update README for v1.1.1

Author: jamorrison

README.md

@@ -45,6 +45,10 @@ make
 
 ### Help
 ```
+Program: dupsifter
+Version: 1.1.1
+Contact: Jacob Morrison <jacob.morrison@vai.org>
+
 dupsifter [options] <ref.fa> [in.bam]
 
 Output options:
@@ -56,15 +60,23 @@ Input options:
     -W, --wgs-only               process WGS reads instead of WGBS
     -l, --max-read-length INT    maximum read length for paired end duplicate-marking [10000]
     -b, --min-base-qual INT      minimum base quality [0]
+    -B, --has-barcode            reads in file have barcodes (see Note 4 for details)
     -r, --remove-dups            toggle to remove marked duplicate
     -v, --verbose                print extra messages
     -h, --help                   this help
+        --version                print version info and exit
 
 Note 1, [in.bam] must be name sorted. If not provided, assume the input is stdin.
 Note 2, assumes either ALL reads are paired-end (default) or single-end.
     If a singleton read is found in paired-end mode, the code will break nicely.
 Note 3, defaults to dupsifter.stat if streaming or (-o basename).dupsifter.stat
     if the -o option is provided. If -o and -O are provided, then -O will be used.
+Note 4, dupsifter first looks for a barcode in the CB SAM tag, then in the CR SAM tag, then
+    tries to parse the read name. If the barcode is in the read name, it must be the last element
+    and be separated by a ':' (i.e., @12345:678:9101112:1234_1:N:0:ACGTACGT). Any separators
+    found in the barcode (e.g., '+' or '-') are treated as 'N's and the additional parts of the
+    barcode are included up to a maximum length of 16 bases/characters. Barcodes are taken from
+    read 1 in paired-end sequencing only.
 ```
 
 ### Option Descriptions
@@ -77,6 +89,7 @@ Note 3, defaults to dupsifter.stat if streaming or (-o basename).dupsifter.stat
 |     -W       |    --wgs-only     |     none      | Process WGS data instead of WGBS (see Documentation for differences in processing) |
 |     -l       | --max-read-length |    integer    | Maximum read length (handles padding for reference genome windows)                 |
 |     -b       |  --min-base-qual  |    integer    | Minimum bae quality (used in determiningg bisulfite strand if tags not provided)   |
+|     -B       |   --has-barcode   |     none      | Use when reads have cell barcodes and you want to mark duplicates accordingly      |
 |     -r       |   --remove-dups   |     none      | Remove reads that are flagged as duplicates                                        |
 |     -v       |     --verbose     |     none      | Print extra messages when running                                                  |
 |     -h       |      --help       |     none      | Print usage help message and exit                                                  |
@@ -120,6 +133,7 @@ categories (descriptions below):
   5. Read 1 Leftmost in Pair?
   6. Orientation
   7. Single-End?
+  8. Cell barcode
 
 Descriptions:
 
@@ -132,6 +146,7 @@ Descriptions:
   forward-reverse, reverse-forward. For reference, forward-reverse is generally
   considered a "proper pair."
   - *Single-End?:* Is the read a single-end read?
+  - *Cell barcode:* Described below
 
 PCR duplicates are found for single-end and paired-end reads using the same
 set of categories, with a few minor notes. First, single-end reads and
@@ -182,6 +197,35 @@ example, the human genome from GENCODE contains over 600 contigs (both primary
 chromosomes and additional contigs). Rather than having 600+ bins, there are
 approximately 25 bins using the described method.
 
+### Cell Barcodes
+
+Cell barcodes are commonly used in single-cell sequencing in order to multiplex
+many cells into a pool, primarily to increase throughput and to overcome
+sequencer input requirements. It also allows for streamlined processing, as many
+cells can be processed at once. These barcodes must be included when defining
+reads that are duplicates as two fragments may be from the same location in the
+genome, but be from two different cells. By default, dupsifter does not look for
+barcodes; however, an option is available (`-B|--has-barcode`) when duplicate
+marking data with barcodes. Dupsifter handles barcodes in the following way:
+
+  1. Looks for the `CB` SAM tag.
+  2. If not found, look for the `CR` SAM tag.
+  3. If neither are found, parse the read name. The barcode must be the last
+  element in the name where the elements are separated by `:`.
+  4. If a barcode can't be found in any of these locations, a warning is
+  printed and a default value is used (thereby negating any benefits of
+  using barcodes).
+
+In all three cases, up to 16 bases are packed into a single integer for defining
+the barcode. If your barcode is longer than 16 bases, it will be truncated to a
+length of 16. Additionally, separators (only `+` and `-` allowed) are treated as
+Ns and count towards the maximum length of 16.
+
+<!-- Room for improvement: -->
+<!--   - Allow barcodes longer than 16 base pairs. -->
+<!--   - Handle barcodes with dual indexes. -->
+<!--   - Include UMI capabilities. -->
+
 ### Bisulfite Strand Determination
 The bisulfite strand for a read (both single-end and paired-end reads) is
 determined with the following priority: