diff --git a/README.md b/README.md
index 4efa947..194a2d6 100644
--- a/README.md
+++ b/README.md
@@ -53,9 +53,9 @@ If you don't have adminstrator privileges, there are other options.
 If you have the `libhts-dev` installed, to build `abismal` the
 following should work:
 ```console
-$ wget https://github.com/smithlabcode/abismal/releases/download/v3.2.2/abismal-3.2.2.tar.gz
-$ tar -zxvf abismal-3.2.2.tar.gz
-$ cd abismal-3.2.2
+$ wget https://github.com/smithlabcode/abismal/releases/download/v3.2.4/abismal-3.2.4.tar.gz
+$ tar -zxvf abismal-3.2.4.tar.gz
+$ cd abismal-3.2.4
 $ mkdir build && cd build
 $ ../configure --prefix=/where/you/want/abismal
 $ make
@@ -84,9 +84,9 @@ be needed below. If you don't already have `abismal` downloaded, the next
 step is to download it. Here we will assume you are using a release rather
 than a clone. To build from a clone involves at least one more step.
 ```console
-$ wget https://github.com/smithlabcode/abismal/releases/download/v3.2.2/abismal-3.2.2.tar.gz
-$ tar -zxvf abismal-3.2.2.tar.gz
-$ cd abismal-3.2.2
+$ wget https://github.com/smithlabcode/abismal/releases/download/v3.2.4/abismal-3.2.4.tar.gz
+$ tar -zxvf abismal-3.2.4.tar.gz
+$ cd abismal-3.2.4
 ```
 Finally, these steps build the software:
 ```console
diff --git a/configure.ac b/configure.ac
index 01ff091..efb38b0 100644
--- a/configure.ac
+++ b/configure.ac
@@ -14,7 +14,7 @@ dnl but WITHOUT ANY WARRANTY; without even the implied warranty of
 dnl MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
 dnl General Public License for more details.
 
-AC_INIT([abismal], [3.2.3], [andrewds@usc.edu],
+AC_INIT([abismal], [3.2.4], [andrewds@usc.edu],
         [abismal], [https://github.com/smithlabcode/abismal])
 
 dnl the config.h is not currently #included in the source, and only
diff --git a/data/md5sum.txt b/data/md5sum.txt
index ed55168..81142e0 100644
--- a/data/md5sum.txt
+++ b/data/md5sum.txt
@@ -3,14 +3,14 @@
 2e492e9d438dee062363449cfcbdb7df  tests/reads_pbat_pe_1.fq
 744e216ed05e34dead8e293721b1376b  tests/reads_pbat_pe_2.fq
 fc153607ee4799cca9d040976f4182ea  tests/reads_pbat_pe.mstats
-533826ad127ec9b5cb95229691cdac43  tests/reads_pbat_pe.sam
+22893c68f28daad043c93d5c8c28eadc  tests/reads_pbat_pe.sam
 6b080ecdc9e7c58c24601ba95f475dcc  tests/reads_pe_1.fq
 3eb9b169c45590eea443715284c80dce  tests/reads_pe_2.fq
 093aa787322a3e5250fb229a62eac201  tests/reads_pe.mstats
-b1c5b9d7a991d22dc1958badb5ef6224  tests/reads_pe.sam
+cb1b28601416069132db0f9a9442abec  tests/reads_pe.sam
 4253b0de3da8715e8851c90962d02c1e  tests/reads_rpbat_pe_1.fq
 18daaa57cde00d36d612495aa4acc35b  tests/reads_rpbat_pe_2.fq
 4be779558f7fb70775c32a80f5d38455  tests/reads_rpbat_pe.mstats
-8b33c64513bd6989823a2c47bf632963  tests/reads_rpbat_pe.sam
-acb6582d5b8def45a0d38d8fee5c0edb  tests/reads.sam
+ca9a943134a9f099b2e8d136088fb978  tests/reads_rpbat_pe.sam
+ae1c1b996c7af56983c5952538d1c8ee  tests/reads.sam
 bcbf01be810cbf4051292813eb6b9225  tests/tRex1.idx
diff --git a/docs/MANUAL.md b/docs/MANUAL.md
index 99bba20..61e1c78 100644
--- a/docs/MANUAL.md
+++ b/docs/MANUAL.md
@@ -49,9 +49,9 @@ substantially.
 
