGATTTATTAAAATGT\n-+\n-@CCFFFFFHHHHHJJJJJIJJJJIBHJJHJIJJIIIJIIGJIHIIGIIJJJJIJJJJJJG<DGIIIJGHIIIGIHGGIG>FH=EHIGIHHHFHHGADFDFF\n-@HWI-ST387:145:B013JABXX:1:1101:6470:5454 1:N:0:\n-ATGGAACAAAAAAGTGTCTTTGCGCTTAGAGGCGCTTAAATATGTACATTATTCCTACTTTTTTATTTAGTATTATGTAAAGACTGAGGTTCTTTGTCATT\n-+\n-?@@DDDDBF>FFHICEEEFHGIIIBHI:F4DF=G@FB<@;C7=C8@;;@CGGGHCH>>E3?;@A=CCC>AACDDC>@B>>CC:AC>(><9AC3::@>CCDC\n-@HWI-ST387:145:B013JABXX:1:1101:6306:5474 1:N:0:\n-TTGACATATTTACAGAAATGTCATTCCTCCCTTCAATGCTATTTTCAAAGCTAGAATGATCGGGTTGGTTTTCTTCCCCGGTTTCTAGCATATCCTGGATG\n-+\n-CCCFFFFFHHHHHIJJJJJJJJJJJJJJJJJJJJJJJJJJIIJJJJJJJJJJJJJGIJIIJJJICHIJEHIJHHHHHHFFDABDDDEDDDEDDDEEDD?CD\n-@HWI-ST387:145:B013JABXX:1:1101:6483:5482 1:N:0:\n-TTTCTTTTTCTCTTGCCTTTCACGATTTCTTCTCTGAGACAGTTTACCTTTGCTTACTTCATCAGCAGCTTCCTTCAGCCTTTCAATTTCTTTATCTTTCT\n-+\n-@C@FFFFFHFGGGJGHHIIHGCHIHIJCHIICHIJJJIEGIJHIJJIEII<<BGGGCHJEGIIHH@8B(7=8C@E:@E@CAEC>>@CBD>@CC;@6;>CCA\n-@HWI-ST387:145:B013JABXX:1:1101:6257:5493 1:N:0:\n-TAGTTTTGAGCCACAATGCTAGGTCTTCTATATTTGGAACTGTTGCACTTAAAGCAACAAACCGAATGTTTTGACACATTGTATTCATCCTTGTCAGAATT\n-+\n-CCCDDFFFHHHHHJJJJJJJJJJFHIIIJJJJJJJJJIJJJJJJJIIJJJIJJJIJJIJJJJJIGGIIDHGHHHFFFFFFEDEEEEEEEDDDDDDED@:@C\n-@HWI-ST387:145:B013JABXX:1:1101:6688:5293 1:N:0:\n-AAATAATGGACTCACTTGTAGAAGAGGAAGCCACTGTTTTCTTGGATGAAGAGGAGGATTGCTTTTCGAATGAACTAATGGAACTAGATGTGGTGACTGAT\n-+\n-@@CFFFFFHHHHHJJJIJFHHHEHGIJHIJHIJJIIFHIJJJJJIGGHDHGHHIFHH=FGGHCHJJIIHEE@=CH>CDDFF@CCCECC@CCCA=B@CCC>@\n-@HWI-ST387:145:B013JABXX:1:1101:6633:5307 1:N:0:\n-ATCTACGAGGCCTCCACTCCCTTTGTGAACATCAATTGGTTCATCATGCAATGTAACGCCAAGAGCAAGAACTCTATCCCTCTGTGGTTTAATGTCGTCAA\n-+\n-CC@FFFFFAFHHHIJGJIJJJJJIJHGHJIIGIJGHGHIHII@GHGIIGIHHIFGHFAHEHFHGFF@DFDECEEEECDDDDDDD@CC?BBCCCC4:ABDD9\n-@HWI-ST387:145:B013JABXX:1:1101:6729:5439 1:N:0:\n-AATCTATCCCTATCTTCTAGTATCCAATTTCTAAAGTCCTCGTAAAAGTTTGTTGTTATGCCCTTTACTTCCAAATCAAGTTCTTCAAGTTCCACATTTTT\n-+\n-CCCFFFFFHHHHGJJJJJIIIHIJJJJIJJHIJJJJIIJIJJIIIJGGBFIJHIJJJIJJIIJIJJIIJJIIEHHEHIHHEHHHHFFEFFFEDECEEEEDC\n-@HWI-ST387:145:B013JABXX:1:1101:6653:5490 1:N:0:\n-TAATATGAAAAGGGAATGGTCAACAGTCATAGTCGCAATTTCTCTCAGGGCGAAATGGACTTTTTGAATGATGATGAACTAGACTTAGATTTACCGGTAAC\n-+\n-@CCFFFFDFFDDFGGIJJICHIEEGHHHCIJIFHGGIGHGIHIIJJJGCHGIHEGHIJH>EHGFFFFEEEECEEECDCCDCDDDCCCDCCDCCDA<95>BD\n-@HWI-ST387:145:B013JABXX:1:1101:6987:5254 1:N:0:\n-GTCACTGACGGTAGCATGCAAGTTCTCATCGGAACGAAATTAGTGACTGAAGGAATTGACATTAAGCAATTGATGATGGTGATCATGCTTGATAATAGACT\n-+\n-CBCFFFFFHHHFHJJIJIJJJJJJJJJIJJIJGIJIEIIJIJJEHIIJJIJJJJJJIJJJJJJJJJHFHDHEFEFFFFDCCCCDE@CADED?CC3;>CCDD\n-@HWI-ST387:145:B013JABXX:1:1101:6900:5255 1:N:0:\n-ATTAAAGAAATTTAATAATTTTGAAAATGGATTTTTTTGTTTTGGCAAGAGCATGAGAGCTTTTACTGGGCAAGAAGACAAGAGATGGAGAGTCCAGCCGG\n-+\n-CCCFFFFFHHHHHIJJJJJJJJJGIJJJJJIJJJJJJJJHIJJJJJJJJJIJIIJIIHJIJHHHHHHFDEFFDDEEDDDDDDCD?CDDDDDDCDDDDDDBB\n"

diff -r f9f71cf4c3e3 -r 890e9a40e2f1 myTools/test-data/mediumTrimmed.fastq
--- a/myTools/test-data/mediumTrimmed.fastq Thu Dec 11 15:42:44 2014 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b"@@ -1,30000 +0,0 @@\n-@HWI-ST387:145:B013JABXX:1:1101:1428:2120 1:N:0:\n-TCTCCTTGCGGGGTCCCGGCTGGGGCCGGGACTAAATATTTTATATATTTATTAATTAAATATTTATCTATTAAATAAAAATTATTAGATAAATTAAGT\n-+\n-@@DDDDDFFFFFI:DGI:D@0:FFI6A;BD//;>@BAABDDD;A@BD>BD;>B>B>A>@B3::BD>BAABDD:B@@ABBBB<AAAD>:ABBAB@B>>::\n-@HWI-ST387:145:B013JABXX:1:1101:1385:2185 1:N:0:\n-TGAGAAATATCATCAAAAAAAAAAAGTGCGACATCACAATGAGACATCAATACTATCAACCACAACCGATGTATTATCAACCACAACCGCAACCTA\n-+\n-@@BDDDEHFHH?FHIIIIIDGIIIID.8B;4';@;=)7?E=)73;;3?>(6@C>;;55;;(5?B<?B=-5;8@CA(+(:@CABDBDD80<9<@<>C\n-@HWI-ST387:145:B013JABXX:1:1101:1701:2127 1:N:0:\n-CGTTATTGATGCTCCAGGTCACAGAGATTTCATCAAGAACATGATTACTGGTACTTCTCAAGCTGACTGTGCTATCTTGATTATTGCTGGTGGTGTCGGTG\n-+\n-@@@DFDDF<FHH>EEGAHCE>FH@HHFEHF>>C?EGGGHGGCGIGIIAF9909?BD?DCHBA<CGGHGG@FFHGGCEEEAAHEEE;?B?@B@?A=;@B?85\n-@HWI-ST387:145:B013JABXX:1:1101:1619:2127 1:N:0:\n-CTGTCTTTTTCACCGCCAAAGAAATGCGCAGCATGTAAAAACTTCTCCGGAGAAAACGCCTACGGATGGGCAGATCGATCGAATTTCCCCGTGCCTAAAT\n-+\n-CCCFFDFFHHHHHJEHJJIGIJJJIJIGJIJIJIJIJIJJIIIIJIJJJHGHHFEHHFFDECDDDDDDDDA<??C>B@BD3<A>?C3>CC3559A@AAC>\n-@HWI-ST387:145:B013JABXX:1:1101:1670:2202 1:N:0:\n-CTGGCCATTACTAGAAGAAGAGAAACAATTAGTGTATTGGATTCGACAAGAGGCAAGCAAGGGAGCCAAGTTTTCCGCATGTCTGGAAGGCAGATCAAAG\n-+\n-@@FFFFFGHDHFHIIJJCGIIJIJJIIDIJJJCFCGIJJIGIJIIGIIJJHGIEIICHGIGGIIG:E;BB?@>CCECD/>BCDDD?5>ABBBD?CDCCDD\n-@HWI-ST387:145:B013JABXX:1:1101:1716:2203 1:N:0:\n-ATTCTTTTAATACCACAGGAACAAAGCGGGCATCGTGGTAGCGGGCCAATCAGGTTGCAGTAAATGAAGAGATATAGAGGAGGACTCTGCTAAAGACCATA\n-+\n-@@@BDFFFGGFAFBHIIII;ECFGGGI1EGGHEHEDGGIGC>@AH<A(6.(-(5>A39>>55>;@;:(5,(3:@@::>CB@89?<ACC::@C34@><3?:@\n-@HWI-ST387:145:B013JABXX:1:1101:1522:2237 1:N:0:\n-CATACAAAATATACCTTTCTCACACAAGAAATATATGCTACTTGCAAAATATCATACCAAAAAACTTTTCACAACCGAAACCAAAACCAAC\n-+\n-?DD@:CEEDEEDF9,<9+A++A:C@DD3CDD9D4B<?B*?<D9DDC<D)?B48==BC##################################\n-@HWI-ST387:145:B013JABXX:1:1101:1971:2120 1:N:0:\n-AGGAACCTACCACTATAACCGGAACTGATAACTTCTTGAGTGAGCTCCACGACGATAATTTAATGCCGTTTAATATAATGTTCCCCACAACCTTTGTACT\n-+\n-@<DFFFFHHHDADHEIIIEGEA@FFA??@FHHIIIIIBBG?BGGIIIBDCFGIIEHEE>B)?@3?BCACBCB:>@BDCA>5@5@><ABB8??C::@CDCD\n-@HWI-ST387:145:B013JABXX:1:1101:1842:2127 1:N:0:\n-TAAATCAATAGTGAATGATTCCAAATATGCCTTCTTTAAAATGGACTCTGGGTTCTTCGCAGTATAAGTCTGTATGGTATGCGAAAGAAAGTGTTTTCTTA\n-+\n-CCCFFFFFHHHHHJJJIJJJJJJJJJJJJJIJJJJJJIIIJJJJJJJJJIJJDGIJJJIJJJIJIJIGHGJJJJJIJDHIHHHDFFDEECDDD;BCDDDDD\n-@HWI-ST387:145:B013JABXX:1:1101:1956:2170 1:N:0:\n-TACGTCGTCTCTGAATTGAGCAACGATGTTGCTATCTGCAGGACCGATTACCCGGGTACCGAAAACATGGTGATTCCTACATATGTGCAAGCAGGTGACTC\n-+\n-CCCFDFFFHGHHHFHHIHGJGIJIIIEIJJJJJIJIJJJJJJEGHIGGIJJJJGGF=BCEDD?BDCDCCC>CCDEDDDDDCCEDECDCCCDDDDD?CC>CC\n-@HWI-ST387:145:B013JABXX:1:1101:1752:2191 1:N:0:\n-GCTCTTGGTGCCTGCATCTCGACTTTGGGAGAAGATGAGACCGATGTTTGTCTCTGACTCAGACTCGAACAGGAATTCTCAGTTTGACAACAACAACAGCG\n-+\n-@@CFFFDDHHFHDBGGGHIIIJJGGIIGGJIGJJIGIGI@DFGIIGIGHGCHEEH=DHH;?)3?B@BAAAC?B??>>CD@;@:>@@CAA:A<??<BAA?BD\n-@HWI-ST387:145:B013JABXX:1:1101:1833:2202 1:N:0:\n-GTATCTGTTTGGTGGAACCTGATTAGAGGAAACTCAAAGAGTGCTATGGTATGGTGACGGAGTGCGCTGGTCAAGAGTGTAAAAGCTTTTTGAACAG\n-+\n-@?DAA>D::?BACG;?ED=GGGIIIB<E<ADEEEGIGHI9??@?FAFBD@FGGE?4B=C/4@EC:A<:BE6;;;;6=@C5(;;3555@@CCB<>@39\n-@HWI-ST387:145:B013JABXX:1:1101:1881:2210 1:N:0:\n-ATTGTTCAAATAACTTCAATAGTTTGTCCATGTTTAATATATTTATATGCAATAGGATTTTTTGAATATGTTATAACAATTGTATATAACATTCAAGATAC\n-+\n-CCCFFFFFHHHHHJJJJJJJJJJJJJIJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJIHIJJJIJJJJIIIJJJHHHGHHHHFFFFFFEDEEEE\n-@HWI-ST387:145:B013JABXX:1:1101:1823:2238 1:N:0:\n-CTATGTCTATTCATCTTTCATCTGACTACCTAATACTATGCAAAAATGTAAAATCATCACACAAAACATAAACAATCAAAATCAGCCATTTCCGCACCT\n-+\n-CCCFFFFFHGHGGJGJJIGGJIIAGIJIJJEHGIIIIGIIIJIIGGIIDGGGFIIJJIIGHEAGHGHGHGGFEIIIHIFHECEFHFCFDBCEECDDBBC\n-@HWI-ST387:145:B013JABXX:1:1101:2164:2119 