Merge pull request #133 from epifluidlab/update-docs

Update docs

CHANGELOG.md

@@ -7,6 +7,12 @@ The format is based on
 and this project adheres to
 [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [0.10.3] - 2024-12-21
+
+### Fixed
+- Update various docstrings and help statements to no longer mention SAM
+files as an accepted format
+
 ## [0.10.2] - 2024-12-19
 
 ### Fixed

docs/_build/html/_sources/documentation/user_guide/inputdata.rst.txt

@@ -7,30 +7,49 @@ Input Data
 SAM
 ^^^^^^^^^^^
 
-A sequence alignment map (SAM) file is a human-readable file format that stores the results of sequence alignment. It contains information about the alignment of each read to the reference genome, as well as information about the read itself. 
+A sequence alignment map (SAM) file is a human-readable file format that stores
+the results of sequence alignment. It contains information about the alignment
+of each read to the reference genome, as well as information about the read
+itself. 
 
 BAM
 ^^^^^^^^^^^
 
-A binary alignment file (BAM) provides the same information as a SAM file, but in a binary format. This can be useful for saving space on disk, but is not human-readable. 
+A binary alignment file (BAM) that stores the results of sequence alignment.
+It contains information about the alignment of each read to the reference
+genome, as well as information about the read itself. This file format is not
+human-readable but relatively space-efficient when compared to its plaintext
+counterpart, the sequence alignment map (SAM) file format.
 
-**FinaleToolkit** requires that BAM files be BAI indexed. Therefore, you should have an associated ``.bam.bai`` file in the same directory of your input data.
+**FinaleToolkit** requires that BAM files be BAI indexed. Therefore, you should
+have an associated ``.bam.bai`` file in the same directory of your input data.
 
 CRAM
 ^^^^^^^^^^^
 
-A compressed read alignment map file is a compressed version of a SAM file. It is a binary file that is smaller than a BAM file, but still contains all of the same information. 
+A compressed read alignment map file is another binary file standard. It
+is a binary file that is smaller than a BAM file, but still contains all of the
+same information. 
 
-**FinaleToolkit** requires that CRAM files be CRAI indexed. Therefore, you should have an associated ``.cram.crai`` file in the same directory of your input data.
+**FinaleToolkit** requires that CRAM files be CRAI indexed. Therefore, you
+should have an associated ``.cram.crai`` file in the same directory of your
+input data.
 
 Fragment File
 ^^^^^^^^^^^^^^^^
 
-A fragment file (`.frag.gz`) file that is derived from information in a BAM file. A fragment file is a block-gzipped BED3+2 file (similar to a tab-separated value file) that contains the following columns (with one row entry for each fragment): ``chrom``, ``start``, ``stop``, ``mapq``, and ``strand``.
+A fragment file (``.frag.gz`` or ``frag.tsv.bgz``) file that is derived from
+information in a BAM file. A fragment file is a block-gzipped BED3+2 file
+(similar to a tab-separated value file) that contains the following columns
+(with one row entry for each fragment): ```chrom``, ``start``, ``stop``,
+``mapq``, and ``strand``.
 
-Here, ``mapq`` is the mapping quality of the fragment, and ``strand`` is the strand of the fragment. The ``strand`` column can be either ``+`` or ``-``.
+Here, ``mapq`` is the mapping quality of the fragment, and ``strand`` is the
+strand of the fragment. The ``strand`` column can be either ``+`` or ``-``.
 
-**FinaleToolkit** requires that fragment files be Tabix indexed. Therefore, you should have an associated ``.frag.gz.tbi`` file in the same directory of your input data.
+**FinaleToolkit** requires that fragment files be Tabix indexed. Therefore,
+you should have an associated ``.tbi`` file in the same directory of
+your input data.
 
 For your reference, here is an example fragment file::
 
@@ -46,4 +65,6 @@ For your reference, here is an example fragment file::
         chr1    10400    10450    60    +
         chr1    10450    10500    60    -
 
-We encourage you to use our comprehensive database, **FinaleDB**, to access relevant fragment files. Learn more about **FinaleDB** `here <http://finaledb.research.cchmc.org>`_ .
+We encourage you to use our comprehensive database, **FinaleDB**, to access
+relevant fragment files. Learn more about **FinaleDB**
+`here <http://finaledb.research.cchmc.org>`_ .

docs/_build/html/_sources/documentation/user_guide/structure.rst.txt

@@ -7,7 +7,7 @@ give you a sense of what is going on under the hood of **FinaleToolkit**:
 
 At the heart of **FinaleToolkit** is the ``Fragment Generator``. This
 generator is designed to be as flexible as possible. It takes BAM, CRAM,
-SAM, and Fragment Files (among other arguments) and filters out the
+and Fragment Files (among other arguments) and filters out the
 reads that are not of interest (e.x. unmapped reads, reads with low
 mapping quality, etc.). The fragments that make it through this filter
 are then passed to the relevant function to be processed.