 Run the following commands to install abismal
 ```
-wget https://github.com/smithlabcode/abismal/releases/download/v3.2.2/abismal-3.2.2.tar.gz
-tar -xvzf abismal-3.2.2.tar.gz
-cd abismal-3.2.2
+wget https://github.com/smithlabcode/abismal/releases/download/v3.2.4/abismal-3.2.4.tar.gz
+tar -xvzf abismal-3.2.4.tar.gz
+cd abismal-3.2.4
 ./configure --prefix=$(pwd)
 make
 make install
@@ -317,7 +317,7 @@ sequence.
 The last line of the headers is a copy of how the program was called
 to generate the SAM output, and is of the form
 ```
-@PG ID:ABISMAL  VN:3.2.2  CL:[command-call]
+@PG ID:ABISMAL  VN:3.2.4  CL:[command-call]
 ```
 where [command-call] is the shell command used to run abismal.
 
diff --git a/docs/abismal.1 b/docs/abismal.1
index 0d3e034..ea5ac19 100644
--- a/docs/abismal.1
+++ b/docs/abismal.1
@@ -57,9 +57,9 @@ Run the following commands to install abismal
 .IP
 .nf
 \f[C]
-wget https://github.com/smithlabcode/abismal/releases/download/v3.2.2/abismal-3.2.2.tar.gz
-tar -xvzf abismal-3.2.2.tar.gz
-cd abismal-3.2.2
+wget https://github.com/smithlabcode/abismal/releases/download/v3.2.4/abismal-3.2.4.tar.gz
+tar -xvzf abismal-3.2.4.tar.gz
+cd abismal-3.2.4
 \&./configure --prefix=$(pwd)
 make
 make install
@@ -364,7 +364,7 @@ generate the SAM output, and is of the form
 .IP
 .nf
 \f[C]
-\[at]PG ID:ABISMAL  VN:3.2.2  CL:\[dq][command-call]\[dq]
+\[at]PG ID:ABISMAL  VN:3.2.4  CL:\[dq][command-call]\[dq]
 \f[R]
 .fi
 .PP
diff --git a/docs/abismal.html b/docs/abismal.html
index 16e2b23..13a4500 100644
--- a/docs/abismal.html
+++ b/docs/abismal.html
@@ -65,9 +65,9 @@ <h1 id="description">DESCRIPTION</h1>
 <p>absimal was built to map short reads of up to 250 bases. It should successfully map reads of size up to 1 million, but because it uses very short seeds for filtration, the mapping time will increase substantially.</p>
 <h1 id="quick-installation">QUICK INSTALLATION</h1>
 <p>Run the following commands to install abismal</p>
-<pre><code>wget https://github.com/smithlabcode/abismal/releases/download/v3.2.2/abismal-3.2.2.tar.gz
-tar -xvzf abismal-3.2.2.tar.gz
-cd abismal-3.2.2
+<pre><code>wget https://github.com/smithlabcode/abismal/releases/download/v3.2.4/abismal-3.2.4.tar.gz
+tar -xvzf abismal-3.2.4.tar.gz
+cd abismal-3.2.4
 ./configure --prefix=$(pwd)
 make
 make install</code></pre>
@@ -204,7 +204,7 @@ <h2 id="output-headers">Output headers</h2>
 <pre><code>@SQ SN:[chrom-name] LN:[chrom-length]</code></pre>
 <p>where [chrom-name] is given by the first word of the chromosome name in the FASTA file (anything after the first white space is deleted), and [chrom-length] is the number of bases in the chromosome sequence.</p>
 <p>The last line of the headers is a copy of how the program was called to generate the SAM output, and is of the form</p>
-<pre><code>@PG ID:ABISMAL  VN:3.2.2  CL:&quot;[command-call]&quot;</code></pre>
+<pre><code>@PG ID:ABISMAL  VN:3.2.4  CL:&quot;[command-call]&quot;</code></pre>
 <p>where [command-call] is the shell command used to run abismal.</p>
 <h2 id="output-mapped-lines">Output mapped lines</h2>
 <p>Following the header lines, reads that are mapped once (or at least once if the -a flag is used) are reported. Each read is a set of thirteen tab-separated fields as follows.</p>
diff --git a/src/bamxx b/src/bamxx
index a9bf187..e7f5a9b 160000
--- a/src/bamxx
+++ b/src/bamxx
@@ -1 +1 @@
-Subproject commit a9bf1878022235cdb331880957eff55889845315
+Subproject commit e7f5a9bd7ef785c2e426141d9f8cc9eaa2b80a07
diff --git a/src/smithlab_cpp b/src/smithlab_cpp
index 005f388..862012d 160000
--- a/src/smithlab_cpp
+++ b/src/smithlab_cpp
@@ -1 +1 @@
-Subproject commit 005f38805e4f2621a3222a274052983fd6a04a84
+Subproject commit 862012de86bed4bde61bc72784aa27f88bd2965a