1:N:0:\n-CTTCTAAATTGGCAAAACTTGGTATTAAGCAAGATAATTCAGTTTTCAAAGAGTTCGATCCAATATCTAAACAACAAGAAGAAAAAACTTTACATGAGGCA\n-+\n-CCCFFFFFHHHGHJJJJJJJJJHIIJIJJJJJJJIJIJJJJJIDFHIJJIHIJFIHJCIIJJJIJJIJJIIIIIJJGHHHFHDFBEC?C@ADCCDCCDABD\n-@HWI-ST387:145:B013JABXX:1:1101:2245:2133 1:N:0:\n-TAGTACATATTGACCTTCTGCACAAGAAGCCATATTGACAGAGCAGTATGTGAGGACCTTTCTTCTACACAATGTAACAGTCAATGGTTGTAGTC"..b"TAGAAAGTATAGGAACTTCAGAGCGCTTTTGAAAACCAAAAGCGCTCTGAAGACG\n-+\n-C@CFFFFFHDHFGJJJJJJGJHIIIJJJIHIJJJFFHJJJIJIJJJJJJIJGIFGIIGJJJJJIJIEGIFHBB<D>>ACEDDDDDDDDDD?<@BC@@CDCD\n-@HWI-ST387:145:B013JABXX:1:1101:6486:5286 1:N:0:\n-ATTAGCTAACAAAAAAAAACTAAAATTTTTTCAAATTCCATCAGTTAGTTTGAGAAGTTGTCGGTAAGCAACCTATAGAACAAGTGTTTCCAGTCA\n-+\n-FFFFFHHHHHJJJJJJJJJJJIJJIJJJJJJJJJJJJJJJJJJIHHJHEHHHHFFFFCEECEDD@BDDDDDDBDCDDEDDDDDDCCCDCDDEDDDC\n-@HWI-ST387:145:B013JABXX:1:1101:6379:5312 1:N:0:\n-CATTATATTGCAAATTTGCCAGGGTCACAATGTCGTTTGCCTCTTGGGTATCAGATTGCATTTTTTCAATACTTTTGGAAAGAATTTTCATGATATCCGTA\n-+\n-C@CFFFFFHHHHHJJJJJJJIJJJAFGGIIJJIJJIJIJJJJGIIJIJDFHIGHIGIIGHHGJJJJH>@DCHHHHGFDCDEECBEEDDEDEDCCDDCCBBB\n-@HWI-ST387:145:B013JABXX:1:1101:6481:5382 1:N:0:\n-ATTCCAATCCTCTCCCTTACTACTTTTTGGAGAAGACGACTTAGAATTACCAGAATACTCTCTTCGAGATAAGGCATGGGGCTCTGAAAGTATCTTTGA\n-+\n-@D?D:=4CF?<ACAEBBF@GA:CBFB?FFI9:::C*C@?@D@FFFBBFCFD@CFAFA8@FEEI>A=(..;@??;76;;>;?'3(>@55::A;(;@B@@:\n-@HWI-ST387:145:B013JABXX:1:1101:6314:5413 1:N:0:\n-TGAAAATGGATTTTTTTGTTTTGGCAAGAGCATGAGAGCTTTTACTGGGCAAGAAGACAAGAGATGGAGAGTCCAGCCGGGCCTGCGCTTAAGTGCGCGGC\n-+\n-??1ADDDADCDFHHIEAGAE?FCAHCEHEGIGGIC@9BDGGHECFIGECHCAEG;@9CH>.?D>@CDCA;A-;-(;?B?;@BBB?89>><<CC########\n-@HWI-ST387:145:B013JABXX:1:1101:6442:5451 1:N:0:\n-ATATATAATAATAAATTATAAATAAATTTTAATTAAAAGTAGTATTAACATATTATAAATAGACAAAAGAGTCTAAAGGTTAAGATTTATTAAAATGT\n-+\n-FFFFFHHHHHJJJJJIJJJJIBHJJHJIJJIIIJIIGJIHIIGIIJJJJIJJJJJJG<DGIIIJGHIIIGIHGGIG>FH=EHIGIHHHFHHGADFDFF\n-@HWI-ST387:145:B013JABXX:1:1101:6470:5454 1:N:0:\n-ATGGAACAAAAAAGTGTCTTTGCGCTTAGAGGCGCTTAAATATGTACATTATTCCTACTTTTTTATTTAGTATTATGTAAAGACTGAGGTTCTTTGTCAT\n-+\n-?@@DDDDBF>FFHICEEEFHGIIIBHI:F4DF=G@FB<@;C7=C8@;;@CGGGHCH>>E3?;@A=CCC>AACDDC>@B>>CC:AC>(><9AC3::@>CCD\n-@HWI-ST387:145:B013JABXX:1:1101:6306:5474 1:N:0:\n-TGACATATTTACAGAAATGTCATTCCTCCCTTCAATGCTATTTTCAAAGCTAGAATGATCGGGTTGGTTTTCTTCCCCGGTTTCTAGCATATCCTGGATG\n-+\n-CCFFFFFHHHHHIJJJJJJJJJJJJJJJJJJJJJJJJJJIIJJJJJJJJJJJJJGIJIIJJJICHIJEHIJHHHHHHFFDABDDDEDDDEDDDEEDD?CD\n-@HWI-ST387:145:B013JABXX:1:1101:6483:5482 1:N:0:\n-TCTTTTTCTCTTGCCTTTCACGATTTCTTCTCTGAGACAGTTTACCTTTGCTTACTTCATCAGCAGCTTCCTTCAGCCTTTCAATTTCTTTATCTTTCT\n-+\n-@FFFFFHFGGGJGHHIIHGCHIHIJCHIICHIJJJIEGIJHIJJIEII<<BGGGCHJEGIIHH@8B(7=8C@E:@E@CAEC>>@CBD>@CC;@6;>CCA\n-@HWI-ST387:145:B013JABXX:1:1101:6257:5493 1:N:0:\n-TAGTTTTGAGCCACAATGCTAGGTCTTCTATATTTGGAACTGTTGCACTTAAAGCAACAAACCGAATGTTTTGACACATTGTATTCATCCTTGTCAGAAT\n-+\n-CCCDDFFFHHHHHJJJJJJJJJJFHIIIJJJJJJJJJIJJJJJJJIIJJJIJJJIJJIJJJJJIGGIIDHGHHHFFFFFFEDEEEEEEEDDDDDDED@:@\n-@HWI-ST387:145:B013JABXX:1:1101:6688:5293 1:N:0:\n-ATAATGGACTCACTTGTAGAAGAGGAAGCCACTGTTTTCTTGGATGAAGAGGAGGATTGCTTTTCGAATGAACTAATGGAACTAGATGTGGTGACTGAT\n-+\n-CFFFFFHHHHHJJJIJFHHHEHGIJHIJHIJJIIFHIJJJJJIGGHDHGHHIFHH=FGGHCHJJIIHEE@=CH>CDDFF@CCCECC@CCCA=B@CCC>@\n-@HWI-ST387:145:B013JABXX:1:1101:6633:5307 1:N:0:\n-ATCTACGAGGCCTCCACTCCCTTTGTGAACATCAATTGGTTCATCATGCAATGTAACGCCAAGAGCAAGAACTCTATCCCTCTGTGGTTTAATGTCGTCA\n-+\n-CC@FFFFFAFHHHIJGJIJJJJJIJHGHJIIGIJGHGHIHII@GHGIIGIHHIFGHFAHEHFHGFF@DFDECEEEECDDDDDDD@CC?BBCCCC4:ABDD\n-@HWI-ST387:145:B013JABXX:1:1101:6729:5439 1:N:0:\n-ATCTATCCCTATCTTCTAGTATCCAATTTCTAAAGTCCTCGTAAAAGTTTGTTGTTATGCCCTTTACTTCCAAATCAAGTTCTTCAAGTTCCACAT\n-+\n-CCFFFFFHHHHGJJJJJIIIHIJJJJIJJHIJJJJIIJIJJIIIJGGBFIJHIJJJIJJIIJIJJIIJJIIEHHEHIHHEHHHHFFEFFFEDECEE\n-@HWI-ST387:145:B013JABXX:1:1101:6653:5490 1:N:0:\n-TAATATGAAAAGGGAATGGTCAACAGTCATAGTCGCAATTTCTCTCAGGGCGAAATGGACTTTTTGAATGATGATGAACTAGACTTAGATTTACCGGTAAC\n-+\n-@CCFFFFDFFDDFGGIJJICHIEEGHHHCIJIFHGGIGHGIHIIJJJGCHGIHEGHIJH>EHGFFFFEEEECEEECDCCDCDDDCCCDCCDCCDA<95>BD\n-@HWI-ST387:145:B013JABXX:1:1101:6987:5254 1:N:0:\n-GTCACTGACGGTAGCATGCAAGTTCTCATCGGAACGAAATTAGTGACTGAAGGAATTGACATTAAGCAATTGATGATGGTGATCATGCTTGATAATAGACT\n-+\n-CBCFFFFFHHHFHJJIJIJJJJJJJJJIJJIJGIJIEIIJIJJEHIIJJIJJJJJJIJJJJJJJJJHFHDHEFEFFFFDCCCCDE@CADED?CC3;>CCDD\n-@HWI-ST387:145:B013JABXX:1:1101:6900:5255 1:N:0:\n-ATTAAAGAAATTTAATAATTTTGAAAATGGATTTTTTTGTTTTGGCAAGAGCATGAGAGCTTTTACTGGGCAAGAAGACAAGAGATGGAGAGTCCAGCCG\n-+\n-CCCFFFFFHHHHHIJJJJJJJJJGIJJJJJIJJJJJJJJHIJJJJJJJJJIJIIJIIHJIJHHHHHHFDEFFDDEEDDDDDDCD?CDDDDDDCDDDDDDB\n"

diff -r f9f71cf4c3e3 -r 890e9a40e2f1 myTools/test-data/small.fastq
--- a/myTools/test-data/small.fastq Thu Dec 11 15:42:44 2014 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,20 +0,0 @@
-@HWI-ST387:145:B013JABXX:1:1101:1428:2120 1:N:0:
-TTCTCCTTGCGGGGTCCCGGCTGGGGCCGGGACTAAATATTTTATATATTTATTAATTAAATATTTATCTATTAAATAAAAATTATTAGATAAATTAAGTT
-+
-@@@DDDDDFFFFFI:DGI:D@0:FFI6A;BD//;>@BAABDDD;A@BD>BD;>B>B>A>@B3::BD>BAABDD:B@@ABBBB<AAAD>:ABBAB@B>>::>
-@HWI-ST387:145:B013JABXX:1:1101:1385:2185 1:N:0:
-TTGAGAAATATCATCAAAAAAAAAAAGTGCGACATCACAATGAGACATCAATACTATCAACCACAACCGATGTATTATCAACCACAACCGCAACCATATATA
-+
-@@@BDDDEHFHH?FHIIIIIDGIIIID.8B;4';@;=)7?E=)73;;3?>(6@C>;;55;;(5?B<?B=-5;8@CA(+(:@CABDBDD80<9<@<X>C:ADD
-@HWI-ST387:145:B013JABXX:1:1101:1385:2185 1:N:0:
-TTGAGAAATATCATCAAAAAAAAAAAGTGCGACATCACAATGAGACATCAATACTATCAACCACAACCGATGTATTATCAACCACAACCGCAACCATA
-+
-@@@BDDDEHFHH?FHIIIIIDGIIIID.8B;4';@;=)7?E=)73;;3?>(6@C>;;55;;(5?B<?B=-5;8@CA(+(:@CABDBDD80<9<@<X>C
-@HWI-ST387:145:B013JABXX:1:1101:1385:2185 1:N:0:
-ATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATAT
-+
-@@@BDDDEHFHH?FHIIIIIDGIIIID.8B;4';@;=)7?E=)73;;3?>(6@C>;;55;;(5?B<?B=-5;8@CA(+(:@CABDBDD80<9<@<X>C
-@HWI-ST387:145:B013JABXX:1:1101:1385:2185 1:N:0:
-AGTATA
-+
-@@@BDD

diff -r f9f71cf4c3e3 -r 890e9a40e2f1 myTools/test-data/smallTrimmed.fastq
--- a/myTools/test-data/smallTrimmed.fastq Thu Dec 11 15:42:44 2014 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,20 +0,0 @@
-@HWI-ST387:145:B013JABXX:1:1101:1428:2120 1:N:0:
-TCTCCTTGCGGGGTCCCGGCTGGGGCCGGGACTAAATATTTTATATATTTATTAATTAAATATTTATCTATTAAATAAAAATTATTAGATAAATTAAGT
-+
-@@DDDDDFFFFFI:DGI:D@0:FFI6A;BD//;>@BAABDDD;A@BD>BD;>B>B>A>@B3::BD>BAABDD:B@@ABBBB<AAAD>:ABBAB@B>>::
-@HWI-ST387:145:B013JABXX:1:1101:1385:2185 1:N:0:
-TGAGAAATATCATCAAAAAAAAAAAGTGCGACATCACAATGAGACATCAATACTATCAACCACAACCGATGTATTATCAACCACAACCGCAACCAT
-+
-@@BDDDEHFHH?FHIIIIIDGIIIID.8B;4';@;=)7?E=)73;;3?>(6@C>;;55;;(5?B<?B=-5;8@CA(+(:@CABDBDD80<9<@<X>
-@HWI-ST387:145:B013JABXX:1:1101:1385:2185 1:N:0:
-TGAGAAATATCATCAAAAAAAAAAAGTGCGACATCACAATGAGACATCAATACTATCAACCACAACCGATGTATTATCAACCACAACCGCAACCATA
-+
-@@BDDDEHFHH?FHIIIIIDGIIIID.8B;4';@;=)7?E=)73;;3?>(6@C>;;55;;(5?B<?B=-5;8@CA(+(:@CABDBDD80<9<@<X>C
-@HWI-ST387:145:B013JABXX:1:1101:1385:2185 1:N:0:
-AT
-+
->C
-@HWI-ST387:145:B013JABXX:1:1101:1385:2185 1:N:0:
-AGTA
-+
-@@@B

diff -r f9f71cf4c3e3 -r 890e9a40e2f1 myTools/trtr

Binary file myTools/trtr has changed

diff -r f9f71cf4c3e3 -r 890e9a40e2f1 myTools/trtr.c
--- a/myTools/trtr.c Thu Dec 11 15:42:44 2014 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,221 +0,0 @@
-/**********************************************************************
-* Author: Jonathan Richards
-* Date: 12/11/2014
-*
-* This tool removes tandem repeats from ends of unaligned sequencing
-* reads (leaving one copy). This prevents reads that don't span the
-* repeated region from overlapping and leading to innaccurate SNPs
-* calls.
-*
-* The maximimum repeat length is adjustable (use 1 to trim only
-* homopolymers).
-*
-* The "aggressive" option should not be touched in general. Setting to
-* 0 will prevent the program from trimming to exactly 1 copy of the
-* repeat, instead leaving between 1 and 2 copies. Why this would be
-* useful, I don't know.
-*
-* This program could also be a useful first step before assembly. More
-* testing needs to be done.
-*
-* Special thanks to my advisor, Professor Alison Gammie, for bringing
-* this problem to my attention and to my reseach partner, Mitchell
-* Vollger, for help testing and finalizing.
-**********************************************************************/
-
-#include <stdio.h>
-#include <stdlib.h>
-#include <stdbool.h>
-#include <sys/types.h>
-#include <assert.h>
-#include <errno.h>
-
-//use my getline for portability
-//adapted from getline.c written by Jan Brittenson, bson@gnu.ai.mit.edu
-//http://www.opensource.apple.com/source/cvs/cvs-19/cvs/lib/getline.c
-ssize_t getline(char** lineptr, size_t* n, FILE* stream) {
- size_t nchars_avail;
- char* read_pos;
- int save_errno;
- ssize_t ret;
- register int c;
-
- if (!lineptr || !n || !stream) {
- errno = EINVAL;
- return -1;
- }
- if (!*lineptr) {
- *n = 128;
- *lineptr = malloc(*n);
- if (!*lineptr) {
- errno = ENOMEM;
- return -1;
- }
- }
- nchars_avail = *n;
- read_pos = *lineptr;
- for (;;) {
- c = getc(stream);
- save_errno = errno;
- if (c != '\r') { //for portability...
- assert((*lineptr+*n)==(read_pos+nchars_avail));
- if (nchars_avail < 2) {
- *n *= 2;
- nchars_avail = *n + *lineptr - read_pos;
- *lineptr = realloc(*lineptr, *n);
- if (!*lineptr) {
- errno = ENOMEM;
- return -1;
- }
- read_pos = *n - nchars_avail + *lineptr;
- assert((*lineptr+*n) == (read_pos+nchars_avail));
- }
- if (ferror(stream)) {
- errno = save_errno;
- return -1;
- }
- if (c == EOF) {
- if (read_pos == *lineptr)
- return -1;
- else
- break;
- }
- *read_pos++ = c;
- nchars_avail--;
- if (c == '\n')
- break;
- }
- }
- *read_pos = '\0';
- ret = read_pos - *lineptr;
- return ret;
-}
-
-int main(int argc, char *argv[]) {
- char *line = NULL;
- size_t len = 0;
- ssize_t line_length;
-
- int count = 0;
- size_t leftTrim = 0;
- size_t rightTrim = 0;
- size_t i;
- size_t i_max = 10;
- size_t j;
- size_t r;
- size_t length;
- size_t longest_region;
- char *ptr;
- bool matched = false;
- bool aggressive_trim = true;
-
- FILE *file = fopen(argv[1], "r");
-
- if (argc >= 3) {
- i_max = strtol(argv[2], &ptr, 10);
- if (argc >= 4) {
- aggressive_trim = strtol(argv[3], &ptr, 10);
- }
- }
- if (file != NULL) {
- while ((line_length = getline(&line, &len, file)) != -1) {
- count++;
- switch (count) {
-
- //read name
- case 1:
- fputs(line, stdout);
- break;
-
- //read sequence
- case 2:
- //find leftTrim
- longest_region = 0;
- for (i=1; i<=i_max && i<=line_length/2; i++) { //size of repeat
- if (line[0] == line[i]) {
- matched = true;
- j=1;
- r=0;
- while (matched == true) {
- if (j == i) {
- r++;
- j=0;
- } else if (line[j] != line[(r+1)*i+j]) {
- //no length comparison needed because of \n at end
- matched = false;
- if (aggressive_trim) {
- length = r*i+j;
- } else {
- length = r*i;
- }
- if (length > longest_region && r>0) {
- longest_region = length;
- }
- } else {
- j++;
- }
- }
-
- }
- }
- leftTrim = longest_region;
-
- //find rightTrim
- longest_region = 0;
- for (i=1; i<=i_max && i<=line_length/2; i++) { //size of repeat
- if (line[line_length-2] == line[line_length-2-i]) {
- matched = true;
- j=1;
- r=0;
- while (matched == true) {
- if (j == i) {
- r++;
- j=0;
- } else if ((line[line_length-2-j] != line[line_length-2-(r+1)*i-j])
- || line_length-2-(r+1)*i-j == leftTrim) {
- matched = false;
- if (aggressive_trim) {
- length = r*i+j;
- } else {
- length = r*i;
- }
- if (length > longest_region && r>0) {
- longest_region = length;
- }
- } else {
- j++;
- }
- }
- }
- }
- rightTrim = line_length-longest_region-1;
-
- //print trimmed line
- line[rightTrim] = '\n';
- line[rightTrim+1] = '\0';
- fputs(line+leftTrim, stdout);
- break;
-
- //+
- case 3:
- fputs(line, stdout);
- break;
-
- //read qualities
- case 4:
- count = 0; //reset to read title
- line[rightTrim] = '\n';
- line[rightTrim+1] = '\0';
- fputs(line+leftTrim, stdout);
- break;
- default:
- break;
- }
- }
- free(line);
- fclose(file);
- } else {
- perror(argv[1]);
- }
- return 0;
-}
\ No newline at end of file

diff -r f9f71cf4c3e3 -r 890e9a40e2f1 myTools/trtr.xml
--- a/myTools/trtr.xml Thu Dec 11 15:42:44 2014 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,34 +0,0 @@
-<tool id="trtr" name="TRTR Trim Reads of Tandem Repeats">
-  <description>Recommended before calling SNPs. </description>
-  <command>trtr $input $max_repeat $aggressive > $output</command>
-  <inputs>
-    <param format="fastq" name="input" type="data" label="Source file"/>
-    <param name="max_repeat" type="integer" value="10" label="Maximum repeat length" />
-    <param name="aggressive" type="integer" value="1" label="Aggressive? See description."/>
-  </inputs>
-  <outputs>
-    <data format="fastq" name="output" />
-  </outputs>
-
-  <tests>
-    <test>
-      <param name="input" value="small.fastq"/>
-      <output name="output" file="smallTrimmed.fastq"/>
-    </test>
-    <test>
-      <param name="input" value="medium.fastq"/>
-      <output name="output" file="mediumTrimmed.fastq"/>
-    </test>
-  </tests>
-
-  <help>
-This tool removes tandem repeats from ends of unaligned sequencing reads (leaving one copy). This prevents reads that don't span the repeated region from overlapping and leading to innaccurate SNPs calls.
-
-The maximimum repeat length is adjustable (use 1 to trim only homopolymers).
-
-The "aggressive" option should not be touched in general. Setting to 0 will prevent the program from trimming to exactly 1 copy of the repeat, instead leaving between 1 and 2 copies.
-
-This could also be a useful first step before assembly. More testing needs to be done.
-  </help>
-
-</tool>